知识库文章

How is the FDR calculated in the peptide-spectrum matching step in the BioPharmaView™ software?

This article describes how the false discovery rate (FDR) is calculated in BiopharmaView™ and BPV Flex software.

How can I enable the MSServiceLog Script in Analyst® software to record readbacks from a mass spectrometer?

By default, readbacks from a mass spectrometer are recorded in the MS Service log file. Use the MSServiceLog script to turn off the recording of the readbacks or to start recording the readbacks from the instrument in the MS Service log file. The MSServiceLog script is only applicable to the SCIEX 3500, 4500, 5500, 5500+, 6500, and 6500+ systems. The MSServiceLog script can be used without an active hardware profile but any changes made to the MS Service log settings take effect only after the hardware profile is reactivated.

Canned Calculation for ICH Guideline M10 – 3.2.2 Specificity Available for SCIEX OS Software

This article provides information on the custom calculations required for processing data according to the guidance found in ICH guideline M10 – 3.2.2. The guidance requires that it is demonstrated that no significant response attributable to interfering components compared to the analyte or IS response in the blank and double blank samples, respectively, is observed. These calculations were created to provide a ready-made solution for determining which samples will need to be re-injected in pesticide reports.

Canned Calculation for ICH Guideline M10 – 3.2.1 Selectivity Available for SCIEX OS Software

This article provides information on the custom calculations required for processing data according to the guidance found in ICH guideline M10 – 3.2.1. The guidance requires that it is demonstrated that no significant response attributable to interfering components is observed at the retention time(s) of the analyte or the IS in the blank samples. These calculations were created to provide a ready-made solution for flagging problematic samples/components.

Canned Calculation for ICH Guideline M10 – 3.2.4/3.3.2 Calibration Standard Accuracy Available for SCIEX OS Software

This article provides information on the custom calculations required for processing data according to the guidance found in ICH guideline M10 – 3.2.4/3.3.2. The guidance requires that the accuracy of the back-calculated concentrations of each calibration standard should be within ±20% of the nominal concentration at the LLOQ and within ±15% at all the other levels. At least 75% of the calibration standards with a minimum of 6 calibration standard levels should meet the above criteria. These calculations were created to provide a ready-made solution for flagging problematic samples/components.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 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.

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.

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.

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 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.

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. 

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

Link is provided and installations instructions are described

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 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.

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.

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.

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.

Which Glycan Notation Is Used in the BioPharmaView™ Software?

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

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."

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.

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.

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.

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.

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.

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.

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:

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 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.

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.

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.

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.

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.

Does BPV Flex Software Support Multiple Period Experiments?

BPV Flex can only open the first period of multiple period experiment runs.

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.

Calculating the Theoretical Average Mass for an Intact Protein in BioPharmaView™ Software

BioPharmaView™ software uses the isotopic masses published by NIST online at: https://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl. Please note that the results generated will be the same throughout all SCIEX software (e.g., PeakView™ and ProteinPilot™ software).

What Is the Organic Solvent Used with iTRAQ® Reagents during Shipment?

All iTRAQ®, aTRAQ™ and mTRAQ® reagents are shipped in acetonitrile from the factory.

Does ProteinPilot™ Software 5.0.2 Support MALDI TOF/TOF™ Systems?

Description of which ProteinPilot™ software versions still support 4800 and 5800 MALDI TOF/TOF™ systems.

Can Skyline Version 4.2.1 and Higher Process .wiff2 File Formats?

Yes , Skyline version 4.2.1 can process .wiff2 files generated using SCIEX OS software.

Compound Parameters Not Loading in Analyze Mode in DiscoveryQuant™ 3.0.1 Software

Compound parameters could not be uploaded in Analyze mode in DiscoveryQuant™ 3.0.1 software after switching from a local database to SQL database due to issues with the database selected as the review database.

List of CE Capillaries with Pre-burned Detection Windows

CE capillaries with pre-burned detection windows are available for purchase; the dimensions and coating information for these products are listed here.

What Causes BioPharmaView™ Software To Stall when Processing Data or Running Batches?

BiopharmaView™ software will stall when processing data when more than one instance of the software is open or if there are some corrupted files in the processing queue folder in the BioPharmaView program files folder.

Changing the Number of Decimals Displayed in Analyst® Software Calibration and Metric Plots

This is a set of instructions for changing the number of decimals displayed in Analyst® software quantitation metric plots and calibration curves. The default number of decimals leaves the significance so low that you can not reproduce the results shown in the results table. A warning is given to let customers know that Regedit is a dangerous utility.

BioPharmaView™ Software 2.x/3.0.x Cannot Open the Data for Subsequent Samples if the Data for the First Sample Is Corrupted

BioPharmaView™ software 2.x/3.0.x cannot open the data for subsequent samples if the data for the first sample is corrupted.

Bio Tool Kit Software License iNeeded for SCIEX OS 1.x and PeakView Software.

The Bio Tool Kit software can be activated within PeakView 2.x and SCIEX OS 1.x software but a separate software license is needed.

What Are the Specifications of the Six-Protein Mixture Supplied with the iTRAQ® Kit?

Specifications of the six-protein mixture (PN 4348363) supplied with the iTRAQ® kit include the accession numbers of the proteins and their mass per tube (in µg and nmol).

What Are the Peptide Sequences in the Six-Peptide Mixture (PN 4465940)?

The six-peptide mixture (part number 4465940) is used for the calibration of mass spectrometers. The kit contains the following six peptides and their mono-isotopic masses: bradykinin (2-9 clip) (904.4681), angiotensin I (1296.6853), glu1-fibrinopeptide (1570.6774), ACTH (1-17 clip) (2093.0867), ACTH (18-39 clip) (2465.1989), and ACTH (7-38 clip) (3657.9294).

Nomencature Used by BiopharmaView™ Software for N-Gylcan Names

BioPharmaView™ software uses predefined N-glycan structures (following the Ludger product names), or software users have the option to build their own custom modifications.

How Are the Samples and Standards for the aTRAQ™ Kit Stored?

The reagents and samples used for the aTRAQ™ kit labeling experiments should be stored at -20 °C or lower.

How Do You Export a Library in LibraryView™ 1.0.1 Software?

The export of a library from LibraryView™ 1.0.1 software is described here.

Difference between Rapid and Thorough Searches in ProteinPilot™ Software

The rapid search and a thorough search settings in ProteinPilot™ software determine which parts of the search algorithm will be invoked and effectively how deep the sample will be searched to find the right answers.

How to adjust, save and export the table settings in an Analyst Quantitation Table

Instructions how to modify (choose and adjust the visible columns, change the significant figures and notation), save and export an Analyst Quantitation Table.

Will ProteinPilot™ 5.0.2 Software Function on a Windows 7 64-Bit System?

ProteinPilot™ 5.0.2 software has only been tested on Windows 10 SP1 64-bit with Microsoft Office version 2016.

Using the 25 Micron ESI Electrode with the DuoSpray™ Source?

A 25 micron ESI electrode can be used with the IonDrive™ Turbo V source and the DuoSpray™ source.

iTRAQ® Reagents: Can Samples Labeled with Both the 4-Plex and 8-Plex Kits Be Mixed?

The iTRAQ® Reagents chemistry for 4plex versus 8plex kits is described.SCIEX does not recommend mixing samples labeled with the reagents from the two separate iTRAQ® kits, 4plex and 8plex, due to the differences in the reagent chemistry.

Which Amino Acids in the PepCalMix Are Labeled?

The PepCal Mix (P/N 5045759) contains 20 heavy-labeled peptides, with the heavy isotopes incorporated in the amino acids, K and R.

Keeping a Nano LC/MS System Running after Sample Acquisition Is Completed

To keep a nano LC/MS system running after sample acquisition has completed, the LC/MS can be configured two different ways, assuming the Nano Eksigent 400 system is used.

Where Can I Find Instructions for the Protein Preparation Kit?

Protein preparation instructions can be found on the SCIEX website at https://sciex.com/Documents/tech%20notes/Protein-Preparation-Kit-Protocol.pdf or https://sciex.com/products/standards-and-reagents/automated-protein-digestion-solution.

Exporting .T2D Files in Batch Mode from the Raw Data Spotset

To export .T2D files in batch mode from the raw data spot set on a MALDI plate, locate the Remote Data Access software in the program files and install the T2DExporter.

Setting Up MRM Transitions if Q1 Mass Is Identical to that of a Second Compound

To set up a MRM transitions where the Q1 mass for one compound is identical to a second compound in Analyst® software, change the Q1 mass of the second compound by 0.1 -0.05 Da. After making this adjustment, the software will accept the duplicate mass for Q1.

Optimal CE Voltages for Peptide Analysis on TripleTOF® Systems

The collision energy (CE) and the collision energy spread (CES) values needed for peptide analysis (during protein IDA identification and SWATH® acquisition) can be optimized using Information in the rolling CE setting embedded in the Analyst® TF software.

Archiving and Purging MALDI TOF/TOF™ Data and Creating Database Backups

Described herein is a general procedure on how to archive/purge data from a MALDI TOF/TOF™ system, as well as how to back up data.

Protocols for Protein Precipitation in Samples before Using iTRAQ® Kits

To prepare samples prior to iTRAQ® reagent labeling, use the following protocols.

ProteinPilot™ 5.x Software: Incorrect Result Output for Instrument Names in the Group File

ProteinPilot™ software uses the incorrect mass spectrometer name in its group file output file. When a TripleTOF® 5600 system was selected, the group file contains the name QSTAR® Elite instead for system information. This causes the wrong results to be output; if the incorrect instrument name is used, then the incorrect tolerance settings are applied.

ProteinPilot Software Datafile Cannot be Searched because two files are acquired under same file name

Searching for ProteinPilot software files using Windows Explorer cannot be done because there are two files acquired under the same file name. This is a long known issue for all ProteinPilot versions that only one file per file name can be searched using ProteinPilot software.

How to Generate MRM Ratios in Analyst Software

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

BioPharmaview™ Software: Simultaneous Analysis of Disulfide Bridges and Cysteine Modification Not Possible

Disulfide bond mapping in BioPharmaView™ software is described in the user guide. However, creating a disulfide bridge table in addition to analyzing cysteine modifications simultaneously is not described and cannot be done.

How Many Vials of Each iTRAQ® Reagent Are in the Multiplex Kit?

Each iTRAQ reagent multiplex kit (PN 4352135) contains 5 vials of of the following iTRAQ reagent labels: 114, 115, 116, and 117.

Separating Concatenated .wiff Files in Analyst® Software

To separate concatenated .wiff file sets, a script called Make Subset File is used. This script might have limitations for Analyst® and Analyst TF software because it depends on the experiments in the file (i.e., the script does not work for IDA methods). The script is found on the Analyst TF software CD in the folder \Extras\Scripts\Make Subset File.

Which Calibration Standards Can Be Used for Intact Protein Analysis on TripleTOF® and X500 Systemss?

An APCI calibrant solution for the SCIEX X500B System and a mAb standard from Waters were compared. Results show that the mass to charge ratio for the calibrant solutions remain constant regardless of the charge state. Secondly, for readings over 500 m/z, the calibration is highly linear for the X500B system.

Tips and Tricks for Cation-Exchange Chromatography for the iTRAQ® Protocol

The manual injection procedure for the iTRAQ® protocol requires a 22-gauge syringe with a 2-inch needle (purchased separately). This article lists some tips and tricks on how to set up the syringe when using cation-exchange columns for samples treated with the iTRAQ reagent.

Where Can I Find a Column Part Number from Eksigent?

The provided link lists all micro and nano columns including nano chip columns.

How Does the Score in the Peptide Sequencing Section of BioPharmaView™ Software 2.1 Work?

Each peptide is displayed in a table after processing the peptide digest in BioPharmaView™ software. A score is given to each peptide after it is compared to the theoretical proteolytic digest.

Reasons for Data File Processing Failure with the Data Converter Version 1.3 Beta

What are the potential issues listed which can cause the SCIEX MS data converter version 1.3 beta to not work correctly?

What Default URL Is Used for Configuring the Mascot Server with ProteinPilot™ Software?

Configuring the Mascot server from the ProteinPilot™ software requires the default URL to be used.

What Is Skyline Software and What Data Types Does It Work With?

This article includes a general description of the features of Skyline software and the possible data formats from SCIEX instruments that work with Skyline.

Acetic Acid Is Needed To Prepare the PepCalMix Peptides in the SWATH® Acquisition Performance Kit

This article describes the experimental issues when formic acid is used to prepare the PepCalMix for the SWATH® Acquisition Performance Kit instead of 5% acetic acid.

Where Can I Download Skyline Software ?

This article includes the link to a free download of Skyline software.

What Is the Full Amino Acid Sequence of BETA-GALACTOSIDASE in the LC/MS Peptide Calibration Kit?

The full amino acid sequence for beta-galactosidase is provided in the FASTA file format. The kit (part number 4465938) contains one vial of beta galactosidase digest (625 pmol/vial).

How Is a Hardware Profile Created in Simulation Mode with an Eksigent 4.x and Analyst TF Software?

Description of the steps to place the Eksigent software in the AAO system of the Analyst® software and how to run it in simulation mode.

How Is the SWATH® Acquisition Variable Window Calculator Excel Sheet Used?

This article includes step-by-step instructions on how to calculate variable windows for your SWATH® acquisition experiment and how to generate the input and output list.

ProteinPilot™ Software 5.0: What Are the Criteria for Including a Peptide in the Feature Tab?

The general filters for peptides are listed here. These are applied through the feature tab in ProteinPilot™ software.

Is ProteinPilot™ Software 5.0.1 Compatible with Windows 10?

Is ProteinPilot™ Software 5.0.1 compatible with Windows10? No, it works only with Windows 7, Service Pack 1, 64-bit.

What Is the Function of the Collision Gas (CAD) on QTRAP® System Instruments?

The various functions of the CAD gas are described for the QTRAP® System instruments and the different scan types.

What Is a Fraglet.exe Error when Running ProteinPilot™ Software 5.0?

A "Fraglet-exe-Error" can have many causes within the ProteinPilot™ software. In some cases, this error is caused when installing ProteinPilot on an incompatible operating system.

How Is a ChemSpider Software License Activated within PeakView® Software?

The software activation procedure is described step-by-step for ChemSpider, which needs to be activated within PeakView® software's FormularFinder feature.

Where Can I Find More Information about Software IQ/OQ Testing Plans?

More information about software validation services can be found by emailing complianceservices@sciex.com.

Intact protein script for TripleTOF™ instruments

This knowledge article summarizes when to use the intact protein script in

PA800 How To - Changing Coolant Tubing

Changing Coolant Tubing on PA800 System

PA800 How To - Trimming a Capillary

Trimming a Capillary

PA800 How To - Installing the LIF Aperture and Probe Stabilizer

Installing the LIF Aperture and Probe Stabilizer

PA800 How To - Cartridge Removal

Video demonstration of Cartridge Removal on the PA800 system

PA800 How To - Capillary Removal

Capillary Removal

PA800 How To - Capillary Storage

Capillary Storage Details for PA800 System

PA800 How To - Installing the Cartridge Aperture

Procedure for Installing the Cartridge Aperture on the PA800 system

PA800 How To - Replacing the Ejector and Electrode

Replacing the Ejector and Electrode

PA800 How To - Uninstalling the LIF Detector

Uninstalling the LIF Detector

PA800 How To - Removing the Ejector and Electrode

Removing the Ejector and Electrode

PA800 How To - Installing the LIF Detector

Installing the LIF Detector

PA800 How To - Cartridge Removal Rebuild Reinstallation

Procedure for Cartridge Removal Rebuild Reinstallation on PA800 System

PA800 How To - Changing a Detector

Changing a Detector

How Are the Method Parameters Chosen for Autocalibration Samples in the X500 Series?

Method parameters for autocalibrations submitted in SCIEX OS batches are automatically chosen from the sample after the autocalibration.

How do I store iTRAQ® labeled peptides?

Store iTRAQ® reagent labeled peptides at -20 or -80 degrees Celsius. Avoid having the peptides undergo multiple freeze/thaw cycles. iTRAQ-labeled peptides can degrade over time.

MALDI TOFTOF: Can I calibrate using a linear mode acquisition method in batch mode?

When calibrating a linear mode acquisition method in batch mode the software reports that a reflector mode acquisition method is required in order to use the batch mode.

Ekspert™ 400 LC system – Change the mobile phase

How to change mobile phase on Ekspert™ 400 LC system

How to remove unused template definitions from DiscoveryQuant 2.1.x

This document explains how to remove unused template definitions from the DiscoveryQuant Analyze setup window

Power Down and Power Up the TripleTOF® System

How to power down and up the TripleTOF systems

TripleTOF® System Vacuum Interface Routine Cleaning

How to clean the vacuum interface of the TripleTOF instruments

How Do I Install SQL Server 2014 for DiscoveryQuant™ 3.0

This article describes the process for building a SQL Server for use with DiscoveryQuant 3.0.

How Do I Migrate Data from a DiscoveryQuant™ 2.1 SQL Server to a DiscoveryQuant™ 3.0 SQL Server

This article describes how to migrate DiscoveryQuant 2.1.x SQL Server Data to a DiscoveryQuant 3.0 SQL Server Installation

DiscoveryQuant Cannot set spectrum for experiment X

DiscoveryQuant Optimize will not complete optimization with the error message Cannot set spectrum for experiment followed by a number which can be any one of your scan functions.

DiscoveryQuant Quicktune DP 0 DP Scan Problem

Using DiscoveryQuant 2.1.3 Quick Tune will set the DP value to 0 and then Fine Tune will fail as it has an invalid DP value. The temporary Q3 MI scan method for the quicktune will show the MH ion with 2 DP scans both at 200v though this voltage may vary.