New software developed for analysis of LC-MS and SRM data

Posted by Tim Clough on June 16, 2013

MSstats2 is now available! MSstats2 is a software package designed for protein significance analysis in both the LC-MS and SRM platforms.

MSstats is an R package that contains tools for protein quantification and significance analysis in label-free LC-MS experiments using the family of linear mixed effects models. The package provides an easy specification of a statistical model, quantities from which can be used to test for differential protein abundance and to quantify abundance of proteins in individual biological samples.

The software is extremely flexible and can be used by researchers with a limited background in statistics and minimal programming experience to analyze data from nearly any label-free LC-MS experiment.

A package vignette containing example code for two case studies is available. See Installation for the latest version of the package, and check release history for specific updates to the package.


The methods implemented in the package were jointly developed by:

  • Tim Clough
  • Melissa Key
  • Dr. Olga Vitek (Departments of Statistics and of Computer Science, Purdue University)


T. Clough, S. Thaminy, S. Ragg, R. Aebersold, and O. Vitek. "Statistical protein quantification and significance analysis in label-free LC-MS experiments with complex designs". BMC Bioinformatics, 13(Suppl 16):S6, 2012.

T. Clough, M. Key, I. Ott, S. Ragg, G. Schadow, and O. Vitek. "Protein quantification in label-free LC-MS experiments". Journal of Proteome Research, 8, 5275-5284, 2009.

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