Perform MS/MS pmd annotation for mgf file

Perform MS/MS pmd annotation for mgf file

pmdanno(file, db = NULL, ppm = 10, prems = 1.1, pmdc = 0.6, scutoff = 0.1)

Arguments

file

mgf file generated from MS/MS data

db

database could be list object from `getms2pmd`

ppm

mass accuracy, default 10

prems

precursor mass range, default 1.1 to include M+H or M-H

pmdc

pmd length percentage cutoff for annotation. 0.6(default) means 60 percentage of the pmds in your sample could be found in certain compound pmd database

scutoff

relative intensity cutoff for input spectra for pmd analysis, default 0.1

Value

list with MSMS annotation results