Single amino acid polymorphisms

[alephreish]

Hi,

AFAICT, MSFragger has no built-in way of addressing known single amino acid polymorphisms (cf. x!tandem). Is such an option on the agenda and/or it there a good workaround recommendation?

Thanks!

[anesvi]

We may add PEFF support at some point, http://www.psidev.info/peff but that will take time You should just built your own custom database and search that. And note that a bigger issue is not the searching itself, but FDR estimation for variant peptides. Best Alexey

…

________________________________ From: Andrey Rozenberg <notifications@github.com> Sent: Tuesday, October 15, 2019 8:57 AM To: Nesvilab/MSFragger Cc: Subscribed Subject: [Nesvilab/MSFragger] Single amino acid polymorphisms (#44) External Email - Use Caution Hi, AFAICT, MSFragger has no built-in way of addressing known single amino acid polymorphisms (cf. x!tandem<https://thegpm.org/TANDEM/api/rsaps.html>). Is such an option on the agenda and/or it there a good workaround recommendation? Thanks! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#44?email_source=notifications&email_token=AIIMM6ZGJ2D5DYOTBBG5OUTQOW43TA5CNFSM4JA4GWBKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HR3VVJA>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIIMM65X73WW2M6QY7TC3VLQOW43TANCNFSM4JA4GWBA>. ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[alephreish]

Thanks for the prompt response! A custom database is of course an option, but with the drawback you mention. I think, in a future solution, polymorphisms should be treated basically the same way modifications are.

[anesvi]

I certainly would not argue with that but we need to do the work to support PEFF format, or read another file (which may include PTMS as well) It’s a question of effort at this point… From: Andrey Rozenberg [mailto:notifications@github.com] Sent: Tuesday, October 15, 2019 2:04 PM To: Nesvilab/MSFragger <MSFragger@noreply.github.com> Cc: Nesvizhskii, Alexey <nesvi@med.umich.edu>; Comment <comment@noreply.github.com> Subject: Re: [Nesvilab/MSFragger] Single amino acid polymorphisms (#44) External Email - Use Caution Thanks for the prompt response! A custom database is of course an option, but with the drawback you mention. I think, in a future solution, polymorphisms should be treated basically the same way modifications are. — You are receiving this because you commented. Reply to this email directly, view it on GitHub<#44?email_source=notifications&email_token=AIIMM62NR2V3LSMORG2JFTLQOYAX3A5CNFSM4JA4GWBKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEBJV7TI#issuecomment-542334925>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIIMM62ZICHHTYHA62U7WETQOYAX3ANCNFSM4JA4GWBA>. ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[jjGG]

Along these lines I do have another question.

How is MSFragger dealing with "X" in the amino acid sequences?

best regards
jonas

[fcyu]

The mass is 0. You can set a fixed modification to let it be any (modified) amino acid you want. Same for B, J, and Z.

Best,

Fengchao

[kichem2043-beep]

Hi Expert,

I saw Professor Nesvizhskii's response that PEFF search is possible in the near future in MS Fragger in 2019. I was considering investigating single amino acid variation using PEFF search. Is it possible to do a PEFF search by FragPipe? Could you please provide any information related if available?

PEFF: http://www.psidev.info/peff

Sincerely,

Ramesh

[fcyu]

No, FragPipe doesn't support it yet.

Best,

Fengchao