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Nesvilab / MSFragger

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics
https://msfragger.nesvilab.org
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Single amino acid polymorphisms #44

Open alephreish opened 5 years ago

alephreish commented 5 years ago

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 commented 5 years ago

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)

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Hi,

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

Thanks!

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alephreish commented 5 years ago

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 commented 5 years ago

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)

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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.

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jjGG commented 1 year ago

Along these lines I do have another question.

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

best regards jonas

fcyu commented 1 year ago

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