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If a peptide in the PSM tsv has a zero for intensity, was it indeed identified and area is incalculable? |
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Replies: 1 comment 3 replies
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There might be different causes for a 0 in the PSM table. In respect to our approach, which is based on moFF, a zero most likely means that the apex peak was not found with the current time window, and m/z tolerance. If this is a special PSM, I suggest you try running the freequant command and adjust these values. |
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Thabk you for your reply. Is there a way to run freequant without having to run the entire analysis. Does my hypothesis still stand that the peptide was indeed identified though? |
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Most likely, yes. To know how well was the assignment to the given peptide check the PeptideProphet probability; the closest it is to 1, the best, or most confident the validation is. You can run the label-free quantification without having to process everything again, just open a terminal window inside the folder where the analysis is, and run the freequant command followed by the report command. If you are by any chance running via FragPipe, then I'm afraid you'll have to process everything again. |
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In FragPipe, you can uncheck the steps before LFQ, no need to run all steps again. |
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There might be different causes for a 0 in the PSM table. In respect to our approach, which is based on moFF, a zero most likely means that the apex peak was not found with the current time window, and m/z tolerance. If this is a special PSM, I suggest you try running the freequant command and adjust these values.