Christie Hunter


Troubleshooting low flow LC – LC-MS peak area is lower than expected

Symptom: LC-MS peptide peak are is smaller than expected in PepCalMix Test

Test: Use PepCalMix Infusion tests to determine if it is a problem with LC or MS


  • First perform the SCIEX recommended performance tests using infusion on your MS system.
  • If these standard infusion tests have all passed, then the problem could be related to LC.
    • Check if autosampler picks up the correct volume. One easy way to do this is to fill an autosampler vial with a volume you want to inject plus 2 µ Then after pickup, check to see if there is only 2 µL remaining in your vial.
    • Check for flow path leaks, both the gradient and trap flow paths
    • Replace trap and/or column
    • Prepare fresh solvents, if solvents have been in use for >3months
    • Prepare fresh PepCalMix, ensure you are using the recommended dilution solution recommended in the protocol


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