Closed animesh closed 2 years ago
You have zero MS1 peaks that passed PTM-Shepherd's minimum PSM cutoff, which is why this happened. If you think your data is fine then you can reduce PTM-Shepherd's minimum PSMs to 1, but I don't think your data is fine.
There are quite a few strange things here...
WARNING: Mixture model quality test failed for charge (1+). WARNING: Mixture model quality test failed for charge (2+). WARNING: Mixture model quality test failed for charge (3+). WARNING: Mixture model quality test failed for charge (5+). WARNING: Mixture model quality test failed for charge (6+). WARNING: Mixture model quality test failed for charge (7+).
Only charge state 4 peptides passed filtering.
You have 242 PSMs and 231 proteins out of 29000 spectra, so less than 1% recovery.
Please check your parameters.
Hi @danielgeiszler ,
Can you make PTM-S give a more informative message in this case?
Thanks,
Fengchao
@fcyu Yes, PTM-Shepherd should crash more gracefully here and I can fix that. But datasets with <1% of spectra identified should probably be throwing errors or warnings much earlier.
Thanks @danielgeiszler for looking into this. I ran MaxQuant before and it has even worse IDs <html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">
MS | MS/MS | MS/MS identified -- | -- | -- 25564 | 37770 | 112 25564 | 37770 | 112
Describe the bug I am running open workflow in the headless mode over a timsTOF-pro data/file and got the following error
Is this because of low number of spectra? The protein.tsv has 231 entries though.
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