Protein grouping in protein.tsv output file
KR-15 opened this issue · comments
Hi,
First of all, thanks again for the great work done ! I am a new user of FragPipe so maybe I have missed something:
Is it normal that when I performed a FragPipe analysis using either the "Default" workflow or the "Speclib" workflow, I do not have "protein groups" in the protein.tsv file as we could get with protein_group.txt file output with MaxQuant for instance? Each line is assigned to a unique protein ID.
Thank you in advance for your response.
Kind regards.
KR
We do not have protein groups. Instead, we list the proteins after razor assignment in our file. Each line has one protein.
Best,
Fengchao
Indistinguishable proteins are listed at the end of the raw for each entry. Subsumed proteins that are a part of a larger protein group are not listed in that file. That would be misleading.
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Subject: Re: [Nesvilab/MSFragger] Protein grouping in protein.tsv output file (#175)
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We do not have protein groups. Instead, we list the proteins after razor assignment in our file. Each line has one protein.
Best,
Fengchao
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