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Utilities for plotting 3D mass spec data, XIC etc from mzML data files

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MS Plotting utilities

These scripts provide some simple utilities for mining and plotting MS data. The data is expected to be available in mzML or the openMS featureXML format.

Script files can be run as standalone apps or as a library.


Command Line Usage: [options]

-h, --help

show this help message and exit

-m MZML, --mzml=MZML

Input mzML file

-f FEATURE, --feature=FEATURE

comma separated list of featureXML files

-o OUTFILE, --output=OUTFILE

output filename (default=’plot.pdf’)

-s, --showX11

Show X11 interactive plot.

-x XROT, --xrot=XROT

Xaxis rotation for plot (default (30)

-y YROT, --yrot=YROT

Yaxis rotation for plot (default: -45)

-l CLIP, --limit=CLIP

Clip threshold for plot

-c COLOURS, --colours=COLOURS

list of colours with which to plot features. Colours will be recycled when needed (default=’r,g,m,c,y,k’)

-r RTMIN, --rtmin=RTMIN

minimum retention time

-R RTMAX, --rtmax=RTMAX

maximum retention time

-t MZMIN, --mzmin=MZMIN

minimum m/z value

-T MZMAX, --mzmax=MZMAX

maximum m/z value

-w RTWINDOW, --rtwindow=RTWINDOW

Window around plot area in which to identify feature peaks

-p, --plotms2

Plot MS2 events

-d MS2WIN, --ms2win=MS2WIN

MS2 ion capture window size

Module usage: mzml is the only non-named argument. All arguments as per the command line version except that lists should be provided as arrays rather than comma-delimited text.

>>> import MSPlot.msplot3d
>>> MSPlot.plot3d(mzml, featfiles=[], outfile='plot.pdf', show=False, xrot=30, yrot=-45, featcols=['r','g','b','m','c','k'], thresh=100, minrt=None,maxrt=None,minmz=None, maxmz=None, ms2win=2.0, rtwindow=20.0, plotms2=True)


Module Usage:

>>> import Unimod.unimod
>>> import MSPlot.ms1pep
# protein amino acid sequence
>>> frags=MSPlot.ms1pep.digestprotein(peptide, enzyme=1, overlap=True, unfavoured=False)
    # overlap - include 1 missed cleavage
    # unfavoured - include unfavourable sites (see the EMBOSS documentation for more details)
    # enzyme - numerical enzyme selection according to the EMBOSS documentation
    Enzymes and Reagents
         1 : Trypsin
         2 : Lys-C
         3 : Arg-C
         4 : Asp-N
         5 : V8-bicarb
         6 : V8-phosph
         7 : Chymotrypsin
         8 : CNBr
>>> frags
[{'start': '1', 'end': '15', 'sequence': 'ACDEFGHIKLMNPQR'}, {'start': '16', 'end': '23', 'sequence': 'STVWYKK'}, {'start': '24', 'end': '32', 'sequence': 'ACDPRFGHI'}, {'start': '1', 'end': '23', 'sequence': 'ACDEFGHIKLMNPQRSTVWYKK'}]
# list of digested fragment peptides.
>>> camc=Unimod.unimod.database.get_label('Carbamidomethyl')['delta_mono_mass']
# get delta mass for fixed cysteine modification.
>>> MSPlot.ms1pep.listmz(frags[0]['sequence'], charges=[2,3,4], modifications=[], fixedmods={'C': camc })
[908.43562931579208, 605.95969455552802, 454.72172717539604]
# returns a list of mz values
>>> mzlist=MSPlot.ms1pep.listmz(frags[1]['sequence'], charges=[2,3,4], modifications=['2 Phospho (T)',], fixedmods={'C': camc })
>>> mzlist
[536.7538243454826, 358.17182457532175, 268.8808246902413]

# listmz does not permute, so for variable modifications, call it with each permutation.

>>> xics=MSPlot.ms1pep.getXIC("LCMSrun.mzML", mzlist, tolerance=0.01, minrt=0, maxrt=None)
>>> xics.keys()
['rt', '358.171824575', '536.753824345', '268.88082469']
# extracts the XIC for each mz ratio. The keys are a truncated string version of the full precision calculated mass.

MSPlot.ms1pep.plotXIC(xics, colours=[‘r’,’g’,’b’,’m’,’c’,’k’], outfile=”plot.pdf”, title=”XIC plot”): # plot the XICs. Any number can be plotted, but they are separated by 7% max(XIC)


pyMS - OpenMS data parsing and analysis by Niek de Klein pymzml - mzML parsing library pyteomics - package for calculating mz values and more numpy - large scale data handling matplotlib - plotting library EMBOSS (for the digest application) Unimod - module for handling a Unimod database.


Dr David Martin, University of Dundee

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