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Hi, Thanks for the great tool and documentation. I do have a question about the output files however: I used FragPipe v 15.0 with MSFragger 3.2 and Philosopher 3.4.13 to analyze timsTOF data. When counting the number of unique PSMs per protein by selecting all PSMs for which the From the description in the Wiki I would have expected these two columns to match, is there any reason for this difference? Thank you for your help |
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Hi Beni. Thanks for the kind words. We found an issue that affected the counts in the protein table, and we will have a new version released soon. For now, please consider the PSM table as being correct. |
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Hi Beni. Thanks for the kind words. We found an issue that affected the counts in the protein table, and we will have a new version released soon. For now, please consider the PSM table as being correct.