search

MSGFPlus / msgfplus

MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.
Other
72 stars 36 forks source link

Protein FDR #146

Closed qzhang503 closed 1 year ago

qzhang503 commented 1 year ago

I am new to MS-GF+. An earlier post indicated that QValue may be used for FDR controls at the levels of PSM. Is there a similar way to compile the PSM outputs to attain 1% protein FDR? Many thanks.

alchemistmatt commented 1 year ago

MS-GF+ does not compute a protein level FDR, just PSM level (QValue) and peptide level (PepQValue).

qzhang503 commented 1 year ago

Thank you for the note.

On Wed, Mar 29, 2023 at 2:06 PM Matthew Monroe @.***> wrote:

MS-GF+ does not compute a protein level FDR, just PSM level (QValue) and peptide level (PepQValue).

— Reply to this email directly, view it on GitHub https://github.com/MSGFPlus/msgfplus/issues/146#issuecomment-1489152225, or unsubscribe https://github.com/notifications/unsubscribe-auth/AK5U2SURL7S6HKGZQOEVDV3W6SB47ANCNFSM6AAAAAAWKWHG4Y . You are receiving this because you authored the thread.Message ID: @.***>