Help to specify modification

[pnnl-comp-mass-spec]

Help to specify modification

[alchemistmatt]

There are example modification definitions in the text files at https://github.com/PNNL-Comp-Mass-Spec/Informed-Proteomics/tree/master/Example_Files

The format of the file is
EmpiricalFormula, AffectedResidue, ModType, PeptideLocation, ModName

• EmpiricalFormula is the elements to add or remove from the peptide
• AffectedResidue is the single letter amino acid abbrevation
• ModType is opt or fix, corresponding to a dynamic mod or a static mod
• PeptideLocation is any, N-term, C-Term, Prot-N-term, or Prot-C-term
• ModName is the name of the modification, preferably corresponding to a Unimod name (see the PSI-MS-Name and Interim Name columns at http://www.unimod.org/modifications_list.php?pagesize=200)

The file with a bunch of example mod definitions is https://github.com/PNNL-Comp-Mass-Spec/Informed-Proteomics/blob/master/Example_Files/Mod_Examples.txt

Note that the modification file format mirrors the one used by MS-GF+. For additional information, see the comments at https://raw.githubusercontent.com/sangtaekim/msgfplus/master/doc/examples/Mods.txt