I have a number of pep.xml files from performing spectrast spectral library searching with tierwise scoring that I'm trying to analyze by PeptideProphet. However, when I analyze the search results by PeptideProphet in Petunia it appears to get "stuck" during the PeptideProphetParser step, specifically when it is running iterations to construct the model. Normally, for 30 pep.xml files from tandem searches PeptideProphet would complete in about 30 iterations. Now, when running ~10 (~100,000 to- 200,000 total spectra) search files from spectrast sometimes PeptideProphet will finish, other times there will be >100 iterations with no end in sight. Is this just the number of iterations it takes to construct a model with spectrast searches? I have tried running PeptideProphet with and without decoy modeling, and changing the number of files analyzed to no effect. I have also tried analyzing different pep.xml files to check if there were problematic files that might be interfering with the algorithm also to no effect. Is there any way to fix this issue?
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