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MSGFPlus / msgfplus

MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.
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Semi-specific sequences #71

Open oliverschilling opened 5 years ago

oliverschilling commented 5 years ago

I would like to make a small feature request and I hope that this way of communication is the right one:

In N-terminomics, we look at sequences that are N-terminally truncated but always have a tryptic / ArgC / etc C-terminus.

At present, msgf+ offers “semi-specific” in silico digestion; yielding sequences that have either a non-specific N-terminus or a non-specific C-terminus. Would it be possible to add a feature to restrict semi-specifity, such that only sequences with non-specific N-termini are being probed?

Example (peptide sequence kept unrealistically short for illustration):

AVGER present semi-specific: AVGE AVG AV A VGER GER ER R

my wish for a restricted semi-specificity (here: focus on non-specific N-terminus) AVGER VGER GER ER R

It would be fantastic to have this possibility!

Thanks again for developing msgs+.

Kind regards and best wishes

Oliver Schilling

patrick-willems commented 1 year ago

Hey,

I was wondering whether this enhancement would still be implemented in a future version? It would also be very interesting to me to restrict the specificity to either N- or C-terminus only.

Thanks! Patrick