Understanding protein report & protein grouping

[mziehm]

Using FragPipe v14.0 and a label-free workflow I obtained a combined-protein.tsv as well as for each experiment a specific protein.tsv and I found this documentation https://github.com/Nesvilab/philosopher/wiki/Protein-reports
However, I still have a couple of questions understanding these files:

1. How do I have to understand the protein group / subgroup? Is there a documentation on this anywhere?
   What defines a protein group? What defines a subgroup?
   How is the quantification to be understood, i.e. is each subgroup quantified based on overlapping peptides, or independently?
   If there are subgroups, is there an overall proteingroup quantification?
   Does the order of the subgroups a,b,c,... mean anything / how is it determined?

2. Give an entry in the protein/combined-protein tsv with one or more "Indistinguishable Proteins".
   How is it determined which protein is listed as protein and which one as Indistinguishable Proteins?

Thanks for building this tool
Matthias

[anesvi]

Ok, give us a bit of time to respond ( and add That info to our websites)

…

Sent from my iPhone On Oct 19, 2020, at 5:11 AM, mziehm <[email protected]> wrote:  External Email - Use Caution Using FragPipe v14.0 and a label-free workflow I obtained a combined-protein.tsv as well as for each experiment a specific protein.tsv and I found this documentation https://github.com/Nesvilab/philosopher/wiki/Protein-reports However, I still have a couple of questions understanding these files: 1. How do I have to understand the protein group / subgroup? Is there a documentation on this anywhere? What defines a protein group? What defines a subgroup? How is the quantification to be understood, i.e. is each subgroup quantified based on overlapping peptides, or independently? If there are subgroups, is there an overall proteingroup quantification? Does the order of the subgroups a,b,c,... mean anything / how is it determined? 2. Give an entry in the protein/combined-protein tsv with one or more "Indistinguishable Proteins". How is it determined which protein is listed as protein and which one as Indistinguishable Proteins? Thanks for building this tool Matthias — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#161>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIIMM6ZJ6KAM5GIF74DPJFTSLP7D3ANCNFSM4SV3RBSA>. ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[Jokendo-collab]

I also have a question. I did set the PTM prophet to get the PTMs but I can only see the combined results for protein and peptides. I have not seen the PTMs results.

[anesvi]

You should see interact.mod.pep.xml file, with localization parsed and shown in PSM.tsv files However, you need to pass to PTM-Prophet all variable modifications that you specified in MSFragger E.g. if you only used Met oxidation and Phosphorylation: --keepold --static --em 1 --nions b --mods STY:79.966331,M:15.9949 --minprob 0.5 But if you also used N-term Acetyl: --keepold --static --em 1 --nions b --mods STY:79.966331,M:15.9949,n: 42.0106 --minprob 0.5 So things must match. Alexey From: Javan Okendo <[email protected]> Sent: Monday, October 26, 2020 2:40 PM To: Nesvilab/philosopher <[email protected]> Cc: Nesvizhskii, Alexey <[email protected]>; Assign <[email protected]> Subject: Re: [Nesvilab/philosopher] Understanding protein report & protein grouping (#161) External Email - Use Caution I also have a question. I did set the PTM prophet to get the PTMs but I can only see the combined results for protein and peptides. I have not seen the PTMs results. — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub<#161 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIIMM64UZ6PE2NOTD5LZYILSMW673ANCNFSM4SV3RBSA>. ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[Jokendo-collab]

@anesvi see the screenshot of the results which I got. I did use the open_search.params for the MSfragger, meaning that I was doing the open search.