A quantitation module for isotope-labeled peptides integrated into PatternLab for proteomics

J Proteomics. 2019 Jun 30:202:103371. doi: 10.1016/j.jprot.2019.04.021. Epub 2019 Apr 26.

Abstract

We present a new module integrated into the widely adopted PatternLab for proteomics to enable analysis of isotope-labeled peptides produced using dimethyl or SILAC. The accurate quantitation of proteins lies within the heart of proteomics; dimethylation has shown to be reliable, inexpensive, and applicable to any sample type. We validate our algorithm using an M. tuberculosis dataset obtained from two biological conditions; we used three dimethyl labels, one serving as an internal control for labeling a mixture of samples from both biological conditions. This internal control certified the proper functioning of our software. Availability: http://patternlabforproteomics.org, freely available for academic use.

Keywords: Bioinformatics; Differential proteomics; Dimethyl; PatternLab.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / metabolism*
  • Databases, Protein*
  • Isotope Labeling*
  • Mycobacterium tuberculosis / metabolism*
  • Peptides / chemistry*
  • Peptides / metabolism
  • Proteomics / standards*

Substances

  • Bacterial Proteins
  • Peptides