Documentation

pyTMT - automated tandem mass tag (TMT) data quantification for Comet and Percolator.

Abstract

This page provides the documentation for the pyTMT package, which is a tool for analyzing tandem mass tag (TMT) labeled quantitative proteomics data.

Example command:

$ python -m pytmt /path/to/mzml/ /path/to/percolator/psms.txt -o /path/to/output/

To test installation of test data files and download two test mzml files from ProteomeXchange:

$ pip install tox
$ tox

To run pytmt on the test data files and print the file to Desktop:

$ pytmt tests/data/mzml tests/data/percolator/percolator.target.psms.txt -o ~/Desktop/pytmt2

TMT tags

Below are the accurate masses used to find the TMT tags signals, and the channels corresponding to each option in the -m argument:

Tag mass	Tag name	0	2	6	10	11	16	18
126.127726	126	✅	✅	✅	✅	✅	✅	✅
127.124761	127N		✅		✅	✅	✅	✅
127.131081	127C			✅	✅	✅	✅	✅
128.128116	128N				✅	✅	✅	✅
128.134436	128C			✅	✅	✅	✅	✅
129.131471	129N			✅	✅	✅	✅	✅
129.137790	129C				✅	✅	✅	✅
130.134825	130N				✅	✅	✅	✅
130.141145	130C			✅	✅	✅	✅	✅
131.138180	131N			✅	✅	✅	✅	✅
131.144500	131C (11-plex)					✅	✅	✅
132.141535	132N (Pro)						✅	✅
132.147855	132C (Pro)						✅	✅
133.144890	133N (Pro)						✅	✅
133.141210	133C (Pro)						✅	✅
134.148245	134N (Pro)						✅	✅
134.154565	134C (Pro-18)							✅
135.151600	135N (Pro-18)							✅

All Options

python -m pytmt -h
usage: __main__.py [-h] [-u] [-q QVALUE] [-m MULTIPLEX] [-p PRECISION] [-o OUT] [-v] [-c CONTAM] [-n] mzml id

pytmt returns ms2 tmt quantification valuesfrom Percolator output and perform contaminationcorrection

positional arguments:
  mzml                  path to folder containing mzml files
  id                    path to percolator target psms output file

optional arguments:
  -h, --help            show this help message and exit
  -u, --unique          quantify unique peptides only
  -q QVALUE, --qvalue QVALUE
                        quantify peptides with q value below this threshold [default: 1.0]
  -m MULTIPLEX, --multiplex MULTIPLEX
                        TMT-plex (0, 2, 6, 10, 11, 16, 18) [default:10]
  -p PRECISION, --precision PRECISION
                        ms2 spectrum mass shift tolerance in ppm [default: 10]
  -o OUT, --out OUT     name of the output directory [default: tmt_out]
  -v, --version         show program's version number and exit
  -c CONTAM, --contam CONTAM
                        Path to contaminant matrix csv file. Leave blank to get tmt output without correction
  -n, --nnls            uses non-negative least square for contamination correction