Filtering for sequence motives/peptide modifications

[sgoetze74]

Dear FragPipe team,
I am currently processing some phophoenrichment samples using FragPipe. I was wondering whether there is not only the option to filter out modified peptides for protein quantification but reversely only filter for the modification (in this case STY 79.966331) for deriving protein quantities.
Best Regards,
Sandra

[fcyu]

HI Sandra,

I am not sure if I understand your question correctly, but can you try the "excluded mods" option in "Quant (MS1)" if you are doing LFQ. If it is TMT, I am not sure if there is such an option.

Best,

Fengchao

[anesvi]

I think Sandra wants to derive protein abundance using phosphopeptides only? For TMT, this is how it works already. TMT-Integrator will use only phosphopeptides to get protein abundance when doing phospho experiments But for LFQ with IonQuant, we do not have such an option at the moment. Perhaps we can add in the future. Alexey From: Fengchao ***@***.***> Sent: Wednesday, February 15, 2023 2:07 PM To: Nesvilab/FragPipe ***@***.***> Cc: Subscribed ***@***.***> Subject: Re: [Nesvilab/FragPipe] Filtering for sequence motives/peptide modifications (Issue #1009) External Email - Use Caution HI Sandra, I am not sure if I understand your question correctly, but can you try the "excluded mods" option in "Quant (MS1)" if you are doing LFQ. If it is TMT, I am not sure if there is such an option. Best, Fengchao — Reply to this email directly, view it on GitHub<#1009 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIIMM64RKLRGZM3BBWBZ5VTWXUSOTANCNFSM6AAAAAAU5HHEKU>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.******@***.***>> ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[sgoetze74]

Hi Alexey, yes exactly, this is what I was trying to do for a DDA (unlabelled) dataset. If you could consider implementing such an option for IonQuant in the future that would be great (also for our glycocapture workflow). Thank you and greetings from Zurich, Sandra <http://wollscheidlab.org/> <http://wollscheidlab.org/>

…

________________________________ From: Alexey Nesvizhskii ***@***.***> Sent: Wednesday, February 15, 2023 8:09:47 PM To: Nesvilab/FragPipe Cc: Goetze Sandra; Author Subject: Re: [Nesvilab/FragPipe] Filtering for sequence motives/peptide modifications (Issue #1009) I think Sandra wants to derive protein abundance using phosphopeptides only? For TMT, this is how it works already. TMT-Integrator will use only phosphopeptides to get protein abundance when doing phospho experiments But for LFQ with IonQuant, we do not have such an option at the moment. Perhaps we can add in the future. Alexey From: Fengchao ***@***.***> Sent: Wednesday, February 15, 2023 2:07 PM To: Nesvilab/FragPipe ***@***.***> Cc: Subscribed ***@***.***> Subject: Re: [Nesvilab/FragPipe] Filtering for sequence motives/peptide modifications (Issue #1009) External Email - Use Caution HI Sandra, I am not sure if I understand your question correctly, but can you try the "excluded mods" option in "Quant (MS1)" if you are doing LFQ. If it is TMT, I am not sure if there is such an option. Best, Fengchao — Reply to this email directly, view it on GitHub<#1009 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIIMM64RKLRGZM3BBWBZ5VTWXUSOTANCNFSM6AAAAAAU5HHEKU>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.******@***.***>> ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues — Reply to this email directly, view it on GitHub<#1009 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AMMDC2I32DQL5XRMKKEKSSLWXUSXXANCNFSM6AAAAAAU5HHEKU>. You are receiving this because you authored the thread.Message ID: ***@***.***> [ { ***@***.***": "http://schema.org", ***@***.***": "EmailMessage", "potentialAction": { ***@***.***": "ViewAction", "target": "#1009 (comment)", "url": "#1009 (comment)", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { ***@***.***": "Organization", "name": "GitHub", "url": "https://github.com" } } ]