Shimadzu LC-40 systems troubleshooting tips and tricks


日期: 11/15/2023
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Shimadzu HPLC systems are commonly used with SCIEX mass spectrometers. The table below shows the most common symptoms encountered for Shimadzu LC-40 systems and details possible causes with the appropriate corrective action. Design changes in this model versus older Shimadzu models may require a different approach to troubleshooting your LC-MS system.

SymptomPossible causesCorrective Action
Liquid waste has backed up out of the waste port and spilled onto the floor or the leak sensor has been triggered1. The waste line is too long1. Cut the waste tubing to the correct length so that the waste drains out of the line steadily
2. The waste line is blocked2. Unblock or replace the waste tubing so that the waste drains out of the line steadily
A system fault has occurred because the autosampler needle is clogged or damaged1. Adhesive from the plate cover has stuck to the autosampler needle1. Always use plate covers that do not contain any adhesives
2. You are using a silicone plate cover that is not pre-split2. When using a silicone plate cover, make sure that it is pre-split
3. The sample plate is not seated correctly in the autosampler3. Fully remove the sample plate tray and place it onto a firm surface. Place the sample plate into position in the autosampler, ensuring that it is fully seated at the corners and the base.
4. The sample plate is not a type recommended by Shimadzu or SCIEX for use with the LC system4. Only use Shimadzu- or SCIEX-recommended HPLC plates
5. The sample plate type is not the same as manually selected in the batch5. Update the autosampler configuration to use the correct plate type. It is recommended to use plates labeled with a bar code to allow the autosampler to automatically determine the plate type.
A batch or results processing failure occurs due to inconsistent injection volumes1. Adhesive from the plate cover has stuck to the autosampler needle1. Always use plate covers that do not contain any adhesives
2. A silicone plate cover that is not pre-split is being used2. When using a silicone plate cover, make sure that it is pre-split
3. The sample plate is not seated correctly in the autosampler3. Fully remove the sample plate tray and place it onto a firm surface. Place the sample plate into position in the autosampler, ensuring that it is fully seated at the corners and the base.
4. The sample plate is not a type recommended by Shimadzu or SCIEX for use with the LC system4. Only use Shimadzu- or SCIEX-recommended HPLC plates
5. The sample plate type is not the same as manually selected in the batch5. Update the autosampler configuration to use the correct plate type. It is recommended to use plates labelled with a bar code to allow the autosampler to automatically determine the plate type.
6. The value for the needle stroke setting for the vials or plates is incorrect.6. Update the needle stroke setting to the correct value.
The retention times are inconsistent or the chromatography is poor1. The check valves are sticking1. Sonicate the check valves and replace them if the check valves are still sticking after sonication.
Note: When using acetonitrile as the organic mobile phase, it is recommended to use a minimum of 5% water to maintain the integity of the check valves and prevent them from sticking. If it is not possible to use a minimum of 5% water, flush the pumps with 100% water at least once a week.
2. The incorrect wash sequence is being used for the advanced wash or internal needle wash programs.2. Use Mobile Phase A or a bottle of premixed mobile phase of the starting LC conditions for the assay as the RO wash.
3. The pump seals have degraded due to the use of a mobile phase modifier with a concentration that is too high or when the modifier is incompatible with the Shimadzu LC system.3. Replace the pump seals and reduce the modifier concentration or type of modifier used. Note: ensure that you always use modifiers that are compatible with the Shimadzu LC system at a suitable concentration.
4. The equilibration time in the LC method is too short.4. Modify the method to increase the length of time for equilibration.
A system fault has occurred due to condensation in the autosampler1. The autosampler cover has been removed1. Always keep the autosampler covers installed
A system alarm is triggered when the sample plate is removed for an extended period of time1. The sample plate is removed for an extended period of time when sample cooling is set as On1. Place the sample plate back in the autosampler and close the door
The PDA or UV-vis detector lamp has burnt out earlier than expected1. The unit was left powered on for an excessive period of time or when not in use1. When the detector is not in use, power the unit off
The SCIEX MS and Shimadzu LC are not synchronized during acquisition.1. The acquisition method is corrupted1. Create a new acquisition method
Carryover is observed1. The analyte is not soluble in the wash solvent1. Replace the wash solvent with one in which the analyte is soluble
2. The flow path has dead volume.2. Inspect the fittings and adjust or replace any fittings as required.
3. The wash program uses a wash time that is too short or a flow rate that is too low.3. Increase the wash time or the flow rate used in the wash program.
4. The volume of wash solvent used in the wash program is too low.4. Increase the volume of wash solvent used in the wash program.