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cox-labs / CoxLab_Bug_Reporting

MaxQuant and Perseus Bug Reporting
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Discrepancy between Reported and Expected Fragmentation Methods #33

Open 227BaronChen opened 1 year ago

227BaronChen commented 1 year ago

Describe the bug Upon using MaxQuant version 2.4.2.0 for peptide identification with the digestion parameter set as Unspecific and other parameters set to default, the resulting PSMs in the output file are labeled as CID instead of HCD, which is the expected fragmentation method.

To Reproduce Steps to reproduce the behavior:

  1. Use MaxQuant version 2.4.2.0 for peptide identification.
  2. Set the digestion parameter to Unspecific.
  3. Keep other parameters as default.
  4. Analyze the output file and observe that the reported fragmentation method is CID instead of HCD

Expected behavior The expected behavior is that the resulting PSMs in the output file should be labeled as HCD, which corresponds to the fragmentation method used in the spectra acquisition.

Desktop (please complete the following information):

Additional context I have thoroughly reviewed the MaxQuant documentation and ensured that the appropriate settings were selected for HCD fragmentation. However, the obtained results indicate that the fragmentation method is being incorrectly reported as CID. I kindly request your assistance in understanding the possible causes of this issue and identifying any misconfigurations or overlooked steps. If additional information or data files are required for further investigation, please let me know, and I will promptly provide them. Your support is highly appreciated in resolving this matter and ensuring the accuracy of the peptide identification results.

Thank you for your attention to this matter, and I look forward to your response.

Best regards, Baron

pisistrato commented 1 year ago

As a possible workaround, would it make sense to set the ITMS settings to match the FTMS ones in the MS/MS analyzer tab? image

In the case of HCD-OT for the MS2, this will probably guarantee that the mass tolerance will not be the one to use for CID-IT, but I am not sure if the scoring algorithms are the same between HCD and CID. Any comments?