知识库文章

Shimadzu LC-40 systems troubleshooting tips and tricks

The table shows the most common symptoms encountered for Shimadzu LC-40 systems and details possible causes with the appropriate corrective action. This HPLC system is commonly used with SCIEX mass spectrometers. Design changes in this model vs older Shimadzu models may require a different approach to troubleshooting your LC-MS system.

How to generate reports in CSV format with SCIEX OS if no comma-separated report style is visible

If no comma-separated report style is visible, you must change the extension of the TXT file to CSV when saving the file.

How To Perform A Master-Reset For PA800 Series

32 Karat Software and Pa800 Plus transport problems can occur due to faulty EEPROM values. These corrupt EEPROM values can be fixed with a Master-Reset

Replacing the electrode in the SCIEX ion source that is compatible with the Eksigent microLC 200 LC system

A YouTube video demonstrates how to replace the electrode in the SCIEX ion source that is compatible with an Eksigent microLC 200 system connected to a SCIEX mass spectrometer and operated by the Analyst® software.

Molecule Profiler software 1.3 supports the entire sequence of an antibody drug conjugate (ADC) in a dedicated workflow

Molecule Profiler software version 1.3 supports a dedicated workflow for antibody drug conjugates (ADCs). The entire antibody sequence can be copied into the software for processing.

How does increasing column temperature affect LC methods?

Increasing the column temperature can affect liquid chromatography (LC) parameters positively by decreasing column pressure, reducing retention times, and lowering the overall analysis time. Fluctuation in column temperature can result in unstable retention times and peak shapes.

Name conflict error when creating a new quantitation method in MultiQuant™ software

The error message, "The specified name conflicts with an analyte in another period/experiment" appears when making a new quantitation method in MultiQuant™ software. This error is the result of one or more analyte names in the current experiment being identical to one of the analyte names(s) in another experiment within the same processing method.

How To Report Out Regression Types in Reporter Template Suite 3.2

To report out the regression type used in a curve fit, a combination of IF, ELSEIF, and ELSE tags are required in the report template in Reporter Template Suite 3.2.

Inputting known concentrations of analytes into a batch in SCIEX OS software

In SCIEX OS software it is possible to input known concentrations of analytes and internal standards for Quality Control and Standard sample types. This prevents having to add the values directly to the results table and saves time when analyzing data.

Processing parameters for an antibody drug conjugate (ADC) Workflow in Molecule Profiler software 1.3

The antibody drug conjugate (ADC) workflow in Molecular Profiler software 1.3 helps to identify and further characterize cytotoxic drugs, their breakdown products, and the linker connected to the entire antibody sequence. This article describes how to set up the processing parameters for the ADC workflow.

What Are the Different Data File Types in Analyst® and SCIEX OS Software?

In the data sub-project within a project folder in Analyst® or SCIEX OS Software, there can be a multitude of file types associated with one set of raw data. The file types and the software they are associated with are listed in this article.

Optimization Report (XPS File) in SCIEX OS Software Does Not Display Graphs

After completing a multiple reaction monitoring (MRM) infusion in SCIEX OS software, the optimization report (.xps file) does not have any graphs displayed even though the graphs appeared in the software after the optimization was completed. This is due to a Windows update (update for Microsoft Windows KB5020866) that restricts .xps files.

How to Reduce the Column Pressure during Liquid Chromatography?

When a new liquid chromatography (LC) method is developed, the pressure might be too high and close to the maximum pressure allowed by the hardware. It is important to address this issue before validating the method.

Is sensitivity lowered for MRM acquisition methods with polarity switching for a SCIEX 5500 system and other instruments?

If user adds polarity switching to a MRM acquisition method that includes both negative and positive experiments, it is possible in theory to have a different signal intensity (usually lower). But having the appropriate settling time in the MRM method will prevent this in most cases.

How to Adjust LC Flow Rates after Changing a Column’s Inner Diameter (ID)

If a user is following an existing liquid chromatography (LC) method but is using a column with an inner diameter (ID) that differs from the original method, how should the LC parameters change?

What is matrix effect and how is it quantified?

The loss of analyte signal due to presence of matrix in sample is called matrix effect in analytical chemistry. Here the quantitation of matrix effect is also explained.

How can I quantify efficiency of my extraction method in SCIEX OS software?

Extraction efficiency is the percentage of analyte recovered through the extraction process, from the start of extraction to the final step of sample preparation prior to LC/MS analysis. This article explains how to quantify the extraction efficiency in SCIEX OS software.

What are the suggested time intervals when using a diverter valve?

Efficient use of diverter valve will keep the mass spectrometer source and ion optics from unnecessary and excessive contamination. This article provides guidance on how to set an appropriate time range for use of a diverter valve during an acquisition method.

How is low resolution set up and tuned in Analyst® software?

To set up low resolution for mass calibration in Analyst® software during instrument optimization, users can choose unit and low resolution and then set it up the parameters accordingly under the Tuning Options screen.

Calibration peak list is missing during instrument optimization in Analyst® software

During instrument tuning and calibration in Analyst® software, the calibration peak list can be obtained by right clicking on the final spectrum and selecting the List Data option. This will open a new pane that contains the calibration peak list. In this tab, the exact expected masses of the calibration components (e.g., PPG positive) are listed.

Which mass spectrometers and ion sources are supported by SCIEX OS software?

If a new flow rate is desired for a LC/MS experiment, a different ion source may be needed for your SCIEX mass spectrometer. Included here is a list of current mass spectrometers and ion sources that are supported by the most recently released of SCIEX OS software, version 3.3.

What is the best way to flush a liquid chromatography system to remove contamination?

Contamination of a liquid chromatography (LC) system usually requires flushing the system with an organic solvent to remove unwanted background. Here an effective way to flush the entire LC system is discussed.

Why do extracted samples and quality controls have lower signal compared to neat standards?

When a sample or a spiked quality control is extracted, the signal is usually lower than that of the corresponding standard made in pure solvents.

How to check if the CAD gas is properly working in Analyst® software

The collision associated dissociation (CAD) gas is an inert gas that breaks parent compound ions into smaller fragments, making it an important component of multiple reaction monitoring (MRM) methods in Analyst® software. It is introduced by diffusing a small stream of nitrogen through a small orifice into the Q2 of a mass spectrometer. On rare occasions, this orifice might become blocked or out of calibration.

Batch submission error in Analyst® software: Exceeding the maximum number of waiting samples

When submitting a batch in Analyst® software, an error message appears: You are exceeding the maximum number of waiting samples configured in the queue options. The solution is to increase the maximum number of waiting samples in the Queue Options under the Settings menu in Configure mode.

Where can I read the vacuum gauge pressure for a SCIEX mass spectrometer in Analyst® software?

For current vacuum gauge pressure readings, double click on mass spectrometer icon at the bottom right corner of Analyst® software to open the MassSpec Detailed Status window. Under the Vacuum System Status section, the real-time readout for the vacuum gauge pressure is visible.

What Curtain Gas (CUR) Settings Should Be Used on SCIEX 3500, 4500 and 5500 Systems?

The curtain gas (CUR) is an important parameter that protects the mass spectrometer from contamination. However, the proper amount of curtain gas depends on the LC flow introduced into ion source and the model of SCIEX mass spectrometer used. This article provides the CUR settings for the SCIEX 3500, 4500 and 5500 (5500+) series systems.

What Curtain Gas Settings Should Be Used on SCIEX 3200, 4000 and 5000 Series Systems?

The curtain gas (CUR) is an important parameter that protects SCIEX mass spectrometers from contamination. The proper amount of curtain gas depends on the LC flow introduced into ion source and the model of SCIEX mass spectrometer used. This article explains the CUR value used for SCIEX 3200, 4000 and 5000 series systems.

Understanding the ion source parameters in Analyst® and SCIEX OS software: GS1, GS2, TEM and CUR

For mass spectrometry acquisition methods in Analyst® or SCIEX OS software, values will need to be set for source parameters that influence the degree of ionization in an electrospray ionization (ESI) source. These values include GS1, GS2, TEM and CUR gas.

How to change source, gas and other default acquisition method parameters in Analyst® software?

When a new method is opened in Analyst® software, the source and gas parameters, including the declustering potential (DP), the collision energy (CE) and the collision cell exit potential (CXP), are populated based on the software's default parameters. Automatic compound optimization method also uses these default values.

Common installation issues when upgrading SCIEX OS software

Some of the most common issues encountered while upgrading the SCIEX OS software and how to prevent them are listed here. Please consult the SCIEX OS software installation guide found in the installer package for step-by-step instructions for correctly upgrading the software.

Is PeakView® software required when processing data in the OneOmics™ suite 3.4?

PeakView® software 2.2  is not required when processing data in the OneOmics™ suite 3.4, but it is required to upload data to the OneOmics suite using the CloudConnect app.

Restoring Missing Toolbars and Menus in Analyst® Software

If the toolbars in Analyst® software disappear, leaving a blank, grey area. they can be restored using the command ALT T.

How To Create Personalized Toolbars in Analyst® Software

To create custom toolbars In Analyst® software and have more personalized access to shortcuts and icons, select the View menu and click on Toolbars. Selecting the New or Customize options will allow for new new toolbars to be created or for customized icons to be added to the toolbars.

Common Installation Errors for SCIEX OS Software

This article describes the common installation issues that occur when installing SCIEX OS software for the first time. To install SCIEX OS software successfully, the Installation Guide should be consulted and each section should be read prior to installing the software.

How To Change the Number of Available Rows in the Batch Workspace in SCIEX OS Software

In SCIEX OS software, it is possible to change the number of available rows in the batch. To do this, select the View button in the top right of the batch workspace.

The Metabolomics Workflow in OneOmics™ Suite 3.4 Offers a New NIST Library Search

The OneOmics™ suite 3.4 offers a new feature in its metabolomics workflow where the NIST library can be selected as a library option in the Merge workflow.

Reporter 3.2 Error In Analyst® Software: Unable To Cast COM Object

When attempting to generate a report in Analyst® software with Reporter 3.2, an error appears immediately after clicking on create report: Unable to cast COM objectnof type System_ComObject' to interface.

How To Utilize the Quick Batch Option in SCIEX OS Software

A new option for creating batches quickly was introduced in SCIEX OS software version 3.1.6 and is called Quick Batch. To utilize Quick Batch, an icon in the upper right corner of the Batch screen will need to be selected.

Error when Opening Analyst® Software: Error 1067

After installing Analyst® software 1.7 alone or with Hotfix 1, attempting to open the software results in an error: Error 1067: The process terminated unexpectedly.

How to set Root Directory in SCIEX OS Software?

Per default, the root directory of SCIEX OS Software is set to C:\SCIEX OS Data. The Managment part of the software provides the possibility to define another root directory path and folder name.

Can a different user log into Analyst® software set to integrated or single user mode?

No, opening the Analyst® software as a different user when the security configuration is set to integrated mode or single user mode is not supported.

Calculating the MS2 Score in the BioPharmaView™ Software for Confident Selection of Peptides for Quantification

In BioPharmaView™ software, the MS2 score evaluates the quality of a match between MS/MS peaks and a set of theoretical fragments. The MS2 score is based on the probability of the MS/MS peaks matching the set of theoretical fragments of the molecule by chance. The score is calculated automatically by the software.

Can two analytes have the same transitions in an MRM method in SCIEX OS software?

Occasionally two different analytes in the same MRM method in SCIEX OS software may have identical Q1 and Q3 masses for their respective MRM transitions. The question is if this could cause problem in quantitation and what should the user do to avoid errors.

Can SCIEX OS software be used for acquisition on all SCIEX instruments?

To determine if a particular version of SCIEX OS software supports acquisition on a SCIEX instrument, please consult the installation guide for that version of the software. SCIEX OS software does not support acquisition on legacy instruments such as the API™ 3200 and 4000 systems.

Considerations when Creating a Library-Free Proteomics Experiment without the OneOmics™ Suite

Library-free proteomics experiments require highly reproducible sample-handling protocols and data analysis and can be done directly in DIA-NN software without any other SCIEX software or ion libraries. 

Recommendations for lower and upper temperatures for an Exion 2.0 method in Analyst® software

When working with an acquisition method that uses an Exion 2.0 LC system in Analyst® software, the lower and upper temperature settings should be set slightly higher or slightly lower, respectively, than the safety limits to prevent column oven errors.

Performing a ProteinPilot software search with the Mascot server enabled

ProteinPilot™ software 5.0.1 can perform searches using the Mascot server. To use the Mascot server, a license is required, and this must be purchased from Matrix Science. Step-by-step instructions are provided in this article for setting up a search with ProteinPilot software 5.0.1 and Mascot version 2.6 or higher.

Accessing ProteinPilot™ Software Searching in the OneOmics™ Suite

To log into the SCIEX Cloud workspace and access the ProteinPilot™ software searching features with a CloudConnect license, follow the instructions below.

Where are print templates stored in SCIEX OS?

A new print template feature appears in SCIEX OS software starting in version 3.1 that allows for batch, queue, and processing methods to be printed for record-keeping purposes. The templates can be accessed from the Configuration tile by selecting the Print Templates tab. Users can customize templates and apply them to specific projects.

Removing an ESI probe to change the capillary on a SCIEX mass spectrometer

Capillaries can get blocked and will need to be replaced from time to time to maintain high quality spray from an electrospray ionization (ESI) probe. This article provides a link to a YouTube video that shows how to remove an ESI probe to change the capillary on a SCIEX mass spectrometer.

How can I set up contact closure in SCIEX OS software for my SCIEX instrument?

To set up contact closure for a SCIEX mass spectrometer to communicate with an external LC system, the contact closure check box must be selected in the instrument's hardware profile in SCIEX OS software. SCIEX OS software 3.1.6 supports many of the same legacy instruments that were controlled by Analyst® software even if contact closure is required for a third-party vendor LC system.

Where can I find general security recommendations for my PC running SCIEX software?

The security guidance provided in the link in this article contains supplemental instructions for protecting acquisition and processing computers that are running SCIEX software. This guidance is intended to supplement rather than replace current IT policies, requirements and practices.

What MRM modes are available on SCIEX TripleQuad and QTRAP systems?

There are four different multiple reaction monitoring (MRM) modes that can be acquired using SCIEX TripleQuad or QTRAP systems with SCIEX OS software: MRM, scheduled MRM, scout triggered MRM RT mode, and scout triggered MRM group mode.

Will my old workflow templates or data be lost when upgrading Biologics Explorer software?

The Biologics Explorer software will automatically save all workflow templates and data from previously installed versions.

Upgrading the Biologics Explorer software

General steps for the upgrade process for the Biologics Explorer (BE) software are described in the release notes. Versions of SCIEX OS software 3.1.5 and greater, have an embedded BE software tile. For those versions of SCIEX OS software containing the BE tile, the SCIEX OS software must first be closed, and all SCIEX OS services stopped before proceeding with the BE software upgrade.

Adding MS/MS information to the MRMHR processing method's Components tab in SCIEX OS software

To add the MS/MS information to a MRMHR processing method in SCIEX OS software, a compound name, a unique name for the fragment ion, and the fragment mass information are required in the table under the Components tab.

How to upgrade your SCIEX mass spectrometer's firmware after upgrading the SCIEX OS software

After upgrading SCIEX OS software on an acquisition PC, the instrument firmware also needs to be upgraded. To do this, follow the instructions in the SCIEX OS software installation guide in the sections MS FW Updater Utility and Mass Spectrometer Firmware Versions.

How to report Dell PC hardware issues for computers not under service contract

For Dell computers experiencing hardware issues that were purchased from SCIEX but are no longer under a service contract, users can reach out directly to Dell for support using the link provided in this article.

Enabling ChemSpider funtionality in SCIEX OS software

To enable the ChemSpider feature within SCIEX OS software, the ChemSpider add-on license must be added to the SCIEX OS software program files and the Formula Finder feature must be enabled in the processing method.

How To Ramp Parameters in SCIEX OS Software during Compound Optimization

When using SCIEX OS software to optimize compounds that are being infused using a syringe pump, it is possible to ramp individual compound parameters such as collision energy (CE), entrance potential (EP), and collision cell exit potential (CXP), and Q0 dissociation (Q0D). This process may be preferred to guided MRM optimization in the event that a more manual and controlled optimization is desired.

Where are print templates located in SCIEX OS software?

A new print template feature appears in SCIEX OS software starting in version 3.1 that allows for batch, queue, and processing methods to be printed for record-keeping purposes. The templates can be accessed from the Configuration tile by selecting the Print Templates tab.

What version of SCIEX OS software includes a tile for Biologics Explorer software?

A tile for Biologics Explorer (BE) software appears in SCIEX OS versions 3.1.5 and higher. The BE software can be launched from this tile, but the BE software needs to be installed from a separate installer as described in this article.

Where is the file for the hardware profile used in Analyst® or Analyst TF software located?

The file corresponding to the hardware profile used in a Analyst® or Analyst TF software is located in the API Instrument project in the Analyst Data folder.

Impermissible Symbols for Root Directory Paths and Project Names in SCIEX OS Software

There are some symbols which cannot be used when naming a root directory path or a project in SCIEX OS software. They are detailed in this article.

What is the maximum project size in the SCIEX OS Data folder that still permits software efficiency?

There is no limit on the number of projects created in the SCIEX OS Data folder.  Additionally there is no limit to the number of subproject folders under a current project.

Proteases such as trypsin and beta galactosidase sold by SCIEX have no certificates of analysis (CoA)

Certificates of analysis (CoA) are available for various reagents; however for proteases such as trypsin and beta galactosidase that are sold by SCIEX, no CoA is available.

How is the Default Column 'Asymmetry Factor' calculated in SCIEX OS?

Asymmetry Factor: Asymmetry factor is a measurement of how well the peak matches the ideal peak shape. As = b/a where b is the distance from the peak apex to the trailing edge of the peak measured at 10% of peak height and a is the distance from the leading edge of the peak to the peak apex measured at 10% of peak height. If As > 1 : tailing, et si As < 1 : fronting

How to reduce matrix effect and increase analyte signal in extracted samples?

Presence of matrix could result in lower analyte signal and reducing matrix effect could potentially increase signal and result in better (lower) limits of detection

How do I create a new entry in the automatic calibration editor in SCIEX OS software

For the batch calibration of high-resolution instruments within SCIEX OS software the Automatic Calibration Editor can be used. Some "ion reference tables" are pre-installed, but they can be customized, or new tables can be added.

What are Metric Plot Settings in SCIEX OS software and where are they saved?

Metric Plot Settings allow the user to customize the appearance of the Metric Plot pane.

How to modify ParameterSettings for APCI “Compound Optimization” in Analyst® software?

The automated “Compound Optimization” within Analyst® software takes over the values set in the parameter settings. The values are optimized for infusion flows around 10 µl/min. For APCI, a flow of at least 200 µl/min is needed, which is why the values for the gases and the temperature must be adjusted.

How to initiate and activate Auxiliary traces in Analyst® Software version1.7.3

How to initiate and activate Auxiliary traces in Analyst® Software version1.7.3

How to perform a source back out (Pyrolysis) in SCIEX OS software or Analyst® software?

In some circumstances, e.g., infusion of very high concentrations of standards or matrices, the source may be contaminated. Baking out helps to remove the impurities.

How To Change the Instrument Idle Time In SCIEX OS Software

After a set time (the instrument idle time) has elapsed, the system will go into Standby state – whereby the LC pumps, column oven and some mass spectrometer voltages are turned off. To change the instrument idle time in SCIEX OS software, navigate to the Configuration pane, and select the Queue tab. The instrument idle time can be changed by typing the desired time into the field.

How to initiate injection counter in Analyst® Software version 1.7.3

How to initiate injection counter in Analyst® Software version 1.7.3

How do I create a Shortcut in SCIEX OS Software and which shortcuts are available?

Overview of available combinations of keystrokes that provides easier access to a command or operation in the SCIEX OS software.

Purpose of a Lockfile Alongside a Results Table File in Analyst® Software

In Analyst® Software, when opening a results table, an additional file - the lockfile - appears in the Quantitation Results folder for a particular project. The purpose of the lockfile is to prevent a second user from opening the same results table simultaneously and trying to modify it.

Error with MPX™ Software 1.2: Unable To Access Autosampler Database

When launching MPX™ software 1.2 on a Windows 7 64-bit operating system, an error appears, "Unable To Access Autosampler Database".

Locating the List of Isotopic Amino Acid Symbols in Bio Tool Kit Software

The Bio Tool Kit microapp can be used for peptide sequencing or fragment matching in PeakView™ or SCIEX OS software. The one-letter codes for amino acids are used when entering potential fragment ions. To represent isotope-labeled amino acids, square brackets encompassing the mass shift are used to the right of the one-letter code. In Bio Tool Kit software, the information for all heavy amino acids is stored in the AA Modifications tab in the Mass Calculator.

Calculating Mass Properties using a Compound's Formula In Analyst® Software

The mass properties of a compound (e.g., average mass, exact mass, nominal mass) can be calculated from its chemical formula using the calculators found in the Tools menu in Analyst® software.

What to do if a service package cannot be created in SCIEX OS or Analyst® software?

If a service package cannot be generated in SCIEX OS or Analyst® software, the event logs, installed programs and other important system information can be manually provided for trouble shooting purposes.

Changing the Y-Axis Scale from Relative Intensity Percent in Analyst® Software,

When opening raw data in Analyst® software, the Y-axis label reads Rel Int. % with values from 0-100% instead of showing the true intensity value. In the Appearance Options window, select Other Graph Options. Under Percent Y Axis, change the value under the Chromatogram column from Yes to No to set the Y-axis scale back to intensity.

Where is the folder location for LibraryView 1.6 software license file?

This will help the user to access the existing LibraryView (version 1.6) license file, or it could help user to place the recently obtained license file into the correct folder on the computer.

ProteinPilot™ software 5.0.3 is needed to view group files from OneOmics™ suite

In order to view group files generated by ProteinPilot™ software from the OneOmics™ suite, users must install ProteinPilot software 5.0.3, a beta version of the software that is not currently available from the SCIEX software downloads page. The link to the installer is provided in this article.

How Do I Work with LC Devices Not Directly Controlled by SCIEX OS Software?

To synchronize signals between a SCIEX mass spectrometer, the SCIEX OS software and LC devices that are not directly controlled by the SCIEX OS software, contact closure can be used.

DIP Switch Positions when Connecting Agilent LC Systems to SCIEX Mass Spectrometers

When connecting Agilent LC Systems to a SCIEX mass spectrometer, the dual-in line packet (DIP) switches on the Agilent LC systems should be in the down (off) position, except for switches 7 and 8 which must be in the up position for the pump and detector.

How to Save Application, System and Security event logs in Windows®10

The Windows event logs often contain crucial data about the performance of SCIEX software. Follow this guidance to save your System, Security and Application event logs so that they can be analyzed by the SCIEX support team.

How can I generate a Batch-Import-Template for SCIEX OS to set up my manual LIMS connection?

SCIEX OS can import batch information from a LIMS system if the import file (*.csv/*.txt) follows defined layout rules. To have the proper layout an example batch can be exported from SCIEX OS to be used as a template.

Can the New Dry Pump MSR 90 for the 6500+ System Be Installed with Analyst® Software?

The new Dry Pump MSR 90 can only be operated with SCIEX OS software on the 6500+ system. It is not compatible with the Analyst® software for data acquisition.

Maintaining the Ion Spray Voltage when Using the Nano OptiFlow® Turbo V Ion Source

In order to maintain the ion spray voltage while operating the nano OptiFlow® Turbo V ion source, one option is to leave the mass spectrometer in Standby mode (LC pumps are turned off and some instrument voltages are turned off) at the end of a run.

What Is a DIA-NN Library-Free Search in a Data-Independent Acquisition (DIA) Proteomics Workflow on ZenoTOF 7600 System?

A library-free search, or direct-DIA (data-independent acquisition), is a proteomics strategy to identify unknown proteins and peptides by generating a theoretical spectral library from a FASTA file and then searching the DIA data against this spectral library using the DIA-NN software.

How Does the Channel Alignment Function on a SCIEX TripleTOF® System?

The purpose of channel alignment is to re-align the signals from each detector/TDC channel in time on a TripleTOF® system. Channel 2 is used as the reference channel, and a simple linear transformation is applied to the other three channels to align them to the refrence.

Which Molecule Profiler Software Version Can Process EAD Fragmentation Data?

The Molecular Profiler software 1.3 is embedded in the SCIEX OS software version 3.1.6 and can assign structures by using fragments from both electron-activated dissociation (EAD) and collision-induced dissociation (CID) techniques.

How To Install the DIA-NN Software 1.8.1 To Process SCIEX WIFF Files?

To process SCIEX data files (.wiff) with the DIA-NN software, the DIA-NN software must be installed using the downloaded executable file. In addition to installing DIA-NN software, the ProteoWizard software must be installed and the dll files in the ProteoWizard installer folder named Clearcore and SCIEX must be transferred to the DIA-NN installer folder.

Canned Calculation for SANTE Guideline 12682_2019 - C16 - Available for SCIEX OS Software

This article provides information on the custom calculations required for processing data according to the guidance found in SANTE 12682_2019 - C16. The guidance requires that analyte response in the extracted pesticide samples should lie within the range tested for calibration standards. These calculations were created to provide a ready-made solution for determining which samples will need to be re-injected in pesticide reports.

What Are the Minimum Cycles Needed To Obtain Quality Optimizations in DiscoveryQuant™ Software?

When setting up an optimization experiment in DiscoveryQuant™ software, the minimum number of cycles needed to obtain quality optimizations is two.

How Are Entries Added to the Compound Database in DiscoveryQuant™ Software?

To add entries to the compound database in DiscoveryQuant™ software, the Edit Compound Workspace must be opened.

Why Can't I Print My Audit Trail Record from Analyst® Software?

For Windows 10 operating systems, if the user who logs on to the Analyst® software in mixed mode is different than the user who logged on to the computer, then the audit trail record printing function will not be available.

What Is the Username and Password for the Empty Compound Database in DiscoveryQuant™ Software?

To open the empty compound database - CompoundDB3.mdb - for DiscoveryQuant™ software, a username and password are required. The username is Admin and the password is !DQO2.

How Can I Customize the Project Information in DiscoveryQuant™ Software?

To customize the project information in DiscoveryQuant™ software, open the Setup Optimization workspace.

Where Are the Report Templates Located for Analyst® Software?

To edit a report template or add a new template to create reports in Analyst® software, users must access the folder where report templates are stored. The report template files are located in the Templates sub-folder within the API Instrument project folder in the Analyst Data root directory.

How Do I Select a Compound Database in DiscoveryQuant™ Software?

To select a compound database in DiscoveryQuant™ software, select the Data menu, and then select Database Selection. The Compound Database Selection dialog will open, and the database options are indicated in this window.

How Is the Analyst Response Factor Column Generated in SCIEX OS Software?

In the SCIEX OS Analytics workspace, Response Factor is not one of the standard columns that users can select from the results table, but it can be created and added to the results table by adding a custom column. 

Do Analyst® Software and Analyst Administrator Console (AAC) Support Cross-Domain Logins?

No, the Analyst® software and the Analyst Administrator Console (AAC) do not support cross-domain logins. The computer where Analyst software is installed, the AAC computer, and the network users should be on the same network domain.

Can I Create an API Instrument Project in a Shared Drive for Network Acquisition with Analyst® Software?

No, when using Analyst® software for network acquisition, users should not create a project with the name API Instrument in the network root directory. Doing so causes the instrument audit trail events to be recorded in the API Instrument project on the network instead of in the local API Instrument project.

How to perform System Check on Sciex Exion 1.0 systems from Analyst®

How to perform System Check on Sciex Exion 1.0 systems from Analyst®

Instrument readbacks log from Analyst

Where to locate the instrument readbacks log from Analyst

How Do I Start the Installation Confirmation Tool in SCIEX OS Software?

SCIEX OS 3.1 software has an installation confirmation tool that ensures that the software has been installed correctly. The confirmation tool can be started by tapping or clicking Search on the taskbar and then typing "SCIEX OS Installation Confirmation Tool" in the search box.

Getting Started with OneOmics™ Suite 3.4

This article describes the required registration, browser setup, software setup, and first steps for uploading data to the Data Store in the web-based and cloud-powered OneOmics™ suite.

Can I Install SCIEX OS and Analyst® Software on the Same Computer for Data Acquisition?

Analyst® software and SCIEX OS software can be installed on the same PC, but SCIEX does not support workflows that use both the Analyst and SCIEX OS software to acquire data from the same mass spectrometer.

Unknown Retention Time Values for Analytes in IDA Method Inclusion or Exclusion Lists in SCIEX OS Software

When setting up an information dependent acquisition (IDA) method, there is an option for including the retention time (RT) for analytes in an inclusion or exclusion list. In the inclusion/exclusion table, users can limit the masses in the list to a certain retention time with a specific width. However, sometimes the retention time is unknown, and its not clear what value to add for RT column.

Can the Installation Repair Tool in SCIEX OS Software Be Used for a Central Administrator Console (CAC) Software Install?

No, the Installation Repair Tool in SCIEX OS software can not be used to assess the installation of the Central Administrator Console (CAC) software.

What Are the New Visualization Features in the OneOmics Suite for DIA-NN Software Output Files?

The DIA Results app, a new software feature in the cloud-based OneOmics suite for processing DIA-NN software output (TSV file), helps visualize proteomics data so that protein quantification results can be interpreted in the Analytics and Browser sections.

What Is the Maximum Length of Characters for the Path to the Installation Folder for SCIEX OS Software?

Please ensure that the path to the installation folder for SCIEX OS software is 118 characters or less. If it is longer, the installation of SCIEX OS software will not proceed.

Setting Up the LC Pressure Trace Monitoring for an Acquisition Method in Analyst® Software

Setting up the LC pump pressure trace and column oven temperature trace monitoring supported by Analyst® software 1.7.3 is explained here. The resulting pressure traces can be stored in the data file for each sample. 

Two New Tiles in the OneOmics™ Suite Support Data Processing with DIA-NN Software

The two new software tiles in the OneOmics™ suite are the Ion Library app and the DIA Results app. These apps are used to process data-independent acquisition (DIA) data acquired by the ZenoTOF 7600 system, along with the DIA-NN software module that is embedded in the OneOmics suite.

How To Configure the OptiFlow® Turbo V Ion Source with the Microflow Probe for Nanoflow Rates

The OptiFlow® Turbo V ion source with the microflow probe can be configured for nanoflow rates, allowing for the continued use of the calibrant delivery system (CDS) for automated calibration.

What File Format Can Be Used for RNA Data Sets in the OneOmics™ Suite 3.4?

To import RNA data sets into the OneOmics™ suite, the RNA data sets need to be in the Cuffdiff output file format from CuffLinks.

How to modify the Project Results Table Settings in Analyst

All available project results table settings can be accessed and modified via Tools.

Creating an Ion Library for DIA-NN Software Using the Ion Library Generator in OneOmics™ Suite 3.3

This article describes how to create an ion library for DIA-NN in the OneOmics™ suite 3.3 using the Ion Library Generator.

What Are the New Features in the ProteinPilot™ Software Found in the OneOmics™ Suite 3.3?

This article describes the new software features recently implemented in ProteinPilot™ software 5.0.3 in the OneOmics™ suite version 3.3. The version of ProteinPilot software found in the OneOmics suite has nearly the same features as the desktop version of ProteinPilot software.

How to use Mixed Mode in SCIEX OS

Explains the different Security Modes and how to use them. More details can be found in SCIEX OS Laboratory Directors Guide

Troubleshooting Common LC Issues on SCIEX Triple Quad™ and QTRAP® Systems

Pressure issues, shifting retention times, and no peaks are common issues when running LC-MS methods. The guides linked tp this article provide step-by-step instructions to troubleshoot these common issues.

How Can I Tell if Zeno SWATH Pulsing Is Working Correctly on My ZenoTOF 7600 System?

To verify that Zeno SWATH pulsing is working on a ZenoTOF 7600 system, users should run a SWATH® acquisition method with and without additional Zeno pulsing using standards from the SWATH acquisition performance kit.

Troubleshooting the ZenoTOF 7600 System: In-Run Calibration Failures

If a calibration failure occurs while acquiring data on the ZenoTOF 7600 system, then certain measures can be followed to mitigate this issue. The troubleshooting guide provided in this article is a step-by-step path for resolving any problems with in-run calibrations. To begin troubleshooting in-run calibration failures, users should open the calibration report in the Analytics workspace of SCIEX OS software to identify the reasons behind the failure.

Microsoft Office 365 Cannot Be Activated on SCIEX Acquisition PCs

Because of the version of Microsoft Windows that is installed, Microsoft Office 365 may not be able to be activated on certain SCIEX acquisition PCs.

How To Create a Metric Plot in Analyst® Software

In Analyst® software, there are multiple ways to view a metric plot in order to see trends quickly after generating a results table.

Communication Issues when Switching Between ExionLC and Eksigent Hardware Profiles in Analyst® Software

Switching from a hardware profile that contains an ExionLC (or Shimadzu LC) system to a hardware profile with an Eksigent LC when both LCs are connected to the PC can cause Analyst® 1.6.3 software to crash, resulting in communications issues.

Diverter Valve Would Not Work While Using Delay Time in Analyst® Software

The diverter valve will not work properly when using Delay Time in the acquisition method of Analyst® Software due to a mismatch between diverter valve timing and MS acquisition timing. This results in the diverter valve timing not aligning with the MS acquisition time.

Error In MultiQuant™ Software When Generating a CSV Report

The error "Cannot save report with graphical or table elements as a text/csv file" appears when attempting to generate a report as a CSV file in MultiQuant™ software using a report template that has figures, pictures, or tables. This is due to CSV reports not being able to display figures or tables.

Troubleshooting the ZenoTOF 7600 System: Tuning and Calibration

Before using the ZenoTOF 7600 system, users should run a system check to verify their instrument's performance. In the event that the MS Quick Status check fails, a link to a troubleshooting guide is included in this article.

How To Create Metric Plots In MultiQuant™ Software

To create a metric plot In MultiQuant™ software, users should highlight the column they wish to see plotted versus the sample index and then select the metric plot icon (trend line with red peaks) in order to view trends such as the peak area of internal standards and analytes.

How Can I Adjust the Dynamic CE Table in SCIEX OS Software?

Sometimes the dynamic collision energy (CE) for peptides needs to be adjusted to get better fragmentation of the precursor ion. This article describes how to adjust the dynamic CE table.

What Fittings Are Needed To Add a Waters M-Class LC to My ZenoTOF 7600 System?

This article explains which fittings are needed to add a Waters M-Class LC to a ZenoTOF 7600 system and includes part numbers and pictures of tubing and trap loop connections.

Device Driver Error During Acquisition with Analyst® Software While Using a Shimadzu LC-40 System

While acquiring data with Analyst® 1.7.3 Software while using a Shimadzu LC-40 system, the run will intermittently fail and the following error will appear: "Integrated System Shimadzu LC-40 Controller 0: ERROR: Operation failed. device driver exception." To resolve this error, Hotfix1 for Analyst 1.7.3 will need to be installed when it becomes available. Alternatively, change the LC method so that it is 0.1 min longer than the MS method.

Why Can't Users with Non-US English Language Settings Create an FDR Report in ProteinPilot™ Software?

When running a search in ProteinPilot™ software as an admin or non-admin user, there should be no difference in FDR report creation as long as full Windows permissions have been provided for Excel report creation. For ProteinPilot software version 5.0.2 with the latest patch (ProteinPilot 5.0.2 Patch for UniProt Issue - Rev. 2), users with a non-admin role may not be able to create reports if the language and font settings are not set to US English.

How To View Metric Plots in the Analytics Mode in SCIEX OS Software

To view trends (such as internal standard peak area) over a range of samples in a results table, a metric plot can be created in the Analytics mode of SCIEX OS software by selecting the column with the values of interest and then selecting Create metric plot from the More menu.

How Can I Set the Integration Algorithm in the SCIEX OS Software?

To set the integration algorithm prior to processing quantitation data, select the Project Default Settings option in the Projects menu in the SCIEX OS software under the Analytics tile.

How To Install Templates in Biologics Explorer Software

This article describes how to install the template packages in Biologics Explorer software.

Can the SCIEX OS Software Central Administrator Console (CAC) Run on a Citrix Server?

The SCIEX OS Software Central Administrator Console (CAC) should run on a Citrix Server, but this configuration has not been tested and is not officially supported.

Will the SCIEX OS Software Central Administrator Console (CAC) Run on Windows Server 2019 in a Virtual Environment?

Yes, the SCIEX OS Software Central Administrator Console (CAC) software installed on a Windows Server 2019 will run in a virtual environment and is officially supported.

What Is the Minimum Accumulation Time in Analyst® TF Software for TripleTOF® Systems?

This article provides guidance on the minimum accumulation time that can be entered in Analyst® TF software for TripleTOF® Systems.

How To Review Statistics for Standards and QCs in Analyst® Software

To review the statistical information for standard and QC samples after creating a results table in Analyst® software, select the statistics button in the software's toolbar. This will open a new window with statistics for the standards and QCs that can be copy and pasted to a spreadsheet.

How To Change Results Table Peak Review Settings in Analyst® Software

While reviewing a results table in the Quantitate mode of Analyst® software, the peak review settings can be changed to view more than one chromatogram and to adjust the x-axis and y-axis automatic zoom settings.

Custom Calculations or Flagging Rules Not Working after SCIEX OS Software Upgrade or Reinstall

After a reinstall or upgrade of SCIEX OS software, the custom calculations and flagging rules of a processing method may not work properly. A config file for the software will need to be edited to restore functionality.

How Do I Open a Port in Windows Firewall for the Central Administrator Console (CAC) Software?

This article describes how to open the port for the Central Administrator Console (CAC) server when Windows Defender is used as the Windows firewall software.

MultiQuant™ MD 3.0.2 Software Will Not Open and No Error Message Appears

If MultiQuant™ MD 3.0.2 software will not open when the desktop icon is selected and there is no error message appearing, this usually indicates that the software was installed on a non-compatible operating system. MultiQuant MD 3.0.2 software must be installed on Window 7, and it will not launch in a Windows 10 enviroment.

Data Not Visible for New Results Table Processing in SCIEX OS Software

To create a new results table in SCIEX OS software, users must browse to data sets (.wiff files) from the Analytics mode through the Results menu. When New and then Browse are selected to start a new results table, no data set is seen when the data folder is selected in the Select Folder menu. It appears as if the raw .wiff files are missing.

Where Do I Put Query Files Used with Reporter Templates for MultiQuant™ or SCIEX OS Software?

Queries are used by report templates to process specific data from results tables in either MultiQuant™ or SCIEX OS Software. For a report template to utilize a query, the query file must be placed in the same directory as the report template.

Do I Have the Central Administrator Console (CAC) Server Installed for SCIEX OS Software on My PC?

Users can determine if the Central Administrator Console (CAC) server is installed on their PC by checking if the splash screen at startup displays the name SCIEX OS Central Administrator Console or by checking the About menu in the Configuration mode of the software. Also, one of the four workspace tiles on the home screen says Central Administration once the software loads.

Is the Settings File for the Central Administrator Console (CAC) Software Forward Compatible?

Yes, the Central Administrator Console (CAC) software settings are forward compatible with future versions of the CAC for SCIEX OS software. This means that the setting files (.eac files) from older versions of the CAC software can be imported into newer CAC versions (when they become available), and all the information regarding users, workstations, projects and workgroups will be able to imported into a new version or new installation of the CAC software.

Can I Install the Central Administrator Console (CAC) Software on a Server Also Running a FlexNet Licensing Server?

Yes, the SCIEX OS software Central Administrator Console (CAC) software can reside on the same server as the FlexNet Licensing Server.

Is a Special Administrator Account Required for the Central Administrator Console (CAC) Software?

A special administrator account is not required for the Central Administrator Console (CAC) software. The CAC server uses the standard SCIEX OS software roles to manage CAC administration permissions.

What Are the Hardware Specifications for the Central Administrator Console for SCIEX OS Software?

The hardware recommendations for the Central Administrator Console for SCIEX OS software are for a PC with a minimum of an i5 quad core, a 3 GHz processor or above, a minimum of 20 GB hard drive space, and a minimum of 8 GB RAM.

Where is the Database for the Central Administrator Console (CAC) Software Stored?

Central Administrator Console (CAC) software is used to create and manage projects and users for laboratories using SCIEX OS software on multiple workstations and instruments. The CAC software database is stored in the following location: C:\ProgramData\SCIEX\Clearcore2.Acquisition\CacServerDataBackup

How Does a Client PC Connect to the Central Administrator Console (CAC) Server?

The Central Administrator Console (CAC) software client connects to the CAC server using TCP ports 63333 and 44144. Users need to open the Windows firewall port when Windows Defender is used as the default firewall software. If different firewall software is used, then users must follow instructions specific to that software to open these ports.

Unable To Connect to Shimadzu LC In Hardware Configuration in Analyst® Software

When trying to activate a newly installed Shimadzu LC in a hardware configuration in Analyst® Software, an error will appear stating that the LC could not be connected.

Where Are the Log Files Located for ProteinPilot™ Software?

The log files are needed for troubleshooting error messages in ProteinPilot™ software and can be located at C:\AB SCIEX\ProteinPilot Data\Temp\ProteinPilot.log.

How Can I Install the Free Extractables & Leachables Library in SCIEX OS Software?

This article describes how to download and install the free Extractables & Leachables library into SCIEX OS software to test a library matching workflow.

MultiQuant™ Software: Concentration Upper Limits Flag Incorrectly Assigned when No Peak Detected

In Multiquant™ software using a quantitation method with upper limits for concentrations set causes samples with N/A for peak area to be flagged for concentration.

How Many Client Workstations with SCIEX OS Software Does the Central Administrator Console (CAC) Software Support?

The Central Admin Console (CAC) software can support 100 client workstations with the SCIEX OS software installed.

What Happens to the SCIEX OS Software when the License for the Central Administrator Console (CAC) Software Expires?

If the license expires for the Central Administrator Console (CAC) software, the server data is maintained in the CAC database, but users won’t be able to launch the CAC application. The SCIEX OS software installed on the client workstations will continue to launch and work with last retrieved data while the CAC server is not reachable.

Fatal Error in MultiQuant™ Software: The File or Directory Is Corrupted and Unreadable

While opening a file or creating a results table in MultiQuant™ software, users may receive the error message "The file directory is corrupted and unreadable." Running the Windows file explorer drive check can resolve this issue.

Internal Standard Recovery Calculations in MultiQuant™ and SCIEX OS Software

SCIEX OS and MultiQuant™ software both calculate internal standard (IS) recovery but use different approaches. SCIEX OS software uses a built-in functionality for creating custom formulas to calculate IS recovery. MultiQuant™ software requires a query to be applied to the results table to perform the IS recovery calculation and to add a custom IS recovery column to the results table.

How To Change Chromatography Peak Shading In MultiQuant™ Software

To change how peaks are shaded in MultiQuant™ software in the Peak Review section, right click on the chromatogram and click on Options. Under the Appearance tab, there will be a drop-down section for Fill Peaks.

How to Export the Settings for the Central Administration Console (CAC) Software

Users can export the security settings from a Central Administration Console (CAC) server used to manage SCIEX OS software users and projects. The settings are exported as an ECAC file and can be imported into another CAC server installation to transfer the security settings. 

Adding a New Fragmentation Rule for EAD Data from a ZenoTOF 7600 System to the Mascot Server

The steps for adding Mascot server fragmentation rules for an electron activated dissociation (EAD) cell on a ZenoTOF 7600 system are discussed in this article, as well as how to set up these rules in the Mascot Daemon client software version 2.6 or 2.8.

Unable To Change Sample Loop Volume With Analyst® Hardware Configuration For ExionLC™ AD System

After replacing the sample loop for a different volume on an ExionLC™ AD system, the volume of the loop can be changed on the LC controller panel but not within Analyst® software hardware configuration.

Valve Model Will Not Stop Equilibrating In SCIEX OS Software 2.1

When equilibrating any MS method on a SCIEX 7500 system, the "Valve Model" will never finish equilibrating even after the specified time when using SCIEX OS software 2.1.

How Can I Get a Biologics Explorer Trial License?

To obtain a Biologics Explorer (BE) 1.x trial license, send an email to biologics.explorer.orders@sciex.com with a request for a 30-day trial.

How to Electronically Reset a SCIEX 7500 System

This article describes the steps for resetting the SCIEX 7500 series instruments.

Implementing Zeno SWATH Functionality on the ZenoTOF 7600 System

To enable the Zeno SWATH pulsing function in the SCIEX OS software for the ZenoTOF 7600 system, upgrade the software to version 3.0 and then add the Zeno SWATH extension license for SCIEX OS software.

Clearing an Integrated Syringe Pump Error in Analyst® Software

Different approaches are provided here to resolve an error message that appears in Analyst® software while using the integrated syringe in manual tune mode: "The current sample cannot be run because the syringe pump has reached the end of its travel. To solve this problem please refill the syringe, press "Clear Error" and resubmit the sample".

Resolving the Error "Unexpected Error Has Occurred" when opening Reporter In Analyst® Software

When opening Reporter in Analyst® software, an error message appears reading "Unexpected error has occurred."

Analyst® Software Error: Please Enter Positive Numeric Value Only

While attempting to select manual tune mode, users of Analyst® software may see the error message "Please enter positive numeric value only." This error results from commas instead of periods being used as decimal points in non-English based operating systems.

Can Results Tables Created in MultiQuant™ Software Be Opened in SCIEX OS Software?

It is not possible to open a results table (.qsession file) that was generated in MultiQuant™ software in SCIEX OS software.

Transferring Acquisition Methods Between Analyst® Software and Analyst MD Software

Is it possible to move an acquisition method that was created in Analyst® software to Analyst MD software?

How Do I Convert Acquisition Methods Created in Analyst® Software for Use in SCIEX OS Software?

Users can convert existing acquisition methods created in Analyst® software for use in SCIEX OS software by using the Convert File option in the Open menu in the MS Method tile. Only the MS portion of the method will be converted; there is no conversion function for the LC portion of the method.

Issue with Ion Ratio Calculations in MultiQuant™ Software 3.0.3 Resolved with HotFix 2

When removing a standard from the calibration curve of an analyte in MultiQuant™ Software 3.0.3, an error occurs where the ion ratio for analytes farther down the list gets improperly calculated and changed. This issue is resolved by installing HotFix 2.

How Do I Find the Build Number for Analyst® Software Version 1.7.3?

With Analyst® software version 1.7.3, the build number no longer appears in the About Box due to a new requirement that the displayed information in Analyst 1.7.3 had to be in sync with the MD version of the software. Users can check the version (build) number by navigating to the Programs and Features section of the control panel by using the Details view to see the version for each installed software.

Special Acquisition Account (SAA) - a must have for Network Acquisition with Analyst in a regulated environment

This article explain what a Special Acquisition Account is, when to use and how to set it up properly for Analyst Software. This is valid for all Analyst versions from 1.0 up to latest 1.7.3. Also in a non regulated environment, it is recommended to use SAA if Acquiring into a Network.

How to create a new Wellplate in SCIEX OS for Agilent Autosampler

Will explain how to use an existing wellplate to modify accordingly to be able to use a new customized wellplate for Agilent Infinity II Multisampler. Same procedure will also works for other Agilent Autosampler, but have some slightly different names for some of the steps.

Unable to Export IDA Table From SCIEX OS Software into Excel

When viewing IDA data in the Explorer mode of SCIEX OS software, the IDA table data will not export into Excel. Exporting the data directly to Excel is not supported in SCIEX OS software, and the best workaround is to select the top row of the table and select Ctrl, Shift, End to copy the IDA data directly to Excel.

Unable to Install MultiQuant™ Software 3.0.3 on Windows 10 Version 20H2

MultiQuant™ software 3.0.3 is not compatible with and cannot be installed on Windows 10 version 20H2. In order to install MultiQuant software 3.0.3, Windows 10 must be downgraded to an earlier version.

Download a Free Ion Library for LibraryView™ Software

A free-of-charge ion library for LibraryView™ software is available from the SCIEX Software Downloads page. No license is required to use the Accurate Mass E&L Open Access HR-MS/MS Spectral Library, the so-called Extractables & leachables library.

What Happens During Q0 Dissociation when "Simple" or "Enhanced" Options Are Used in SCIEX OS Software?

Declustering is achieved with the SCIEX Triple Quad 7500 system using a voltage differential between the QJet® ion guide and the IQ0 lens or a voltage differential between IQ0 and Q0 (the quadrupole ion guide before Q1). This article explains how Q0 dissociation is achieved using simple or enhanced modes in the SCIEX OS software and how the D Jet™ ion guide is involved in enhanced-mode dissociation.

Can the Lipidyzer™ Platform Be Upgraded to a Windows 10 Compatible Version?

Lipidyzer™ platform 1.0.5 is only Windows 7 compatible, and there are no upgrades available that allow the software to be used on a Windows 10 system.

How to Activate the Molecule Profiler Software Module in SCIEX OS Software

The Molecule Profiler software is a processing-only software module within the SCIEX OS software suite that can identify and characterize parent molecules and their metabolites. Activating the Molecule Profiler software version 1.1 simply requires the installation of an additional license; however, activation of version 1.0.1 requires an additional software download as well as license installation.

Can I Use the SWATH® Variable Window Calculator 1.2 with All SCIEX QTOF Systems?

The SWATH® Variable Window Calculator 1.2 is a new updated calculator that supports all SCIEX QTOF instruments with Analyst® TF and SCIEX OS software versions.

What Are the Current Limitations of the SWATH® Variable Window Calculator Tool?

The SWATH® Variable Window Calculator tool can be used with Analyst® TF 1.7 software and SCIEX OS 1.7 software and higher for many QTOF instruments. This article lists the maximum target number of Q1 windows and the maximum upper m/z limit for each QTOF instrument.

Do I Need To Revalidate My Software Workflow after Upgrading from Analyst® to SCIEX OS Software?

Yes, the software workflow will need to be revalidated after upgrading from Analyst® to SCIEX OS software. SCIEX OS software is a completely different software platform than Analyst software, and because even minor changes require revalidation, the switch from Analyst to SCIEX OS software will also require a revalidation.

Does the SCIEX 7500 System with SCIEX OS Software Work with StatusScope® Remote Monitoring Service?

Yes, the SCIEX 7500 System with SCIEX OS Software is compatible with StatusScope® remote monitoring service version 2.0.

Can Analyst® and SCIEX OS Software be Installed on Separate Computers and then Used Alternately for Acquisition?

Switching between Analyst® and SCIEX OS software for acquisition, either on the same or different computers, is not a supported workflow.

Can Both Analyst® Software and SCIEX OS Software be Used for Acquisition on the Same PC?

No, Analyst® and SCIEX OS software cannot be used for acquisition on the same computer. Analyst software will be removed from an acquisition PC if it is upgraded to use SCIEX OS software for acquiring data.

Are Validation Services Available To Install and Test the SCIEX OS Software in My Lab?

Yes, the SCIEX validation services team has helpful and cost-effective services for SCIEX OS software validation.

How to Report Regression Parameters in a Results Table Created in SCIEX OS Software

Regression parameters values (e.g., r squared, slope, linear coefficient) can now be added to a results table created in SCIEX OS software from the calculated columns that are saved under the processing method.

Can Audit Maps Be Easily Transferred from Analyst® Software to SCIEX OS Software?

No, audit maps cannot be directly transferred from Analyst® to SCIEX OS software.

Are There Differences in LIMS Column Headers between Analyst® and SCIEX OS Software?

As users switch from Analyst® to SCIEX OS software, there may be concerns about column header or formatting differences between the two software versions when importing or exporting information using a LIMS. Although similar, there are format and column differences between the SCIEX OS and Analyst software systems, and SCIEX can provide examples for both formats.

Is the SelexION® Device Compatible for Acquisition with SCIEX OS Software?

No, the SelexION® device is not yet supported in SCIEX OS software.

Can I Modify or Add an Enzyme in Bio Tool Kit Software?

The Bio Tool Kit software micro-app characterizes biomolecules within SCIEX OS and PeakView® software through features such as intact protein spectral deconvolution and manual sequence tagging. The software does not allow users to add or modify proteolytic enzymes themselves, but there is a workaround that can be used to modify an existing enzyme.

Converting WIFF2 Files from SCIEX OS Software to the mzML and mzXML Format

The ProteoWizard tool (http://proteowizard.sourceforge.net/downloads.shtml) for mzML and mzXML conversion has been updated to work with the WIFF2 files that are produced by SCIEX OS software.

How to Generate a Service Package in Analyst® Software

Generating a service package allows the technical support team to pinpoint and resolve software issues more quickly. To diagnose an issue with Analyst® software, download and install the Analyst Diagnostics Tool (ADT).

Locating the Computer ID(s) on a PC with a Windows Operating System

The computer ID, also known as the physical or MAC address, is a number used when activating a software license on Sciex.com and contains a series of 12 characters followed by a space and then another 12 characters. This article explains a few different ways to generate the computer ID on a Windows 10 system. (These same steps apply to a Windows 7 system as well.)

Exporting Mascot Searches from QTOF and MALDI TOF/TOF™ Systems for PRIDE Submission

Mascot searches can be exported from the Mascot server; but the data needs to be converted to the mzIdentML file format and then submitted to PRIDE. This article only describes how to export a Mascot search.

When Does Analyst® Software Start Generating the Archive for Audit Trail Records?

Once the instrument audit trail or a project audit trail contains 1000 audit records, the Analyst® software automatically archives the records and begins a new audit trail.

How to Save Application and System Event Logs in Windows 10

The Windows event logs often contain crucial data about the performance of SCIEX software. Follow these steps in Analyst® software to save your system and application event logs so that they can be analyzed by the SCIEX support team.

What is the Maximum Sampling Speed of the Echo® MS System?

There are two modes for the Echo® MS system, normal and fast. The normal mode maximum sampling speed is 1 sample/s. In fast mode, the maximum sampling speed is 3 samples/s.

How to Export and Import Processing Methods in SCIEX OS Software

Processing methods can be exported or imported in the Analytics workspace of SCIEX OS software.

Setting Up Email Notifications and Emailed Reports in Cliquid® Software

To set up email notifications in Cliquid® software, launch the software and select the User Profile option. To start email notifications and the option to have reports emailed, the user's email address will need to be entered in the user profile.

What Sample Plate Formats Are Supported on the Echo® MS System?

The Echo® MS System is only compatible with specialized, acoustically clear microplates that were specifically designed to ensure the optimal and repeatable performance of droplet ejection. These specialized plates are available in both 384- and 1536-well formats.

Creating a Hardware Profile in Simulation Mode in SCIEX OS Software

To create a hardware profile in simulation mode in SCIEX OS software, select Simulate Device under the Settings tab when adding instruments to a hardware profile in the Configuration mode.

How to Restore the Batch Rack Code in Analyst® Software when Using CTC Autosampler

While creating a batch in Analyst® software with a CTC autosampler in the hardware profile, the drop-down menus appear blank for rack position, plate position, and plate code and do not contain the usual text selections. Reselecting the rack code value of 1 will restore the drop-down menu text.

Setting Up Manual Integration (Percentage Rule) in SCIEX OS Software

To set up the parameter Manual Integration (Percentage Rule) in SCIEX OS software, a results table and peak review will need to be open in Analytics mode. In the peak review pane, select the Peak review display settings button under the Options menu. Then select the Appearance tab. The manual integration percent rule can be set by clicking the drop down arrow as shown below.

How to Create an Ion Ratio Flag in a Report Template

To flag an ion ratio as pass or fail in a report, an If/Else statement needs to be added using the MQ_Ion_Ratio tag.

Setting the Security Configuration to Single User Mode in Analyst® Software

To set the security configuration to single-user mode in Analyst® software, navigate to the Configure mode, and then select the Security Configuration option. Select More from the bottom left side of the splash screen, and then select the Security tab at the top of the screen. Under the Security Mode tab, choose the Single User Mode option. Click Apply and OK.

Returning the Results Table Settings to Defaults in Analyst® Software

If custom settings are applied to a results table in Analyst® software, they can be reversed by selecting the default settings option. To do so, right click within the results table to generate a secondary menu. Select the Table Settings option and then select Default.

How to Remove "No Data" from Report Output Generated from SCIEX OS Software

An IF/ELSE statement can be created to filter out the “No data” response in a report in SCIEX OS software.

How is the GETSTAT Function Used in SCIEX OS Software?

The calculated columns for a processing method in SCIEX OS software allow users to add a formula that pulls the statistics pane calculations into the results table as a custom column. This can be done using the GETSTAT function.

Can a Method Built in MPX™ Software Be Converted to a Method Used with SCIEX OS Software?

No, methods built in MPX™ software cannot be converted for use in SCIEX OS software. Files built in MPX software are not supported in SCIEX OS software.

Is It Possible To Convert an Acquisition Method Built in Analyst® Software to a MS Method for SCIEX OS Software?

A MS acquisition method built in Analyst® software cannot be opened directly in SCIEX OS software 2.2, but it can be converted to a usable MS method in SCIEX OS software using the Convert file feature in the MS Method workspace.

Changing the Comparison Sample Assignment in Analytics in SCIEX OS Software

When reviewing a results table in the Analytics workspace of SCIEX OS software, users can change the comparison sample assignment from the one that was originally included in the processing method by selecting the option, Use the selected sample as the comparison sample.

What Are the Specifications for Installing SCIEX OS Software 2.2 on an Acquisition PC?

To install SCIEX OS software version 2.2 on an acquisition workstation, the PC needs to meet specific requirements. The following PCs are supported: 1) SCIEX workstation or workstation+ and 2) SCIEX Alpha workstation 2020.

Is the Database for DiscoveryQuant™ Software Limited to 1 GB?

Yes, the size of the Microsoft Access database file is limited to 2 GB. However, the reliability of the database degrades before reaching the 2 GB limit, so it is suggested that DiscoveryQuant™ software users create a new database before the database exceeds 1 GB.

Can a Processing Method Built in ChemoView™ Software Be Converted for Use in SCIEX OS Software?

No, a processing method built in ChemoView™ software cannot be converted for use in SCIEX OS software. Files built in ChemoView software are not supported in SCIEX OS software.

Can a Method Built in Cliquid® Software Be Converted to a Method for SCIEX OS Software?

No, methods built in Cliquid® software cannot be converted for use in SCIEX OS software. Cliquid software method files are not supported in SCIEX OS software.

Is Watson LIMS Software 7.6.1 SP1 Compatible with Analyst® Software 1.7.2 on Windows 10?

Yes, Watson LIMS software 7.6.1 SP1 is compatible with Analyst® software 1.7.2 on Windows 10. Please run as administer when installing both the Watson and the Analyst software to ensure LIMS integration between the two.

Enabling and Disabling the Data File Checksum Feature in SCIEX OS Software

To enable or disable the data file checksum feature in SCIEX OS software, navigate to the Configuration workspace in SCIEX OS software. Under the Projects tab under Data File Security, select the checkbox for Enable checksum writing for wiff data creation.

Where Are the SCIEX OS Software Project Audit Trail Archives Stored?

The audit trail records for a SCIEX OS software project are stored in the Audit Data sub-folder for the project. The audit trail file name is ProjectAuditEvents.atds.

When Does SCIEX OS Sofware Start Archiving Audit Trail Records?

In SCIEX OS software, the audit trail will be archived when it reaches 20,000 records.

How To Reset a QTOF System Mass Spectrometer

Power cycling a QTOF mass spectrometer can help resolve communication issues. The The TripleTOF® system, the X500 QTOF system, and the ZenoTOF system instruments (X500-, 5600-, 6600- and 7600-series instruments) are all reset in the same way. This article describes the reset procedure for these instruments.

Where Are Acquisition Method Files (Both LC and MS) Saved for SCIEX OS Software Projects?

Each SCIEX OS software project has its own, separate MS and LC acquisition method files. This article describes where the method files are typically stored.

Where Is Guided Optimization Found in the SCIEX OS Software?

The SCIEX OS software offers various guided optimization methods in the MS Method mode.

Can a WIFF or WIFF2 File from SCIEX OS Software Be Split into Subset Data Files?

There is currently no script or software that allows for splitting a multi-sample data file from SCIEX OS software (i.e., .wiff or .wiff2) into individual subset files.

How Can I Export Results Table Data in Encrypted Text Files in SCIEX OS Software?

Users with the administrator role have access to the project settings for secure export in the Analytics workspace under the Projects drop down menu in the SCIEX OS software.

Should I Revalidate My Software?

Periodic reviews of validated systems must be performed to ensure that no changes have been made that affect the validated state of the system. If there is a change, then the software needs to be revalidated.

What Do SCIEX Validation Services Include?

SCIEX qualification services include testing and documentation that demonstrates that the instrument is operating correctly and includes objective evidence showing what was tested, the specification for each test, and the results.

Will Software Validation Ensure that Our Lab Is 21CFRpart11 Compliant?

The SCIEX software validation service ensures that Analyst® software is configured correctly, that the necessary procedures are documented, and that objective evidence of these activities is provided to ensure 21CFRpart11 compliance.

What Normalization Can I Use in MarkerView™ Software 1.3.1 when Processing My Peptide Data?

MarkerView™ software 1.3.1 software has a new Most Likely Ratio (MLR) normalization algorithm incorporated info this newest version of the software.

Can Biologics Explorer Software Be Installed on a PC with One Partition?

Biologics Explorer software needs to be installed on a computer with both a C: and D: drive partition; however, it is also possible to install this software on a PC with just one (C: drive) partition if a patch is also installed.

Can I Use the TOMKit Library with SCIEX OS and/or LibraryView™ Software?

The TOMKit Libraries are newer library entities, and they are not compatible with SCIEX OS or LibraryView™ software. The TOMKit libraries are for use with Agilent instruments only currently.

Building a Quant Method in SCIEX OS Software for DAD Data

Peaks from DAD or UV chromatograms that were acquired during an LC/MS experiment can be quantified in SCIEX OS software. Open a new quantitation method in SCIEX OS software, and then select the representative sample. On the Components tab, select the drop down menu in the Experiment Index column. Select the DAD experiment for each transition and add the desired wavelength to quantitate in the Start - Stop (Wavelength) column.

My Annual SCIEX License Suddenly Stopped Working Before It Expired, Why?

A new annual SCIEX subscription license stopped working suddenly despite having many months of use remaining.

Is It Possible to View Extracted Ions in Separate Panes in SCIEX OS Software?

To show extracted ions in SCIEX OS software, the data file must be opened in the Explore module and then Ctrl+E is used to extract the ions of interest. The Split Traces into Separate Panes option in the Graph menu allows for the extracted ions to be displayed in separate panes.

How to Print an XPS Report after Running MS Tune in SCIEX OS Software

To print the XPS report from the most recent or a prior tuning in SCIEX OS software, navigate to this location: D:\SCIEX OS Data\Optimization and then print the file report.xps.

DiscoveryQuant™ Software Produces SQL Error during Migration from Windows 7 to Windows 10

To resolve an error that prevents the SQL database from connecting with DiscoveryQuant™ software 3.0.2 in Windows 10, SQL user accounts with the password enabled must be used.

Extra Backslashes Added when Using Network Location for Root Directory in Analyst® Software

If extra backslashes are added to a network location for a root directory for Analyst® software, a registry edit will be needed to prevent this issue from continuing to occur. The extra backslashes in the data file name can cause errors when trying to create a new project or save files (including results tables).

Compounds Need to be Assigned to a Library to be Recognized in Cliquid® Software

A MS/MS spectra was added to a compound record in LibraryView™ software, but subsequent confirmation runs in Cliquid® software failed. The root cause of the issue was the compound in the LibraryView software database was not associated with any named library.

Password Guidance for Secure Network Account or Special Acquisition Account for SCIEX OS or Analyst® Software

This article provides some guidance for using a secure network account (SNA) with SCIEX OS software or a special acquisition account (SAA) with Analyst® software.

Analyst® TF Software Error: Instrument Optimization Parameters Are Not Available

If the error message "Instrument optimization parameters are not available" appears when running Analyst® TF software, check the region and language settings and ensure that English (United States) is set as the default language in the Windows operating system settings.

Generation of a New Root Directory for SCIEX OS Software Called C:\ClearCore Data

Some users have reported the appearance of a new root directory created by SCIEX OS software that is not on the D: partition where the root directory (D:\SCIEX OS DATA) is typically located, but rather on the C: drive. This C: drive root directory has a different name (C: \Clearcore Data) and does not match the root directory that appears in the Configuration mode of SCIEX OS software in the Projects menu.

Is It Possible To Convert a Shimadzu High-Flow LC to a Microflow LC System?

In order for a microflow LC system to perform optimally, the correct LC hardware must be installed. For example, a high-flow Shimadzu LC-20AD system cannot simply be converted to a microflow system because the 20AD is not equipped with the correct type of solvent mixer.

Mapped Network Drive Issue when Using SCIEX OS Software Version 2.1.6

Many customers reported issues when using a mapped network drive to store for data for SCIEX OS software version 2.1.6; however, if the data was download to a local drive, no errors were received.

Why is Scheduled Ionization in Analyst® TF Software 1.8 Not Working with the OptiFlow® Turbo V Ion Source for Nano Flow?

Scheduled ionization in Analyst® TF software 1.8 is not configured to work optimally with the OptiFlow® Turbo V ion source ion source for nano flow. When using the OptiFlow® Turbo V ion source, scheduled ionization is always on, except when the start time in Analyst software is set to zero during pre- and post-run times. This is an issue for the nano spray users, because they will be unable to have the voltage stay on between runs for perpetual spray.

How to Check if Unknown Samples Are Within Calibration Curve Range in SCIEX OS Software

To check if unknown samples are within the calibration curve range in a SCIEX OS software results table, additional calculated columns will need to be added to the results table.

How Do I Select a Library and Perform a Library Search in SCIEX OS Software?

To select a library to use with a targeted or non-targeted screening method in SCIEX OS software, open an existing processing method or edit an embedded method from a results table. Ensure that the checkbox for Quantitation and targeted identification or for Non-targeted screening is selected. Then navigate to the Library Search option to set the library search parameters.

Why Is There No MRMHR Scan Type when Using the Method Wizard for a TripleTOF® LC-MS/MS System?

This article describes the MRMHR workflow for a TripleTOF® LC-MS/MS System using the Method Wizard in Analyst® TF or SCIEX OS Software. MRMHR is not a scan type. It is a description for a set of looped experiments, which can be used for a targeted approach. The looped experiments include a TOF-MS experiment followed by dedicated product ion experiments either in high-resolution or high-sensitivity mode.

Decreasing Run Time when Using the LCMS Reconstruct Algorithm in ProteinPilot™ Software

This article describes how to modify the configuration file for ProteinPilot™ software to decrease the time needed when using the LSMS Reconstruct algorithm, especially when performing large protein ID searches on data sets from a TripleTOF® 6600 LC-MS/MS System.

What is the Signal-to-Noise(S/N) Integration Threshold in SCIEX OS Software?

A signal-to-noise (S/N) integration threshold was introduced in SCIEX OS software version 2.1.6, which allows users to select peaks for integratin based on the S/N ratio.

How Can I Sum Vitamin D2 and D3 in SCIEX OS Software?

To add the calculated concentrations for vitamin D2 and D3 together and calculate the total vitamin D, a custom calculation in SCIEX OS software will need to be created in the processing method in the Analytics mode. The calculation will add custom column named Total VitD to the results table and provide a sum of the values for the calculated concentrations for vitamin D2 and D3.

Reporter Error: Cannot Retrieve Analyte: the Specific Index ("-1") Is Out of Range

If the following error is received when creating a report for a results table in MultiQuant™ or SCIEX OS software "Cannot retrieve analyte: the specific index ("-1") is out of range", ensure that the individual tags within the loop are for the same sample type (e.g., use internal standard tags if For Each Internal Standard is used for the loop).

Chromatograms Are Not Appearing in Reports Created with Reporter Template Suite

When using MultiQuant™ or SCIEX OS software to create a report with Reporter Template Suite software, chromatograms are not appearing in the report. Instead, the report shows the text "This image is not available" where the image should appear. If the tag, Picture: Peak Review, is used, then the Label field must contain a value that matches the name of a column in the results table or it must be blank.

Reporter Template Suite Software: The Summary Table Always Starts on the Second Page

When a report is generated from a results table in MultiQuant™, Analyst® or SCIEX OS software, the summary table will only start appearing on the second page of the report, and the first page is left blank after the header. To resolve this issue, open the report template and select and highlight the summary table. In the Microsoft Word Layout menu, select Paragraph. De-select the option Keep with next.

Adding a Custom Column to a Results Table in SCIEX OS Software

To add a custom column to a results table in SCIEX OS Software, select Add custom column from the More menu. Provide a name for the custom column and then select OK.

Reporter Template Suite Software: How Do I Get Rid of "No Data" in Report if Sample Comment Is Empty?

When using the Reporter Template Suite Software with MultiQuant™, Analyst® or SCIEX OS software, the report output may indicate "no data" in the sample comment column if there is no text in the corresponding column in the results table. To eliminate "no data" as a response in the report, try using the following IF/ELSE statement: IF EMPTY($Sample_Comment) (Text Field: none) ELSE (Text Field: Sample Comment)

How to Export Results for Specific Analytes from SCIEX OS Software

To report only the results for specific analytes from SCIEX OS Software, a results table will first need to be opened in the Analytics mode. Start by selecting one of the analytes of interest from the Components and Group Tab. If multiple analytes need to be reported, then select additional analytes by holding the Ctrl key down and selecting each additional analyte with the mouse. Then in the Reporting menu, select Export Results > Export and Save Results Table.

Cliquid® Software Does Not Show Quantitation Values for Qualitative Transitions in the Sample List

When Cliquid® software is used to submit samples, the sample list shows only the group name instead of each individual transition (e.g., only Testosterone is shown, instead of Testosterone 1 and Testosterone 2) so only one concentration from one transition can be added. To ensure that Cliquid software reads the full transition name, an underscore in between the name and number must be added (e.g., Testosterone_1 and Testosterone_2).

What Are the Standard Addition Columns in a SCIEX OS Software Results Table?

Sciex OS software allows users to process standard addition results by selecting the Standard Addition option in the Components tab of the processing method in the Analytics mode. What do the new standard addition column headers mean?

How to Setup Standard Addition in SCIEX OS Software

If the standard addition feature is enabled in SCIEX OS software, then the results table contains new columns, including Standard Addition Accuracy that compares the Standard Addition Calculated Concentration for a sample to the Standard Addition Actual Concentration. Standard addition is enabled in the quantitation method on the Integration tab under the Options menu.

Unable to Add Users to the Security Database in Analyst® Software

When Analyst® or SCIEX OS software is launched under the local admin account, an error message is received: “The current user is not added to the security database.” This error message appears because the software was originally installed under a non-admin account.

Reporter: Unable to Report Custom Columns Created in the Analyst® Software Results Table

When a user creates a custom column in an Analyst® software results table and creates a report template using a custom tag for the custom column, the data for this custom column is not output to the report. The report template will not read the custom column unless [Custom] is added to the column name in the results table

Custom Calculations and Flagging Rules for Carryover in SCIEX OS Software

This article contains instructions on how to set up a new processing method in SCIEX OS software that has the custom calculations and flagging rules for carryover.

How Is the Full Screen Option Enabled in SCIEX OS Software?

Select the Full Screen Mode option to use SCIEX OS as the primary application. Users cannot close the software or access other software programs.

Reporter Templates Cannot Be Edited Due to Missing XML Tags

When opening a template, an error was received from the Template Content Control Manager, "Error: Specified argument was out of range of valid values." To resolve this error, the Template Content Control Manager needs to be reinstalled.

How To Organize Data Using Sub-Folders in Analyst® Software

When setting up a batch in Analyst® software, a sub-folder can be created in the project's data folder to organize data by date or acquisition time. To create the sub-folder, type a backslash next to the data file name in the Data File column.

Chromatograms Are Randomly Missing from the Report after Upgrading Microsoft Office

When a report is created using Sciex OS, MultiQuant™, or Analyst® software, one of the chromatograms is randomly missing. This issue is due to Microsoft Office 365 Apps for Enterprise or Business being installed, and this version of Office is not currently compatible with the current versions of SCIEX software.

Multiwash Section in Analyst® Device Driver 1.3 Software Is Grayed Out when Configured with Agilent 1290 MultiSampler

The Analyst® Device Driver 1.3 software includes a Multi-wash section on the Multisampler tab when the LC portion of an Analyst software method is open, but it is grayed out. If the multi-wash hardware accessory is not installed on the autosampler, the Multi-wash screen will not be available for editing.

Reporter Error: Template Not in Your Trusted Location

If a reporter error shows that the template is not in the trusted location when trying to save or move a report template, then the Trusted Locations list in Word must be updated to include locations where SCIEX reports and templates are edited.

MultiQuant™ or SCIEX OS Software: The Ion Ratios on the Report and Results Table Do Not Match

When a query file is used to calculate the ion ratio calculations in a MultiQuant™ or SCIEX OS software report, the values for the internal standards ion ratios in the report output will not match those in the results table. This issue is observed when the internal standards are not assigned to the analytes in the order in which they are listed on the quantitation/processing method.

IF Statement Syntax for Calculated Columns in SCIEX OS Software 2.1.6

Reports created with SCIEX OS software use templates with embedded tags. One of the commonly used tags is the IF statement, and the basic syntax for this tag is as follows: if(<condition>;<value if true>;<value if false>)

Adding or Removing Samples from the SCIEX OS Software Results Table

Open a results table in the Analytics workspace in SCIEX OS Software. Select the More menu > Add samples. In the Select Samples dialog, select the required samples.

Library Hits Are Missing from the Library Search Reports in Analyst® Software

When using the library search report templates in Analyst® software, the library hits or the name of the compounds that has a library match does not show up in the report. This is due to an IF statement present in the pre-installed, standard, library-search templates that checks if the library hit is greater than zero ($Libs_Max_Hit_Count>0).

Adding a Syringe Pump To a Hardware Profile in Analyst® Software

Adding a syringe pump to a hardware profile in Analyst® software is necessary if the user needs to use the syringe pump to infuse sample during manual tuning. This article provides instructions on how to update a hardware profile to include a syringe pump.

What is the Difference Between an EMC and an EMS Scan on a QTRAP® System?

The EMS and EMC scans are two different scan types that can be run on a QTRAP® system, making use of the linear ion trap (LIT) functionality. The EMS or enhanced mass scan is a full mass range MS scan in the LIT. The EMC or enhanced multiple charge scan is carried out in the LIT, where high charge state ions are selectively trapped and scanned.

Setting Up a New Project in SCIEX OS Software

Projects can be created in the Status panel by selecting the white plus sign in a circle icon next to the projects drop down menu. Selecting the button will bring up the New Project screen where the name of the New Project will be entered. Projects can also be created in the Configuration module by selecting the Projects tab.

Can Data Files Be Renamed after Acquisition Is Complete?

It's possible to change the name of a raw data file after it has been acquired in Analyst® or SCIEX OS software. Both the .wiff and .wiff.scan files would have to be named in the exact same manner or they may become corrupted.

SCIEX OS Software: Unable to Upload Exported Text File to Watson LIMS

In SCIEX OS software 2.1.6, if the internal standards appear in any location in the results table, instead of being grouped together at the bottom of the analyte list, and are distributed throughout the processing method, then the exported results text file cannot be uploaded to Watson LIMS.

How To Create Sub-project Folders in SCIEX OS Software

Within projects, data can be further organized in sub-folders in SCIEX OS software. This article explains how to create a sub-project using the Add Data Sub-Folders dialog in the Configuration workspace.

Analyst® Software: Where Are the Library Search Parameters Set?

In Analyst® software, the library search parameters such as maximum number of hits, minimum purity, hit, etc. are set in the config files that are saved under C:\Program Files (x86)\AB SCIEX\AnalystReporter\Resources\AlgorithmConfigFiles.

How to Export the Peak List in SCIEX OS Software

SCIEX OS software users can save the peak list for the currently active spectrum or chromatogram to a tab-delimited text file. This file contains information such as the centroid X-value (mass or time), peak area, height, etc.

How to Apply Regional Settings in SCIEX OS Software

This article describes how to have the Windows regional settings (language, time/date formatting and regional preferences) match the formatting in SCIEX OS software.

Is Installing a SCIEX Software Hotfix on an Unsupported Instrument Problematic?

There are no negative effects caused to software or instruments by installing SCIEX software hotfixes on an instrument model not expressly covered by the hotfix (as indicated in the release notes).

What Should I Do if the Scrollbars Are Missing in DiscoveryQuant™ Software 3.0.2 Hotfix2?

When working with DiscoveryQuant™ software 3.0.2, the scrollbars are missing, making it difficult to view the data. This issue can be resolved by installing the patch, DiscoveryQuant 3.0.2 Patch for Scrollbars and Plot Resize issue.

How Does SCIEX OS Software Calculate the Ion Ratio for a Component?

SCIEX OS software uses the regression parameter defined for the first component in the results table to calculate the ion ratio for all of the components in the results table.

Saving Consecutive Batches for the Echo® MS System to the Same Data File Impairs Peak Splitting, Automatic Processing

For data acquired with the Echo® MS system, peak splitting is performed after acquisition is complete. If a subsequent batch is acquiring data to a file while the system is splitting peaks written to that file during the previous acquisition, then a resource conflict occurs.

What Fields in DiscoveryQuant™ Software Standard Template Are Default Names?

In DiscoveryQuant™ software version 3.0.2 and version 3.0.2 with HotFix 2, default names are generated for the sample, acquisition method, and data file name fields if they are not defined in the imported LIMS file.

Queue TIC Plot Does Not Resize Properly when the Window Size Is Adjusted in DiscoverQuant™ Software 3.0.2

The patch, DiscoveryQuant™ 3.0.2 Patch for Scrollbars and Plot Resize Issue, needs to be installed to resolve the TIC plot not resizing when using DiscoveryQuant software 3.0.2.

Data File Sample Information Is Incorrect for Data acquired with Different SCIEX OS Software Versions

If data is acquired with one version of SCIEX OS software, and then data is appended to the data file (.wiff) with another version of SCIEX OS software, then the software version recorded in the data file is incorrect. The earlier software version will be shown in the File Info section, and the newer version will not be captured in the file information.

The ExionLC 2.0 System Status Icon in the Analyst®Software Is Red But Shows as Ready

Sometimes when an error occurs on the ExionLC 2.0 system, the LC status icon in the Analyst® software turns red — but the LC status may be listed as Ready. To reset the LC system, deactivate the hardware profile and then activate it again.

Differences in Date-Time Stamp for a Results Table Audit Map in Analyst® Software

In the Audit Trail Manager in Analyst® software, the audit map associated with a Results Table (accessed under the Results Tables node) might have a modified date-time that is different than the modified date-time shown with the project node (accessed under the Projects node) or in a Windows folder.

Why Does Activating the Hardware Profile in Analyst® Software Change the Date of the Instrument Data File?

For SCIEX Triple Quad™ and QTRAP® Systems, the Analyst® software creates backup instrument data parameter setting files when deactivating a hardware profile. Each time the hardware profile is activated, it loads the correct backup file according to the mode of the default instrument data and parameter setting files; because the file is changed, the date on the instrument data file also changes.

Is SCIEX OS Software Compatible with Cliquid® Software?

No, SCIEX OS software cannot coexist with the Cliquid® software on the same PC.

Location of the Analyst® Software Configuration Files

The configuration files contain the processing parameters for library searching in Analyst® software. These parameters can be changed under the ConfirmationLibrarySearch.config or MultipleCandidateLibrarySearch.config files, and these files are typically saved under C:\Program Files (x86)\AB SCIEX\AnalystReporter\Resources\AlgorithmConfigFiles.

What is the Limit of the Path Length for the SCIEX OS Software Installer to Ensure a Successful Install?

The SCIEX OS software installation folder path is limited to 118 characters or less.

Is the Shimadzu LC-40 Fluorescence Detector RF-20AXS Supported in Analyst® Software?

Yes, Analyst® software 1.7.2 can directly control the Shimadzu Nexera LC-40 fluorescence detector RF-20AXS.

Which Version of DiscoveryQuant™ Software Supports the Acquity LC on Windows 10?

The Windows 10 compatible version of DiscoveryQuant™ software that supports Acquity LC is version 3.0.1 Hotfix 2.

Can SCIEX OS Software Be Installed on a PC with Windows 10 Hotfix2?

No, SCIEX OS software cannot be installed on a PC with Windows 10 hotfix2.

Can Analyst® Software Directly Control the Shimadzu SPD-M40 Detector?

Analyst® software 1.7.2 can directly control the Shimadzu SPD-M40 detector through the Shimadzu MIMIC 2 driver that has been incorporated into Analyst software.

What is the Maximum Length of the Project Path in Analyst® Software to Submit a Batch Successfully?

In Analyst® software 1.7.2, users cannot save or submit an acquisition batch if the name of the project path is longer than 126 characters.

Delete Rights Are Not Needed to Save or Overwrite a PDF Report in Analyst® Software 1.7.2

In Analyst® software 1.7.2, delete rights are not needed to save or overwrite a PDF file to the folder where the original PDF report is saved.

Configuring a SCIEX X500 QTOF System after Downgrading SCIEX OS Software 2.0 to 1.7

After re-installing SCIEX OS software 1.7, stop the ClearCore2 service and then install the Microsoft C++ Redistributable package (vc_redis*.exe) from the install folder in the SCIEX OS 2.0 installation package. This will enable user to configure an SCIEX X500 QTOF System in the Devices workspace.

Unable to See Chromatograms when a MultiQuant™ Software Report is Printed

If the Peak Fill option is set to "Do Not Fill Peaks" in MultiQuant software, chromatograms will be faded out when output to a report and sometimes appear as not legible.

Why Is No Data Acquired in EAD Fragmentation Mode on a ZenoTOF 7600 System?

If EAD fragmentation is used in an acquisition method on a ZenoTOF 7600 system, then the accumulation time must be at least three times the reaction time. If it is not, then no data will be acquired. To resolve the issue, increase the accumulation time in the method in SCIEX OS software.

Why Does the SCIEX OS Software 2.1.6 Installer Disable the System Restore Task?

The SCIEX OS software 2.1.6 installer disables the System Restore task for better performance of the application.

When Do I Click the Confirm Button in SCIEX OS Software during Watson LIMS Data Transfer?

When transferring data to Watson LIMS from SCIEX OS software, the user must wait for the transfer to complete successfully before clicking Confirm in SCIEX OS software. It the user clicks Confirm before the transfer is complete, then the transfer status will show as failed.

Status Display Issue for ExionLC 2.0 Systems with UV/Vis Detectors in Analyst® Software

If an Exion LC 2.0 system contains a DAD or multiwavelength detector, then after the LC system and mass spectrometer go to Standby state, the Analyst® software status icon for the ExionLC 2.0 system turns yellow, but the LC system state is shown as Wait.

How Do I Display the Calibration Peak List in Analyst® Software?

This article describes how to apply the appropriate calibration peak list reference table during a tuning procedure in Analyst® software.

What Version of Analyst® Software Is Required to Run Keystone™ Converter Software?

Keystone™ converter software requires Analyst® software 1.7.2 along with a patch for the Keystone Converter software to be installed on the data-converting PC.

How Can I Create a Custom Enzyme in BioPharmaView™ 3.x Software?

This article describes how to use a different DataDictionary file to add a custom enzyme to BioPharmaView™ software. The BioPharmaView.Data dictionary file cannot be modified. This will result in a reinstall of the software.

Can Wiff1 Files Generated by SCIEX OS Software 2.1 from X500 Series Instruments be Searched with ProteinPilot™ Software?

X500 series instruments generate wiff2 file formats, but with the newest version of SCIEX OS Software 2.1, they can also generate a .wiff1 file. Only .wiff1 files can be used to perform a ProteinPilot™ software search.

Why Are My Run Times Longer after Upgrading to MPX Software 2.0?

Run times may be longer after upgrading to MPX software 2.0 because the acquisition methods may be different for the two streams. Make sure that the methods for both streams are the same.

Can I Do Any Data Processing in Keystone™ Viewer Software?

No, Keystone™ viewer software provides data viewing capabilities only.

What SCIEX Mass Spectrometer Data Files Work with Keystone Converter Software?

Keystone Converter Software can convert nominal mass (.wiff1) files, but it does not work with SCIEX OS software files or TripleTOF system files.

Does SCIEX OS Software Have Functionality To Help My lab Achieve Compliance with Regulations?

Yes. SCIEX OS software has all the key data integrity features required to reduce your regulatory risk, including configurable security, electronic signatures, and audit trails.

Will Keystone™ Viewer Software Open Any AnIML file, or Just ANIML files Converted by Keystone Converter Software?

Keystone™ viewer software displays an AnIML file, including those that were not created by Keystone converter software.

How Does the Size of a Converted AnIML File Compare to the Original Wiff File Size?

The converted AnIML file created using the Keystone™ converter software is 1.6 to 1.8 times bigger for data sets with multiple reaction monitoring (MRM) data. This is because the original .wiff.scan file is compressed, but then it is uncompressed as part of the conversion and storage process when creating the AnIML file.

What is the Source of the Atomic Weight Information in BPV Flex Software?

BPV Flex software uses the same source of atomic weight information as BioPharmaView™ software. The theoretical value required for the intact workflow uses the average molecular weight; the peptide workflow uses the monoisotopic weight.

Can a LIMS System Be Connected Directly to SCIEX OS Software?

Yes, SCIEX OS software supports the ability to send results directly to Watson LIMS. Other LIMS connections are possible through a third-party provider, Data Innovations.

Users Are Unable to Save or Submit Batches with Long File Paths in Analyst® Software 1.7.2

In Analyst® software 1.7.2, users cannot save or submit an acquisition batch if the project path is longer than 126 characters.

Does a POET Error Reflect a Possible Network Connectivity Error or an Unsupported Network Drive Type?

This article describes what to do to identify this POET error in more detail. A POET error can arise when saving a results table in Analyst® software, with the error typically arising when saving the results table file to a network drive.

Is There a "Batch-Convert" Function Available in Keystone™ Converter Software?

Yes, Keystone™ converter software offers a command line option to allow for the creation of automated processes for converting large pools of legacy data.

Can an Analyst® Software Results Table Be Opened in SCIEX OS Software?

No, an Analyst® software results table cannot be opened in SCIEX OS software. The user will have to recreate the Analyst results table in SCIEX OS software.

How Do I Install the Intact Protein Script on the TripleTOF® 5600 and 6600 Systems?

The Intact Protein script can be installed from the Analyst® TF software directory located at: C:\Program Files (x86)\Analyst\Scripts. The ShowInTuneLayout script must be installed and enabled in order to acquire intact proteins.

How to Simulate a Hardware Profile with a Mass Spectrometer and Shimadzu LC in Analyst® Software

In Analyst® software, creating a simulated hardware profile allows a user to create acquisition methods and batches when using the software on a processing PC that is not connected to an instrument. To create a simulated hardware profile, open the Hardware Configuration Editor and select a hardware profile that you would like to simulate. Then select Edit Profile.

Can ProteinPilot™ Software Version 5.0.2 Be Installed on a 2019 Server?

Yes, ProteinPilot™ software 5.0.2 can be run on a Windows 2019 Server. This was not officially tested or mentioned in the release notes, but many users have installed the Windows 10-compatible ProteinPilot software 5.0.2 on the Windows Server 2019 operating system and have run the software successfully in this environment.

What Type of Analyst® Software Data Is Used with Keystone™ Converter Software?

Keystone™ converter software will convert nominal mass .wiff1 files from Analyst® software 1.4.1 and later versions.

Magnifying Chromatogram Peaks Displayed in a SCIEX OS or MultiQuant™ Software Report

The chromatograms of peaks that are displayed in a report generated in SCIEX OS or MultiQuant™ software will retain the format of the original peaks displayed in the peak review pane. To magnify the peaks displayed in a report, the zoom settings will need to be changed in the peak review settings for MultiQuant or SCIEX OS software.

What Is the Peak Split Algorithm when Using a Marker Peak with the Echo® MS System?

The marker well in the Echo® MS System is defined by the user in the acquisition batch to generate a special barcode pattern at the beginning and end of the plate run. The barcode is a pattern composed of a narrow peak, then a pause, a wide peak, then a pause, followed by a narrow peak.

What Information Is in the AnIML File Created by the Keystone™ Converter Software?

AnIML, an open standard XML data format for storage and sharing of experimental data, is the file format that is created when a data file is converted by the Keystone™ converter software. This article details the information that is included in the converted AnIML file.

Where Can I Download Skyline Unplugged for a Windows 10 64-bit PC?

Link is provided and installations instructions are described

How to Interface MultiQuant™ Software with a LIMS System via a LIMS Report Template

Oftentimes MultiQuant™ software results table data needs to be exported and then interfaced with a LIMS system. This article explains how to indirectly transfer data from results tables created in MultiQuant software to a LIMS system via a report template. The report template creates an output file in CSV format that can then be interfaced with a LIMS system.

Can I Submit mzIdentML Files from ProteinPilot™ Software 5.x to the PRIDE Repository?

This article summarizes the issues with ProteinPilot version 5.0 and mzIdentML created files. Submission of mzIdentML files is still not automated with later versions of ProteinPilot™ software, including version 5.0.x. Complete submissions from ProteinPilot software to PRIDE are not possible, but partial submissions of the mzIdentML are, and this partial submission process is described below.

How Are Peptides Named in BPV Flex Software after in Silico Digestion?

The general rule for naming peptides in BPV Flex software is: the first peptide resulting from a proteolytic cleavage is named T1 for sequences displayed from the N-terminus to the C-terminus; moving toward the C-terminus, the second proteolytic cleaved peptide is named T2, and so forth.

How Is the New SCIEX OS Software Quantification Algorithm Better than the Original Analyst® Software Classic Algorithm?

The quantification algorithms for finding and integrating peaks in SCIEX software programs have improved significantly since the Analyst® software classic algorithm was introduced. Users of the SCIEX OS software will see two main advantages when integrating peaks with the new AutoPeak algorithm.

What Are the Advantages of the .wiff2 Data File Format?

The .wiff2 meta data file generated by SCIEX OS software is designed to offer users improved security for their data. One of the primary advantages is the .wiff2 meta data file is encrypted, which prevents software users from tampering with results.

What Is the Difference Between .wiff and .wiff2 Data Files?

There are two data file formats for data sets acquired using SCIEX mass spectrometers: 1) .wiff and 2) .wiff2. Instruments using Analyst® software to acquire data will write data sets in the .wiff format. Instruments acquiring data using SCIEX OS software (version 2.0 or lower) will write data sets in the .wiff2 format. The newer versions of SCIEX OS software (version 2.1 and greater) write data in both the .wiff and .wiff2 format.

How to Use the MAM Script in BioPharmaView™ Software 3.0.2 to Transfer Peptide Information to SCIEX OS Software

BioPharmaView™ software 3.0.2 has improved its multiple attributes monitoring (MAM) workflow, and the software now includes a script, MAM-BPV to Analytics Converter, used to create a quantitative processing method for the Analytics mode of SCIEX OS software.

Top 10 des bonnes pratiques de l’utilisateur pour minimiser les contamination des systèmes LC/MS

French Translation of Knowledge Article 000017896

Top 10 Things Users Can Do to Minimize Contamination of LC/MS Systems

Several things can be done to reduce the contamination of LC/MS systems that require minimal time but increase uptime and robustness. Here, we present a list (in no particular ranking) of the top ten things to consider when trying to lower instrument contamination.

How to Display High-Precision m/z Values in LibraryView™ Software

Select and open a compound in LibraryView™ Software. Then navigate to the MS/MS Spectra tab to view any MS/MS spectra for the compound. Select the ‘i’ button in spectrum panel, and a peak list with high precision m/z values will be displayed.

Location of the Current Instrument Data File for SCIEX Triple Quad™ or QTRAP® LC-MS/MS 7500 Systems

The current instrument data file (current.dat file) for Triple Quad™ or QTRAP® LC-MS/MS 7500 Systems is backed up to a SCIEX OS Software folder located at C:\ProgramData\SCIEX\MassSpec\InstrumentData\YYYYMMDDHHMMSS.

How Is the Peptide Score Calculated in BPV Flex™ Software 2.1?

The BPV Flex™ Software 2.1 peptide score indicates the probability that the peaks in a given MS/MS spectrum will match those of the theoretical peptide fragments by random chance. Therefore, the score calculation is derived from observed MS/MS fragments and the corresponding intensities, as well as the number of theoretical MS/MS fragments.

Can the Existing Ion Source on the X500R QTOF System Be Converted to APCI?

The source on the X500R QTOF System can be used in atmospheric-pressure chemical ionization (APCI) mode, but a different probe with a twin electrode must be installed. In addition, a different APCI tuning solution must be used and is available for purchase from SCIEX.

Reporting Values for Calculated Concentration that Are Not Equal to N/A from a Results Table

To filter results table data in a report based on the calculated concentration not equal to N/A, add the if statement $Calculated_Concentration<>"N/A".

Creating Reports where Internal Standard Peaks Appear Normalized to the Analyte Peak in Chromatograms

When viewing an analyte's chromatogram in a report, the internal standard peak that is overlaid with the analyte's is not normalized in the report's chromatogram and part of the peak appears out-of-bounds in the peak review image. If you see an internal standard peak in the peak review pane of MultiQuant™ Software or SCIEX OS Software that is not normalized to the analyte's peak size, double click on the x-axis of that particular chromatogram.

I am seeing inconsistent HPLC Peak shape. What may be the cause of this?

Summary of potential causes of poor HPLC peak shape

Displaying Analytes Horizontally and Samples Vertically on a Report

To create a report where the analytes appear horizontally (as column headers) and sample names appear vertically (at the start of a row) in a report, the For Each Analyte tag will need to be nested within the For Each Sample tag.

I am having trouble reaching temperature in the ALS Thermostat. What is the effective range of the ACMP Peltier?

The ACMP Peltier effectivity is based on the ambient temperature of the instrument. The operational range of the ACMP is between 4-40C.

Error Code 50 Appears when Creating Reports in MultiQuant™ Software

When creating reports in MultiQuant™ Software, an error appears, "Error code 50." This error is due to a corrupt file in the project folder, and a new project will need to be created.

Are PPGs Used for Tuning and Calibrating the QTRAP® or TripleQuad™ LC-MS/MS 7500 Systems?

No, a new calibrant, the MS Tuning Solution, was introduced for tuning and calibrating the QTRAP® or TripleQuad™ LC-MS/MS 7500 Systems.

Analyst® Software: How to Increase the Number of Waiting Samples in the Queue

By default the number of samples that can be submitted from the Analyst® Software queue is 100 samples. To change the number of waiting samples shown in the queue, select the Configure mode, and then navigate to the Tools menu. Select Settings and then Queue Options. Type in a desired number for Max Num Waiting Samples, and then click OK.

Can Multiple Users Log In to Windows while Analyst® MD Software Is Acquiring Data?

If a user starts a batch using Analyst® MD Software and then signs out of their Windows account while Analyst Software is acquiring data, the software will close and suspend the run. It is not recommended to sign out of a user's Windows account if Analyst MD Software is acquiring data.

Using an Older Version to Open a Processing Method Created in a Newer Version of SCIEX OS Software

The files created in SCIEX OS Software are not backwards compatible with other versions of the software. An error will appear when a processing method created with a higher version of SCIEX OS Software (e.g., 2.0) is opened with a previous version of SCIEX OS Software (e.g., 1.7). To open a processing method created in the latest version of SCIEX OS Software with the older version, export the processing method as a text file.

How Is Relative Retention Time Calculated?

For analytes using an internal standard, the actual retention time (RT) of the internal standard peak (for the corresponding sample) is first determined. The expected RT for the analyte is determined by multiplying the specified expected RT by the ratio of the actual to the expected RT for the internal standard.

Where Is the Executable File for Excel Saved on My Computer?

The executable file for Excel – Excel.exe – is located in the installation directory for the 64-bit version of Microsoft Office 365 at C:\Program Files\Microsoft Office\root\Office16. 

How to Sum the Concentrations of Isomers in SCIEX OS Software

To add the concentrations of different isomers together when processing data in SCIEX OS Software, open a processing method in the Analytics mode of the software. Select the Calculated Columns tab in the processing method and then select Add Formula to create a custom calculation for adding the isomers.  

How to Open a Reporter Query Used with SCIEX OS or MultiQuant Software Report Templates

This article discusses the three ways to open a query (a file with the extension .query), a file linked to a report template that can be used to perform more complicated calculations or sorting functions in a results table.

Where Is the License File Saved to Activate a SCIEX Library Used with SCIEX OS Software?

For libraries imported into SCIEX OS Software and used with LibraryView 1.x Software, the license file needs to be saved to the directory C:\Program Files\AB SCIEX\LibraryView\LibraryViewFramework\Server in order to unlock the library and activate it.

When Should I Use Retrieve Configuration in Analyst® Device Driver Configure Mode?

In Analyst® Device Driver, when adding or changing a CTC PAL3 autosampler configuration, the Retrieve Configuration command must be performed in the Configure mode in the CTC PAL3 LC sampler dialog.

What Value Should Be Used for the XIC Width in My SWATH® Acquisition MicroApp Processing Settings?

One common error when using the SWATH® Acquisition MicroApp 2.0.1 for processing SWATH data is to relate the XIC width setting in the processing software with the mass accuracy of the instrument, and set the XIC width to a value that is too low. XIC extraction widths should be set to 50 to 75 ppm, regardless of the mass accuracy of the acquired data.

Connecting to a New Compound Database Library in Analyst® Software

The steps needed to connect to a new compound database library in Analyst® Software are detailed in this article.

Unable to Open SCIEX Cloud ProteinPilot™ Software Searches with the Desktop Version 5.0.2

The version of ProteinPilot™ Software in the SCIEX Cloud is version 5.0.3; therefore, group files created in the SCIEX Cloud cannot be downloaded to a desktop and opened in ProteinPilot Software 5.0.2. To download and read a group file on a desktop installation of ProteinPilot Software, the desktop version must be upgraded to version 5.0.3.

Can I Use Windows Experience Enhancers on My SCIEX Acquisition and Processing PCs?

Some PC users prefer different views and/or functionalities in the new Windows 10 interface. There are freeware/shareware programs available that allow for the customization of Windows features (such as emulation of Windows Classic settings). However, these types of Windows accessory programs have not been tested with SCIEX software; their use is not supported.

MasterView™ Software Report Error: Object Reference Not Set to an Instance of an Object

When creating are report in the PeakView®/MasterView™ Software suite, the following error appears: "Object reference not set to an instance of an object." This error occurred because a file other than a report template was selected during the create report process.

Why Do the Results for Some Analytes Shift to a New Column in a CSV Report?

When reporting results table values to a comma-separated values (CSV) report, for some analytes, the reported information is shifted from the correct column to one column over to the left. This column-shifting issue is observed when an analyte name contains a comma.

Which Glycan Notation Is Used in the BioPharmaView™ Software?

The glycan notation used in BioPharmaView™ Software is the Oxford style.

Is the Digital PicoView® Ion Source Compatible with Analyst® TF Software 1.8.x?

Both Analyst® TF Software 1.8.x and the software for the Digital PicoView® Nanospray Ion Source will work together with the Windows 10 operating system. This was tested and confirmed separately by both manufacturers, SCIEX and New Objective. 

Remote Data Access Software Error on MALDI TOF/TOF™ instruments

When setting up ProteinPilot™ Software or the imaging acquisition software for the MALDI TOF/TOF™ Systems, a RDA (Remote Data Access) software error message is received: "TOF/TOF Imaging Acquisition Software. The client components used to communicate with the instrument are newer than those found on the instrument. Please update the Remote Data Access service on the instrument."

Electronically Resetting the X-series QTOF MS Systems (X500R and X500B)

The steps required to reset the X-series QTOF MS Systems (X500R and X500B) are described here.

What File Formats Can Be Converted with the Newest Version of ProteoWizard Software?

This newest version of ProteoWizard software, version 3.0.20258-97f41f698, can now convert files to the txt format, as well as the three original file types (MGF, mzML and mzXML). For SCIEX software users, the txt file might be a useful option; however, the quality of the output file from ProteoWizard has not tested.

Filtering Audit Trail Events Using a Set of Specified Criteria in SCIEX OS Software

The audited events in the audit trail can be filtered using a set of specified criteria in SCIEX OS Software by selecting the Filter icon in the upper task bar on the Audit Trail screen.

ProteinPilot™ Search Error: Unhandled Exception: Out Of Memory Exception

During a search with ProteinPilot™ Software 5.0, 5.0.1 and 5.0.3, the error "Unhandled Exception: Out Of Memory Exception" appears. This issue is due to the LC/MS reconstruct crashing within the ProteinPilot Software when data sets with a high MS1 scan speed are being processed.

How Inclusion or Exclusion Lists Are Imported into Analyst® TF Software

This article describes how a text file can be created to import an inclusion or exclusion list into Analyst® TF software when building an IDA method.

Can I Use My Own Calibrant Solution to Tune the QTRAP® or TripleQuad™ LC-MS/MS 7500 System?

To tune and calibrate a SCIEX QTRAP® or TripleQuad™  LC-MS/MS 7500 system, a new calibrant, called the MS Tuning Solution, was recently introduced and must be used to tune the new instrument.

How Can Audit Trail Records Be Viewed from SCIEX OS Software?

To view audit trail records in Sciex OS Software, open the Audit Trail workspace. The Audit Trial screen will appear. Select Workstation in the left pane to view the audit trail for the workstation. Select Project in the left pane to view the audit trail for the project of interest.

Can the SCIEX QTRAP® or TripleQuad™ 7500 LC-MS/MS System Operate without E Lens™ Technology Active?

Yes, the SCIEX QTRAP® or TripleQuad™ 7500 LC-MS/MS Systems can operate without the E Lens™ Technology active. Each QTRAP and TripleQuad 7500 System comes with a blanking plug that can be inserted should there be a need to operate without the E Lens Technology.

Are the Ion Sources Interchangeable Between the QTRAP® and TripleQuad™ 6500+ and 7500 Systems?

The ion sources for the SCIEX QTRAP® and TripleQuad™ 6500+ and 7500 LC-MS/MS Systems are not interchangeable. The OptiFlow® Pro Ion Source cannot be used on the QTRAP or TripleQuad 6500+ Systems. Likewise, the IonDrive™ Turbo V, Turbo V™, and OptiFlow Ion Sources cannot be used with the QTRAP and TripleQuad 7500 Systems. 

Creating a ProteinPilot Software Winner Proteins Results List as FASTA File

This article describes the steps for creating a FASTA file from a ProteinPilot™ software report of winner proteins.

Flags or Custom Results Are Not Showing Correctly on a SCIEX OS Software Report

A mismatch of index can occur when internal standard values from a SCIEX OS software results table are processed within a query, causing the text for the reported values to appear bolded and in red, even when there is no reason for flagging these values in the report itself. This phenomena is observed for results tables created in versions of SCIEX OS Software 1.6.1 or lower and has been fixed in versions of SCIEX OS software 1.7 or greater.

How to Print an Acquisition Method in Analyst® Software

To print an acquisition method in Analyst® software directly from the .wiff file, open data file under the Explore mode and then click on the i icon in the toolbar for the data file's information. Activate the file info pane by selecting it, and then go to File > Print > Pane.

Is the E Lens™ Technology Used in the OptiFlow® Pro Ion Source Compatible with Atmospheric Pressure Chemical Ionization??

No, the E Lens™ Technology integrated into the SCIEX Triple Quad™ 7500 LC-MS/MS System has been designed for electrospray ionization (ESI) mode of analysis and is not compatible with atmospheric pressure chemical ionization (APCI).

Can the Probes and Electrodes for the OptiFlow® Ion Source Be Used with the OptiFlow Pro Ion Source?

The probes and electrodes for the OptiFlow® Ion Source can be used with the OptiFlow Pro Ion Source.

Does SCIEX OS Software Offer Tools To Assist with Achieving 21 CFR Part 11 Compliance?

The features within SCIEX OS software that help users achieve 21 CFR Part 11 compliance are explored in the article, "SCIEX OS LC/MS Software and 21 CFR Part 11 Regulations".

How to Apply an External Calibration Curve to a Results Table in MultiQuant™ Software

In MultiQuant™ software, a previously-created calibration curve can be imported into a results table and applied to the existing unknown samples. In the old results table with the calibration curve that you would like to export, ensure the standard samples are present and select the Process menu. Then select Export Calibration, name the calibration curve data, and click Save.

Is There an Equivalent to Single User Mode in SCIEX OS Software 2.0?

Single user mode is a security mode in Analyst® software that allows for any user that is logged in to a PC using any Windows account to access the software as an administrator. However, there is not currently an equivalent to single user mode in the SCIEX OS software. The security mode options in SCIEX OS software are limited to integrated mode and mixed mode.

How to Set the Parameter Settings in Analyst® Software Back to Original Factory Settings

The parameters settings in Analyst® software can be set back to the original, default factory settings by selecting the Parameter Settings option from the Tools menu and then using the Factory Settings button to reset the parameters of the selected scan type.

How to Remove the Extra Characters from an Analyte Name in a Report

To report the analyte name in a report without additional characters showing after the name, use the TRIM and LEN functions in the expression written in the Math Field Type tag in the report template.

Controlled Ways to Output Data from SCIEX OS Software

The controlled ways to output data from the SCIEX OS software Analytics workspace include 1) exporting a results table; 2) Transferring  the results table data to a LIMS; and 3) Creating a report though the Reporting tab option Create Report and Save Results Table.

Adding a Flag or a Custom Flag Created in SCIEX OS Software to a Report

After creating a new results table in SCIEX OS software, add the Outlier Reasons column in the quantitation method to the Input tab of a query. Then, in the AnalystCalculations tab of the query, use the search function to find the flag of interest. Have the Outlier Reasons column added to the query's Output tab, and then link the Outlier Reasons column to the report template using a custom tag.

Where Are the Files Containing the Hardware Profiles Stored in Analyst® Software?

The hardware profiles created in Analyst® software are stored in the API Instrument project folder in the Configuration sub-directory: C:\Analyst Data\Projects\API Instrument\Configuration.

What Is a Regular Expression?

A regular expression (regex), also called a rational expression, is a sequence of alphanumeric and/or special characters that can define a search pattern depending on their context.

Does the Echo MS System Support All QTRAP® 6500+ System Functionality?

The Echo® MS System cannot be supported by the QTRAP® 6500+ System; instead, Echo MS is paired with the TripleQuad 6500+ System for data acquisition.

Initiate Transfer to Watson LIMS in SCIEX OS Software Prevents Analyst® Software from Launching

When the feature Initiate Transfer to Watson LIMS is selected in SCIEX OS software, software users find that the Analyst® software installed on the same workstation will no longer launch. This is the expected behavior for Analyst software and depends on the configuration and the installation order of other SCIEX software that were installed on the same PC. 

Adding Custom Columns to a SCIEX OS Software Report Template

In SCIEX OS software, a custom column added to a results table can be included in a report template with a custom tag.

Reporter: Why Did the Outlier Reasons Column Change Color after Running a MultiQuant™ Software Query?

The text in the outlier reasons column will change from black to pink if the column value exceeds the cutoff value in  MultiQuant™ software. If a query is run after creating the MultiQuant software results table, the flagging color of the query overrides the flagging color of the outlier reasons column in the results table.

Can I Change the Sorting Order for Project Folders in Analyst® Software?

Analyst® software does not have not have internal sorting logic, so to sort projects, the API functions, FindFirstFile and FindNextFile, are used to retrieve the files from the directory. The order in which the file names are returned is dependent on file system type (NTFS, CDFS or FAT).

Restoring Icons to the Analyst® Software Toolbar

To restore missing toolbars in Analyst® software, select the Tools menu, and then select the Restore Default Toolbars option. This should restore the icons that were not showing previously. 

Recovering a Lost or Corrupted Acquisition Method in Analyst™ Software

To recover or recreate an acquisition method that was lost or corrupted in Analyst™ Software, click in the information pane of an older data file, and then right click and choose Save Acquisition Method.

How to Improve SCIEX OS Software Performance during Data Analysis

SCIEX OS software may perform slowly during data analysis due to the location of the data files being processed. Relocating data files from a temporary location (such as the Windows desktop) to a SCIEX OS or Analyst software project folder that is located in the root directory mapped in the Configuration module of SCIEX OS software may improve the software performance. 

Watson LIMS Needs To Be in Compatibility Mode for Use with SCIEX OS Software

When transferring data from SCIEX OS software to Watson LIMS, the Watson software did not appear to be importing the data.

Where Are the Event Logs for SCIEX OS Software Archived?

When event logs in SCIEX OS software become too large, the software will create an archive event log file. This file is located in the directory C:\ProgramData\SCIEX\Clearcore2.Acquisition.

Turning the Checksum Option On or Off in Analyst® Software

In order to turn the checksum option on in Analyst® software, select the View menu and then choose Audit Trail Manager.

Where Can I Find My Hardware Profile in SCIEX OS Software?

The hardware profiles for instruments supported by SCIEX OS software are stored in a file called HardwareProfile.hwp that is located in the following directory: C:\ProgramData\SCIEX\Clearcore2.Acquisition.

Adding Custom Columns to a Results Table in Analyst™ Software

To add custom columns to a results table in Analyst™ software, right click within an open results table and select the option Add Custom Column.

Is There a Password Character Limit for Accessing Analyst® Software in Mixed Mode?

Passwords used to access Analyst® software in mixed mode are capped at 13 characters. If your internal IT policy for the Windows password specifies more characters, this longer password requirement may lock the user out of Analyst software in mixed mode.

Where is the SCIEX OS Software Security Database Found?

The SCIEX OS software security database files are located at C:\ProgramData\SCIEX\Clearcore2.Acquisition, and the file is called Security.data.

How to Export a Statistics Table From SCIEX OS Software to Excel

The statistics pane can be accessed from the Views menu in the Analytics module of SCIEX OS software. After opening the results table, select Statistics pane from the Views menu and a new table appears below the results table. To export the contents of the statistics table from SCIEX OS, the table can be copied to Excel by highlighting all rows, and then selecting Ctrl+C. In an open Excel spreadsheet, the selected columns and rows can be pasted using Ctrl+V.

Adding an Arrow in MultiQuant™ Software to Display the Expected Retention Time during Peak Review

In MultiQuant™ software, an arrow can be added to the peak review chromatogram window to represent the expected retention time. To do this, right click within the peak review pane and select Options from the list. A Peak Review Options popup window will appear. Check the option Mark Expected RT with Arrow under the Appearance tab. Then select OK. 

Resolving the Analyst® Software 1.7 Error: Feature Has Expired

The licensing error, Feature has expired, appears when Analyst® software 1.7 is launched. This article explains how to replace the license file to resolve the error.

What Is the SCIEX OS Software Equivalent to the Area Threshold Feature in Analyst® Software?

SCIEX OS software does not have a field for the Area Threshold as found in the Analyst® software quantitation method wizard that allows users to set the criteria for peaks to appear as "not found" in a results table. Instead, a custom flagging rule must be created in SCIEX OS software to enable this type of filtering for peak area.

What Cable Should I Use To Connect PAL3 to an Agilent Pump when Using Analyst® Device Driver?

A sync cable, called the PAL connecting cable APG Remote, should be used to connect the PAL3 autosampler to an Agilent pump when both the devices are configured through the Analyst® Device Driver (ADD).

Can Regular Expressions (Regexes) Used for Data Filtering in SCIEX OS Software Be Saved?

To export and import filter settings so they can be used across multiple results tables and projects in SCIEX OS software, a regular expression (regex) can be created using a custom filter in an existing results table. The custom settings can be exported as a .cset file using the Table Display Settings export feature and reapplied to another table using the Import feature.

Differences between iTRAQ® Reagents Application Kit - Protein (4374321) and iTRAQ® Reagent 4Plex or 8Plex Kits

This article describes the different workflows for the iTRAQ® Reagents Application Kit - Protein (4374321) and the iTRAQ Reagents - 4plex or 8plex kits.

Incorrect Argument Error when Adding Standards to a Results Table in SCIEX OS Software

When adding multiple standard samples with the same name to a results table in SCIEX OS software, an error was generated: "Incorrect Argument. An item with the same key has already been added." This article explains the workflow that generates this error and provides a workaround.

Why Do I Receive Memory Concerns Warning when Processing Data in MultiQuant™ Software?

When processing a large data set in MultiQuant™ software 3.0.3, users may see a Memory Concerns message, "The Results Table you opened may cause out of memory computer issues. To free-up memory close other applications and any other opened results table." This message is a warning, not an error message, regarding the amount of memory required to process and display a large data set.

Differences between “Find Any” and “Find” in FormulaFinder in SCIEX OS Software

In SCIEX OS software, the “Find Any” function in Formula Finder considers just the monoisotopic peak to be within the m/z tolerance. Both odd (in italics) and even electron elemental compositions are provided. When using “Find Any” element ranges “From” and “To” are considered. The “Find” function in Formula Finder uses all constraints, including the mass tolerance for all selected peaks in the isotope pattern and the settings from the Options dialog.

How to Change the Font in a Report Template?

Use these instructions to change the font of the text appearing in a report.

Can I Use a Regular Expression (Regex) to Filter Data in SCIEX OS Software?

A regular expression (regex) can be used to filter data in a results tables and in reports created with SCIEX OS software.

Can BioPharmaView™ and BPV Flex Software Coexist on the Same Computer?

BioPharmaView™ Software 3.x and BioPharmaView (BPV) Flex Software 2.x are compatible and can be installed on the same computer.

Is the Impurity Feature Available in BPV Flex Software?

This is a known issue in the ProteinPilot™ software 5.0.2 and was resolved with a patch.

SQLite Exception Error in the Regulated Version of SCIEX OS Software

While setting up the regulated version of SCIEX OS software (CFR features activated), the following error message appeared when accessing the Audit Map portion of SCIEX OS software: "System.Data.SQLite.SQLiteException : unable to open database file." To resolve this issue, change the Windows permissions so that the user has full access to Audit Trail files.

What Software Is Supported for Analysis of Data from the Echo® MS System?

Once data collection from a well plate has been completed on the Echo® MS System, a .csv file is created for each well, in addition to another file that contains all of the data from the well plate. The .csv files can be imported into any data visualization software for further analysis, or the .wiff2 data can also be reviewed in SCIEX OS software. The data set contains the sample name, well location, component name, peak area, peak height, and peak width.

What is the Supported Control Software for the Echo® MS System?

The Echo® MS System is controlled by SCIEX OS software, version 1.6.10. This is the only supported software for direct control of this instrumentation. SCIEX OS software supports an open application programming interface (API) for the creation of integrated control through third-party automation software packages.

What Sample Matrices Are Supported on the Echo® MS System?

The sample matrices that can be supported on the Echo® MS system must correspond to one of the supported liquid classes, either AQ or SP.

Is It Possible To Monitor More MRMs Per Well than Specified for the Echo MS System?

Yes. The specified four MRMs per well is based on the peak width from a single droplet ejection.

Issue when Exporting and Importing Text Files into MultiQuant or SCIEX OS Software

Excel can insert extra characters in exported forms of the MultiQuant™ or SCIEX OS software data and corrupts this data; the resolution here is to edit the exported file and use another editor, other than Excel, that does not insert extra characters into text.

How To Provide Selective Access to Analyst® Software Projects

To set access for select users at the project level in Analyst® software, the security configuration must be updated.

Why Won't LipidView™ Software Load My Analyst® Software (.wiff) Data Files?

In order to load Analyst® software data files (.wiff files) into LipidView™ software, either Analyst or Analyst TF software must be installed alongside LipidView.

Locating the Name of a Server or PC Using the Command Prompt Window

This article describes the DOS commands used to access the name of the server or PC.

How to Extract Multiple XICs in Separate Windows in Analyst® Software Explore Mode

Sometimes in the Analyst® software Explore mode, it's optimal to view individual extracted ion chromatograms (XICs) in separate panes instead of in the same windows when extracting multiple ions from a total ion chromatogram (TIC). To prevent multiple XICs from appearing in the same window, the Appearance Option settings in Analyst software will need to be adjusted.

Locating the Most Recent Quantitation Method Used in MultiQuant™ Software

To locate the most recently used quantitation methods used in MultiQuant™ software, select the File menu and then select the Recent Quantitation Methods option. This menu option allows for the most recently accessed methods to be viewed.

Resolving the Analyst® Software RackBuilder.exe Error Message: Failed To Open Database AutosamplerPoetDb

When running the RackBuilder.exe, an error message is received: "Failed to open database AutosamplerPoetDb". This error can be cleared by setting the Windows User Account Control (UAC) settings to level 4 (Never notify) and then rebooting the computer.

Removing Rows Releated to Internal Standards from a MultiQuant™ Software Table

If its not desirable to view the internal standard information in a MultiQuant™ software results table, de-select the IS button by clicking on the binoculars icon in the Components & Groups column.

Locating the Name of a Server or PC Using the Command Prompt Window

This article describes the DOS commands used to access the name of the server or PC.

C Drive Free Space Requirements when Using SCIEX OS Software

SCIEX OS software performs best when 20 GB of free space is available on the C drive (C:). Furthermore, SCIEX OS software creates log files in order to monitor both instrument (on an acquisition PC) and software (on both acquisition and processing PC's) performance. These log files incremently increase and can accumulate to a total size of 35 GB. This sets a limit of 55 GB of space needed on the C drive to use SCIEX OS software optimally.

Obtaining Intensity Information from an IDA-EPI MS/MS Spectra

To obtain the intensity information from an IDA-EPI MS/MS spectra, the ProteoWizard data conversion tool, MSConvert, can convert SCIEX data files (.wiff and .wiff.scan) to other formats using MSConvert besides mzML, such as MGF or txt formats. These non-mzML formats create larger files but provide the spectral data in simple mass/intensity text.

Installing ProteinPilot™ 4.5 and 5.0.x Software on the Same PC

For software users who need to view the older group files, maintaining a separate computer with ProteinPilot™ software 4.0 installed is the recommended best approach. Alternatively, both versions, 5.0.x and an older version, can be installed on the same computer, but this is an unsupported configuration.

Obtaining a Smaller Volume Divert Valve for a 4500, 5500 and 6500 LCMS Systems

To obtain a smaller volume divert valve for a 4500, 5500 or 6500 LCMS system, a new part must be ordered from Valco, part number of C52-2006I.

DiscoveryQuant™ Software Will Not Launch Without Analyst® Software Installed

If DiscoveryQuant™ software fails to launch, even after the software is uninstalled and reinstalled, check to see if Analyst® software is also installed. An installed version of Analyst software is a prerequisite to installing DiscoveryQuant software; DiscoveryQuant software will not launch without Analyst software.

Printing an Unsecured Report as a PDF with MultQuant™ or SCIEX OS Software

Reports printed as PDF files from either SCIEX OS or MultiQuant™ software are always secure because they are printed using pdfFactory. A workaround must be used to print unsecured PDF reports.

Altering Parameters in PPG Tuning Methods Causes Mass Shift and Resolution Issues

Changing any of the source or compound parameters in a PPG tuning method (such as Q1PosPPG.dam located in the API Instrument project folder in the Analyst Data folder) causes mass shift and resolution issues in the resulting data file.

What Library Database File Types Can Be Imported into LibraryView™ Software 1.4?

Many different types of compound and library databases can be imported into LibraryView™ software version 1.4. The following options for source files are acceptable for importing library compounds into LibraryView software: LibraryView Package (*.lbp), DiscoveryQuant™ Compound Database (*.mdb), Analyst® Compound Database (*.mdb), Cliquid® Package (.clq), Excel file (*.xls), Overwrite Database with LibraryView Snapshot (*.lbp), and Third Party Library Package (*.tplp)

What Is the Correct Format for the Client License Text for Software Using a Concurrent License?

To create and set up the license on the client PC for software using concurrent license server, the license text should be formatted as follows: SERVER [SERVERNAME.DOMAIN.COM or IP ADDRESS] ANY [PORT NUMBER] VENDOR ScxMSSW0 USE_SERVER

What Is the Best Way to Back Up My Library Compounds in LibraryView™ Software?

This article provides some guidance on best practices for backing up your library compounds stored in LibraryView™ software. Its recommended that a snapshot is created of the library every time the library is updated or edited.

What Are the Most Common Installation Issues for SCIEX OS Software 1.7?

Some of the most commonly observed installation issues with SCIEX OS software 1.7 are summarized here. Instructions on how to uninstall previous versions of SCIEX OS software are also included.

What is the Analyst® Diagnostic Tool and How Can It Help Me?

Analyst® Diagnostic Tool is an information-gathering program that is designed to provide insight on performance issues with Analyst software and the computer's operating system.

ZenoTOF 7600 系统的故障排查：调谐和校准

This is a known issue in the ProteinPilot™ software 5.0.2 and was resolved with a patch.

ZenoTOF 7600 系统的故障排查：运行中的校准不通过

This is a known issue in the ProteinPilot™ software 5.0.2 and was resolved with a patch.

Accessing ProteinPilot™ Software Searching in the SCIEX Cloud Workspace

To log into the SCIEX Cloud workspace and access the ProteinPilot™ software searching features with just your CloudConnect license, follow the instructions below.

How to Determine if the Acquisition PC Has a Bad Ethernet Card?

This article summarizes some issues that might contribute or confirm a bad network card.

Missing Columns when Exporting the Protein Summary from ProteinPilot™ Software 5.0.2?

This is a known issue in the ProteinPilot™ software 5.0.2 and was resolved with a patch.

Checking for Administrator Rights on a Windows 10 PC before Installing Analyst®/SCIEX OS software

There are three simple steps to determine which Windows users are listed as administrators before installing SCIEX software.

Is Cliquid® 3.4 Software Compatible with MPX™ 2.0 Software?

MPX™ Software is compatible with Cliquid® software and can be operated through the Cliquid software console; however, the Cliquid software Walk-up mode is not available.

Which Version of Watson LIMS Is Compatible with SCIEX OS Software 1.7?

SCIEX OS software 1.7 has been tested with Watson LIMS server/client version 7.6, Oracle server/client 12.2.0.1.0 SE (64-bit) and 12.2.0.1.0 (32-bit).

Is Digital PicoView® Source Windows 10 compatible?

Digital PicoView® Source is a nano ion source from New Objectives that is Windows 10 compatible and can be used with many SCIEX mass spectrometers.

Setting Up Email Notifications for Reports in Cliquid® Software

To allow the system to deliver email notifications of reports generated in Cliquid® software, select Run Samples. In the menu option Set report options, users can choose to set up the email notifications for completed reports or indicate their preference to have a pdf version of the report emailed to them directly.

Windows 7 and 10 Operating Systems Are Compatible with Analyst® Administrator Console 3.0

Windows 7 and 10 operating systems are compatible with Analyst® Administrator Console 3.0 software.

How to Export UV Data into a Text File in SCIEX OS Software

Open a data file that also contains UV data in SCIEX OS software in the Explorer module. Locate the Show menu and select UV/DAD/ADC Channel. Once UV trace is displayed, click Data and Peaks Table under the Show menu to display the table. Export the data by right clicking on the table and selecting Export Data as Text from the menu.

Removing Server Path Names in the MultiQuant™ Software LIMS Transfer Dialog

In order to enter the correct server address to enable LIMS transfers in MultiQuant™ software, delete the FilesFolderOptions.xml file in the folder C:\Users\User.Name\AppData\Roaming\AB SCIEX\MultiQuant3 and then restart the software.

Location of the Event Logs for the MPX 2.0 Driver Software System

The event logs for the MPX 2.0 driver software system are saved under C:\Program Data\SCIEX\MPX Driver\Log\.

Unable to Import Batch Files in XLSX Format in the Batch Editor in Analyst® 1.7 Software

Importing an XLSX batch file into Analyst® 1.7 software may cause an error, and the batch file import will not be successful. The XLSX format is only available if the version of Microsoft Office that is installed is a 32-bit application. Users with a 64-bit version of Office will see these batch import errors, and must install additional software components to support XLSX type spreadsheets with Analyst software.

How To Create an Unsecured PDF Report in Sciex OS Software

In order to create reports in SCIEX OS software in the portable document format (PDF) that are unsecured, the PDF setting in the SCIEX OS config file will need to be updated. Please follow below instructions to edit the config file.

How to Install Skyline Software on an Off-Line Computer

To download Skyline software on a computer that is not connected to the internet, use the Unplugged installer or the Administrator installer:

How to Group Analytes in an Analyst® Software Results Table

To place multiple analytes (or multiple transitions for the same analyte) into a group within a results table in Analyst® software results table, follow the steps outlined in this article.

Where Are the Report Templates for BioPharmaView™ Software Stored?

The file folder locations of the report templates for BioPharmaView™ software are listed in this article.

How Do I Create a Dump File?

A SCIEX technical support agent may ask you to create and send a dump file to provide a snapshot of a SCIEX software application's processes, loaded modules and memory at a certain time point. This article explains how a dump file is created.

Can Xcalibur Software 3.x and Eksigent Software 4.3 Operate on Windows 10?

SCIEX's Eksigent software and Thermo Scientific's Xcalibur software have not officially been tested together on a Windows 10 operating system. The Eksignet software can be installed on a Windows 10 PC, but then it cannot be configured with any Xcalibur software versions. However, both software types can be configured together on a system running Windows 7, 64-bit.

How to Add Select Samples to a Report Created in SCIEX OS Software

To add only selected samples from a results table created in SCIEX OS software in a report, uncheck the Reportable column for the sample you do not want to report. Then edit your report template to include an If statement within a ForEachSample loop to include $Reportable="TRUE".

Sciex OS Software Report Error: An Item with the Same Key Has Already Been Added

An error was received while using Sciex OS software to generate a report: "Error during Report generation. An item with the same key has already been added." No report was generated. To resolve this issue, open the report template and see if a query file is linked through the Meta Field tag. If a query is linked, open the query and evaluate it for any duplicate column names. Delete any duplicate columns from the input sheet.

Which Folders Should Be Backed Up Before Upgrading the SCIEX OS Software?

Prior to upgrading or removing SCIEX OS software, back up the SCIEX OS Data folder and the SCIEX folder in the Program Data folder.

Is the MPX™ Driver Software System Compatible with Analyst® MD software?

The MPX™ driver software system is not supported with Analyst® MD software. Compatible LC systems are listed in the installation guide for Analyst MD software.

Using an External Calibration Curve in SCIEX OS-MQ Software

To use an external calibration curve with a results table created in SCIEX OS-MQ software, use the Export calibration (and save results...) feature in the Options menu after the calibration curve has been generated.

How To Enable the New Intact Protein Quant Feature in SCIEX OS 1.7 Software

The Intact Quant feature in Sciex OS 1.7 software platform enables the quantitative processing of intact proteins without sample prep and allows for the complete and compliant intact reconstruction of protein data sets. To activate this feature, an additional, add-on software license, SCIEX OS IntactQuant 1.7 (part number 5078597), must be installed in the C:\ Program Files\SCIEX\SCIEX OS folder.

Common Project Area Folder Write Access Error in SCIEX OS Software

When creating a new project in SCIEX OS software, the following error was received: The current user does not have write access to the requested project. This issue was resolved by copying the common-project-area folder in the SCIEX OS Data folder over from a different PC with an intact root directory.

How To Generate a List of All Installed Programs and Windows Updates

To generate a list of all programs installed on a PC and a list of Windows updates, select the Programs and Features icon in the control panel. A list of all installed Windows updates can be created from the View Installed Updates screen.

Upgrading SCIEX Software Licenses

How to upgrade self-upgrade registered software licenses

General Guidance for Antivirus and Backup Software Used on Acquisition PCs

The antivirus or backup software on Analyst® software acquisition workstations should be configured in a manner that will disable real-time scanning and archiving of files in the Analyst Data folder.

What Is the Exact Mass that iTRAQ® Reagents Add to Peptides?

SCIEX does supply the masses of the labels in the iTRAQ® Reagent 4plex and 8plex kits, but masses with more significant figures can be found at www.unimod.org.

How Is a Formula Column Added to a Result Table in Analyst® Software?

To add a formula column to a results table in Analyst® software, right click on the results table and select Add Formula Column.

Reporter 3.2: How To Report Calculated Concentrations of "<0" or "N/A"

If a MultiQuant™ or Analyst® software results table contains values of "<0" and "N/A" for some calculated concentration values, these text values must be converted to a numerical zero value first using an Excel query. These calculated concentration values cannot be filtered into a Reporter Template Suite 3.2 results template using an if statement that selects for calculated concentration values that are less than or equal to zero.

Why Do the Calculated Concentration Values Show as Degenerate in SCIEX OS Software?

In SCIEX OS software, if a value in the Calculated Concentration column displays as degenerate, this is because the values for Actual Concentration for standard samples have not been added to the results table.

What Parameters in ProteoWizard Are Needed when Converting .wiff2 Files to mzXML Files?

The parameter settings, including the PeakPicking value, that are used for converting .wiff2 files to mzXML or mzML files in ProteoWizard, are explained in more detail here.

Does the XCMSPlus Software Use MS/MS Data Matching to Identify Metabolites?

XCMSplus software does not use MS/MS matching to identify features. Instead, this software identifies features based on the precursor m/z.

Causes of the taglet.exe Error in ProteinPilot™ Software

The taglet.exe error in ProteinPilot™ software is due to a wide range of issues including incorrect language settings, installation of the software on the incorrect operating system, and the incorrect addition of modifications — to name a few.

Saving Custom Columns As Default Columns in MultiQuant™ Software

To routinely add the same custom columns to each newly generated MultiQuant results table, custom columns can be added to the table in the Batch Editor in Analyst® software that is created before acquiring a data set.

AB SCIEX Data Explorer® Software Issue: Periodic Table and Other Software Features Are Grayed Out

The AB SCIEX Data Explorer® software is an embedded software for data processing on the 4800 MALDI TOF/TOF™ and the TOF/TOF™ 5800 Systems and was recently rebranded; however, the rebranding process caused certain applications menu items to become grayed out (periodic table, isotope calculator, and elemental composition). To resolve this issue, install the patch provided in the link in this article.

Does My Acquisition PC Have a Bad Ethernet Card?

This article summarizes some issues that might contribute to a bad network card.

The Peakfinding Algorithm in SimGlycan® Software Improves Search Results on SCIEX Datasets

The Peak Detection & Picking feature in SimGlycan® software versions 5.9.2 and higher offer an improved peak-picking algorithm that is faster and more efficient at handling data from SCIEX TripleTOF® LC-MS/MS System instruments.

Why Use the Enterprise Edition of SimGlycan® Software?

SimGlycan Software (a product of PREMIER Biosoft) predicts glycan and glycopeptide structures from SCIEX mass spectrometer-acquired MS/MS data. Some of the advantages of using the enterprise edition of SimGlycan software include being able to create glycan templates so that novel glycan structures can be added to the database.

What is SimGlycan Software?

SimGlycan® software is a comprehensive glycan and glycopeptide drawing and structure analysis software.

Does SimGlycan® Software Use .wiff2 File Formats from X500 Series Instruments?

This article describes the possible file input formats for SimGlycan® software.

Upgrading to Analyst® TF Software 1.8.1: Batch Editor No Longer Displays Autosampler ekspert nanoLC400 as an Option

After upgrading Analyst® TF software 1.8 to version 1.8.1, the Eksigent control software no longer displayed the option to chose the ekspert™ nanoLC 400 autosampler. To resolve this issue, in the Eksigent control software, the autosampler driver for the nanoLC 400 must be unregistered and then re-registered.

Reporter 3.2: Including Only the Results for the Quantifier Ion in a Report

To include only the data associated with the quantifier ion in a report, group the quantifier and qualifier ion for a particular analyte, and then use the For Each AnalyteGroup loop around the information to be reported.

LightSight® Software Acquisition Mode Is Not Supported on a SCIEX 6500+ LC-MS/MS System

LightSight® software version 2.3.x acquisition mode is not supported on a SCIEX QTRAP® or Triple Quad™ 6500+ LC-MS/MS System.

SCIEX OS Software: How to Choose the Format for a Numerical Field in a Report

By default, the format for a numerical field in a report is taken from the results table itself if the format is not set in the report template tag. If a specific numerical format is desired for a particular field in a report, certain default formats (such as the number of decimals desired or scientific notation) can be chosen in the Format field in the tag for that value. Otherwise, In the SCIEX OS software results table itself, the number format can be set for individual columns by editing the Number Format in the Results Table Display Settings options.

Aliquots of Bulk iTRAQ® Reagent Require Cold Storage Under Inert Gas

When aliquoting bulk iTRAQ® reagent, vials must be stored at -20 °C under inert gas.

What Is the Settling Time in an Analyst® Software Acquisition Method?

In Analyst® software, the settling time is defined as the time that a mass spectrometer pauses after finishing a cycle until it begins the next cycle. The instrument electronics require a settling time in order to function successfully.

SCIEX OS Software: Internal Standard Data in Report Does Not Match the Results Table

If a report generated from SCIEX OS software using a template and a query contains information about internal standard samples, the internal standard information showing in the results table does not appear correctly in the report. To resolve this issue, all internal standard samples must be listed at the bottom of the SCIEX OS software processing method in the components section.

No Help Topics Appear in the SCIEX OS Software Help System

Selecting the question mark in the upper right hand corner of SCIEX OS software launches the SCIEX OS Help System screen. If no information appears for a selected topic, the SCIEX OS Help.chm file located in the C:\Program Files\SCIEX\SCIEX OS\Documentation folder needs to be unblocked.

Modifying a Report Template to Report Select Sample Types Using IF Statements

An IF statement can be added to limit the sample types that need to be output to a report from a results table created in Analyst® software, MultiQuant™ software or SCIEX OS software. Below are few examples of how to write an IF statement within the loops ForEachSample or ForEachAnalyte.

Where are the SCIEX OS Software Report Templates Located on My PC?

If a report template needs to be opened for editing or if a new custom template needs to be added to the template list in SCIEX OS software, then navigate to C:\ProgramData\SCIEX\Analytics\Reporter to locate or add a template.

Direct LIMS Transfer in SCIEX OS Software Does Not Require a Template

Transferring data to a LIMS system from a results table created in SCIEX OS software does not require a template. Once the results table is saved and locked, under the Reporting menu, select Transfer results to LIMS, and two LIMS export options will appear in the LIMS transfer dialog box.

What Are the Functions Available to Each Security Configuration Role in Analyst® Software?

Individual users of Analyst® software can be assigned a particular role in Analyst software in the Security Configuration mode. The various roles are designed to limit a user's access to certain functions within the software depending on the role assigned. Below is a chart that shows how access to these functions decreases for the various default roles.

Adjusting the Dilution Factor Corrects Calculated Concentrations in Analyst® Software for Known Samples

If the dilution factor is not set correctly in an Analyst® software results table, the calculated concentration values for samples of known concentration will be incorrect.

Adding Custom Columns In a Batch in Analyst® Software

To add a custom column(s) to a batch in Analyst® software, right click within the batch table on the Sample tab, and select Add Custom Column.

Can the Loops ForEachSample and ForEachVisibleSample Be Used in the Same SCIEX OS Software Report Template?

No, the loops, ForEachSample and ForEachVisibleSample, cannot be used within the same SCIEX OS software report template. Similarly, ForEachAnalyte and ForEachVisibleAnalyte cannot be used together in the same report template.

MultiQuant™ Software Report Error: Object Reference Not Set to an Instance of an Object

If the MultiQuant™ software error "Object reference not set to an instance of an object" appears when creating a report, then the report template was not selected in the Create Report dialog. Check the file being used in the Report template field is a true report template. If not, replace it with a correctly formatted report template.

Problem Uninstalling SCIEX OS Software Stems from Hidden SQL Driver

While removing the SQL 2008 R2 Setup program during a SCIEX OS software de-installation, an error was received—indicating that the issue was due to the 2008 R2 RsFx driver, a "hidden" program that needs to be manually uninstalled using either the command prompt or regedit Windows functionalities.

Setting Up a New Project in Analyst® Software

To set up a new project in Analyst® software, navigate to the Tools menu and select Project.

How to Update or Link a Query File to a Report Template

If the name of a query is ever changed or updated or if a new query needs to be attached to a report template, the query must be relinked to the template used for reports created in MultiQuant™, Analyst® or SCIEX OS software.

What Integration Algorithms Are Used by SCIEX OS Software?

The SCIEX OS software has three integration algorithms that can be used to integrate peaks, and these options are listed in the Project Default Settings in the Analytics module: MQ4, AutoPeak and Summation.

Resolving the Report Error in SCIEX OS Software: "Error during Report generation"

This is a known issue in the ProteinPilot™ software 5.0.2 and was resolved with a patch.

Report Template Editing Blocked after Upgrading SCIEX OS 1.6.1 Software from a Previous Version

After updating SCIEX OS software from version 1.5 to 1.6.1, report template may be unable to be edited if Analyst® software is installed on the same PC. An error message appears in the Microsoft Word report template document: "Reporter Office addin. The provider with the name Quantitation already added to content control addin.Multiple custom type XML files found for the same provider." This article explains how to resolve this issue.

What Is the Format of a LIMS Template?

A LIMS template is used to transfer data from a MultiQuant™ software results table to a LIMS system. The LIMS template is a comma delimited file with the fields to be output listed across the top of the report. Each field in the template should be separated by a comma.

Changing the Integration Algorithm in SCIEX OS 1.6.1 Software

To change the integration parameter used in a quantitative processing method in the Analytics module of SCIEX OS Software, select the Projects menu, and under the Projects default settings, select Quantitative Processing > Integration Defaults > Integration Algorithm.

Absence of Calibration Curve in Analyst® or MultiQuant™ Software Due to Omitted Standard Concentration Values

If actual concentration values for standards are omitted from a MultiQuant™ or Analyst® software results table, then the data points for standard concentration versus peak area will all be aligned with zero on the x-axis in the calibration curve, looking nothing like the expected diagonal line. Adding the actual concentration information for the standards spreads the points across the x-axis and restores the expected diagonal linear regression line.

What File Format Can Report Templates Be Created In?

Report templates—used to create reports from results tables generated in Sciex OS, MultiQuant™ and Analyst® software—must always be in the format of a Word document with a file extension .docx. However, the output report itself can be created in several formats including Word, HTML, PDF, and CSV.

How to Access the SCIEX OS Software Help Menu

To access the SCIEX OS software help menu, click on the question mark in the upper, right-hand corner.

Where are the Cliquid Software Report Templates Located?

The Cliquid® software report templates are saved in the folder D:\Analyst Data\Projects\Cliquid\Templates\ReportTemplates.

Ensuring the Positive Hits Report Includes Only Positive Hits from a Results Table Generated in SCIEX OS Software

To ensure that only the positive hits appear in a report generated using the Positive Hits template rather than all visible results in a results table, the results table itself first needs to be filtered to show only positives prior to running the report.

Data for Custom Calculations Show as Not Calculated on a Report

In reports created from results tables in Analyst® and MultiQuant™ software, queries are used to compute the values for custom calculations, but occasionally the data appears as "Not calculated" on the report. This issue appears when the query file linked to the report template is not saved to the same folder as the report template.

Centering a Peak in a SCIEX OS Software Peak Review Pane

To adjust the location of the peak in the window and to center it, select the peak review icon in the results table, click Options and then Peak review display settings. In the Zooming tab, select the Zoom time axis to view peak check box and add the desired retention time.

Can the ChemoView™ Software LIMS Template Be Edited?

Yes, the LIMS template for ChemoView™ software can be edited and customized. Once changes are saved in the report template, the report output will reflect the changes.

Creating a New Report Style in Cliquid® Software

To create a new report style in Cliquid® software, go to the Administrator Tasks (Home) menu, then select Manage Report Styles and Create a Report Style.

To Make Reporter Tags Visible in a Report Template Unblock Them

If a report template is emailed or transferred to another computer and then opened, the xml tags may not be visible because they were blocked for security reasons.

Can the Default Location of MultiQuant™ Software Queries Be Changed?

It is not possible to change the default location of MultiQuant™ software queries.

Can Standard Concentration Values Be Stored in a MultiQuant™ Software Quantitation Method?

No, the concentration values for a standard or quality control samples cannot be stored in or saved to the MultiQuant™ software quantitation method.

LeadScape Software and LeadSampler (LS-1) Compatibility with Exion AD Pumps

The Exion AD pumps sold by SCIEX are compatible with Sound Analytics' LeadScape software and the LeadSampler (LS-1) autosampler.

Unlocking the Secure PDF Files Created by SCIEX OS Software

To unlock a secure PDF file created using SCIEX OS software reporter, open the document in a web browser and then print the newly opened document using either Microsoft Print to PDF or Save As PDF.

Reinstalling Analyst® Software without Uninstalling Analyst® Device Driver Will Cause Acquisition Methods To Fail

When installing the Analyst® Device Driver with Analyst® software, the order of installation of the programs is important. The Analyst software must be installed first, and then the Analyst Device Driver is installed next.

File Locking Prevents Addition of Remaining Injections to Existing Analyst® Software Data Files

To add injections to an existing data file, ensure that the Analyst® software data file is not in use or locked by another software program.

Unable to Configure a Shimadzu LC System after Upgrading to Analyst® 1.7 Software

A Shimadzu LC system may not be recognized and may not be able to be configured after an upgrade to Analyst® 1.7 software if a computer image on the PC was not sourced from SCIEX.

Migrating the SQL Server from DiscoveryQuant™ 2.1 Software to Version 3.0.x

Instructions are provided here for migrating the SQL server for DiscoveryQuant™ 2.1 to an installation of DiscoveryQuant 3.0.x software.

Migrating an Analyst® Software Compound Library to Sciex OS Software

To migrate compounds in an Analyst® software library to Sciex OS software, navigate to the Library module in Sciex OS software, and select Analyst Compound Library in the import options. The imported library must be named. Instructions for naming the library are included here.

Increasing the Maximum Injection Volume for an MPX™ Software System

To change the default injection volume in MPX™ 1.2.1 software, the MaxInjectVolume line in the MPX configuration file (Multiplex.INI) can be edited. Additionally, the value added to the injection volume field in the Analyst software batch editor (on the Sample tab) will override the configured MPX injection value during an acquisition run.

How Are Analytes Deleted from a Processing Method in Sciex OS Software?

To delete unwanted analytes from a processing method in Sciex OS software, highlight the rows, right click and select Delete Rows.

Entering the Formula for a Stable Isotope Labeled Compound in SCIEX OS Software

To enter the formula for a stable-isotope-labeled compound in the Components tab of a processing method in SCIEX OS software, some specific rules must be followed. When entering the formula, the atomic mass of the isotope is added before the single letter chemical abbreviation of the element, and then the total number of atoms of each isotope follows the chemical symbol.

Resolving Analyst® 1.6.3 Software Launch Error: Cannot Find the File Usernameanalyst.exe

To resolve the error "Cannot find the file usernameanalyst.exe" when opening Analyst® 1.6.3 software, the format of the Windows username on the computer where Analyst software was installed could not contain a period or a space in the middle of the user name. Reformatting the text of the Windows usernames resolved the issue.

How Can Library Hit Results Be Filtered by Score in a SCIEX OS Software Results Table?

To filter library hit results in a SCIEX OS software by library score and to remove any results without a proper score (presenting with N/A), a custom filter can be used in the Analytics mode.

After Upgrading Analyst® Software, Why Do Data Files Include xx.wiff.scan Files?

After upgrading Analyst® software, some data files now include xx.wiff.scan files. In the Configure mode in Analyst software, navigate to the Tools and Queue Options menu. Deselect the Use flat files for scan data button to prevent the xx.wiff.scan files from being created.

Tips for Setting Up a Test in Watson LIMS™ Software for Use with Analyst® Software

This article summarizes some helpful hints for setting up a test in Thermo Fisher™ Watson LIMS™ software for use with Analyst® software.

Longer Power Cycle May Help To Resume Instrument Connectivity after Power Failure

Even after resetting the mass spectrometer (by following the power-cycling procedure), the instrument would not come back online after a power failure. On some occasions, the mass spectrometer must be completely powered down for at least 1 min in order for the circuits to discharge and fully release any faulty information.

Exporting and Importing a Flagging Rule in SCIEX OS Software

Flagging rules for IS Recovery can be exported from an existing method in the Analytics workspace of Sciex OS software, and then the exported file can be re-imported into a new processing method using the Export/Import functions in the Flagging Rules screen.

Setting the Low Limit Value in the MPX 2.0 Software for Real-Time Data-Dependent Decision (RTD3) Flagging

When setting up MPX 2.0 software's carryover detection feature in the Define limit values screen (step 3), the low limit for each component must be defined using the lower limit of quantitation (LLOQ) or from the cut-off limit determined from the standard curve.

Where Can the Software for StatusScope® Remote Monitoring Service Be Accessed?

To obtain access to the software download for StatusScope® Remote Monitoring service, users who are under warranty or who have purchased the service can navigate to statusscope.absciex.com and select the link to the software download.

Recommendations for Waters Driver Packs with Different Analyst® Software Security Modes

When installing Analyst® software with the Waters' Driver Pack 4 (DP4) or the Driver Pack 4 supplemental release (DP4 SR1), consideration must be given to the Analyst security mode setting that is selected.

Resolving SCIEX OS Software Error: Cannot Open LibraryViewServiceHost Service on Computer

When trying to access the Analytics mode in SCIEX OS software when logged into Windows as a user without administrative privileges, an error is received: "Error has occurred: Cannot open LibraryViewServiceHost service on computer '.'. LibraryView service must be running." The LibraryViewServiceHost was not started when the Analytics mode was opened, and a workaround needs to be used to launch it.

Does BPV Flex Software Support Multiple Period Experiments?

BPV Flex can only open the first period of multiple period experiment runs.

Why Is There a .Special File Placed in the SCIEX OS Software Project Folders?

SCIEX OS software creates a special placeholder file (with a file extension of .special) and places these files in the root of every known SCIEX OS project sub-folder. SCIEX OS software uses both the project folder names and the .special files to identify its known folders, and it will not recognize the folder if the .special files are removed.

How Very High Concentration Samples Are Handled in MPX 2.0 Software

MPX™ 2.0 software contains a feature for automated carryover monitoring, which can identify samples above a certain threshold.

Preventing IP Address Conflicts with SCIEX 5500/6500+ Series MS and Waters' Acquity LC Instruments

To eliminate the possibility of any IP address conflict, the Waters IP addresses should be changed when operating with a SCIEX 5500/6500+ series instrument. To change the IP address on a Waters' LC components, use the Waters DHCP configurator located in the following folder: C:\\Program Files\Waters Instruments\Waters DHCP Server Configuration.exe.

Resolving the PeakView™ 2.2 and MultiQuant™ 3.0.3 Software Error after Upgrading to .NET 4.7.2

After upgrading PeakView™ software to version 2.2 or MultiQuant™ software to version 3.0.3, the following error message was generated: "The procedure entry point nextafterf could not be located in the dynamic link library MSVCR120_CLR0400.dll." The workaround is to remove .NET Framework 4.7.2 and then install the .NET 4.0 software.

Multiple Period Experiments Cannot Be Processed in BioPharmaView™ Software 2.x and 3.x

Data processing for intact proteins and peptide mapping in BioPharmaView™ software versions higher than 2.x do not allow for multiple period experiments.

How Many User Roles Are Available in ChemoView™ Software?

ChemoView™ software supports two user roles, technician and administrator. Each role allows access to different rights and functions within the software.

Creating a Processing Method in ChemoView™ Software

To create a new processing method in ChemoView™ software, select the Add New Processing Method button.