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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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Set of multiple optional modifications #106

Open Stortebecker opened 4 years ago

Stortebecker commented 4 years ago

Describe the question or problem I am working with metablic 15N labelling, meaning that every nitrogen in every amino acid of a protein is replaced by 15N. To search for these modifications, I would either have to use fixed searches for unlabelled and labelled proteins separately or use a high number of optional modifications, which would blow up the search space tremendously.

As all proteins are either fully unlabelled or fully labelled, I would need an option to search for a set of modifications, instead of searching for each modification separately.

Details The 15N labelling could be described by the following settings:

0.997035, ADCEGILMFPSTYV, opt, any, Label:15N(1)    # 15N-labelling for amino acids with one N,
1.994070, NQKW, opt, any, Label:15N(2)              # 15N-labelling for amino acids with two N
2.991105, H, opt, any, Label:15N(3)                 # 15N-labelling for amino acids with three N
3.988140, R, opt, any, Label:15N(4)                 # 15N-labelling for amino acids with four N

A possibility to search for sets of modifications has been implemented into X!Tandem.

alchemistmatt commented 4 years ago

MS-GF+ constructs a dynamic programming grid of residues to consider when examining MS/MS spectra. This means it's not straightforward to adjust which peptides are to be considered or not considered for searching, given a set of dynamic mods. Thus, the only option you have available is to perform two searches, one with normal amino acids, and one with N15-labelled amino acids, which you can define using static mods:

StaticMod=0.997035, ADCEGILMFPSTYV, fix, any, Label:15N(1)     # 15N Labeled ADCEGILMFPSTYV
StaticMod=1.994070, NQKW,           fix, any, Label:15N(2)     # 15N Labeled NQKW
StaticMod=2.991105, H,              fix, any, Label:15N(3)     # 15N Labeled H
StaticMod=3.988140, R,              fix, any, Label:15N(4)     # 15N Labeled R

See also this example file: MSGFPlus_N15_PartTryp_20ppmParTol.txt

Stortebecker commented 3 years ago

Sorry for the late answer: That's the workaround I used so far. But of course it would be more convenient to have a combined results file directly.