Change Log

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

Edward Lau

Published

October 4, 2023

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

v.0.5.0

  • Added support for MS3-based TMT quantification
  • Added additional contaminant matrices for TMT 10-plex and 16-plex
  • pyTMT now uses pymzml v.2.5.2 to read mzML files

v.0.4.3

  • Minor bug fix
  • Corrected standalone mass for TMT 16-plex 133C

v.0.4.3

  • Corrected standalone mass for TMT 16-plex 133C

v.0.4.2

  • Added function to collapse individual peptide TMT intensities into protein TMT intensities
  • Added options to determining parsimony groups in collapsing peptide data into proteins
  • Added option to separate proteins into light and heavy groups based on SILAC labels
  • Patching standalone percolator

v.0.4.1

  • Added support for TMT 18-plex
  • Added non-negative least square method for contamination correction

v.0.4.0

  • pyTMT now supports TMT contaminant correction.
  • Added support for TMT 16-plex

v.0.3.5

  • pyTMT now reads the percolator output log file from crux to assign mzML files to Percolator file_idx
  • When no log file is present, pyTMT falls back on the old method of ordering mzML files by file names

v.0.2.8

  • input changed from specifying percolator directory to percolator file path
  • added preliminary support for standalone percolator output (psms)