A Comprehensive Mass Spectrometry Deconvolution Tool for Analyzing Glycosaminoglycan (GAG)

This software identifies GAG species from a mass spectrum.

spectrum: a spectrum file in plain text format
gag_type: type of GAG ('hs': heparan sulfate, 'cs': chondroitin sulfate, 'ds': dermatan sulfate, 'ha': hyaluronic acid)
accuracy: mass accuracy in ppm
num_charge: minimum number of charge states
length_type: 'Fixed' or 'Variable'
range_low: lower end of length range
range_high: higher end of length range
dHexA: number of unsaturated hexeruronic acid
Mann: number of 2,5-anhydromannose
NH4: maximum number of ammonium
Na: maximum number of sodium ion
K: maximum number of potassium ion
Ca: maximum number of calcium ion
Li: maximum number of lithium ion

from gaginterpreter import GagInterpreter

spectrum = #some spectrum file
gag_type = 'hs'
accuracy = 3
num_charge = 3
length_type = 'Variable'
range_low = 4
range_high = 10
dHexA = 1
exp = GagIdentifier(spectrum, gag_type, accuracy, num_charge, length_type, range_low, range_high, dHexA)
matches = exp.identify_species()

for mass, mz, charge, gag, _ in matches:
    print "%.4f\t%.4f\t%d\t%d %d %d %d %d %d %d %d %d %d %d %d %d" % (mass, mz, charge, gag.dHexA, gag.HexA, gag.HexN, gag.HexNAc,
        gag.Mann, gag.Ac, gag.SO3, gag.NH4, gag.HOHloss, gag.Na, gag.K, gag.Ca, gag.Li)