EasyProt--an easy-to-use graphical platform for proteomics data analysis

J Proteomics. 2013 Feb 21;79:146-60. doi: 10.1016/j.jprot.2012.12.012. Epub 2012 Dec 28.

Abstract

High throughput protein identification and quantification analysis based on mass spectrometry are fundamental steps in most proteomics projects. Here, we present EasyProt (available at http://easyprot.unige.ch), a new platform for mass spectrometry data processing, protein identification, quantification and unexpected post-translational modification characterization. EasyProt provides a fully integrated graphical experience to perform a large part of the proteomic data analysis workflow. Our goal was to develop a software platform that would fulfill the needs of scientists in the field, while emphasizing ease-of-use for non-bioinformatician users. Protein identification is based on OLAV scoring schemes and protein quantification is implemented for both, isobaric labeling and label-free methods. Additional features are available, such as peak list processing, isotopic correction, spectra filtering, charge-state deconvolution and spectra merging. To illustrate the EasyProt platform, we present two identification and quantification workflows based on isobaric tagging and label-free methods.

Publication types

  • Validation Study

MeSH terms

  • Mass Spectrometry / methods
  • Protein Processing, Post-Translational
  • Proteins / analysis
  • Proteomics / methods*
  • Sequence Analysis, Protein / methods*
  • Software*

Substances

  • Proteins