Tuning MS2 by low-quality fragment matches on all DIA PSMs at apex_rt resulted in low-quality MS2 prediction

[jalew188]

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]

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