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MannLabs / alphapeptdeep

Deep learning framework for proteomics
Apache License 2.0
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Tuning MS2 by low-quality fragment matches on all DIA PSMs at apex_rt resulted in low-quality MS2 prediction #124

Open jalew188 opened 7 months ago

jalew188 commented 7 months ago
  1. Using DIA PSMs identified by DIA search engine to refine MS2 model may result in low-quality MS2 prediction due to low-quality precursor matches;
  2. Using spectral library tsv to refine the MS2 model may also result in low-quality MS2 prediction. It depends on how many low-quality matches are there in spectral library;
jalew188 commented 6 months ago

It turns out that this is not “catastrophic forgetting”, this is due to low matching quality of DIA data.