SWATH2stats: An R/Bioconductor Package to Process and Convert Quantitative SWATH-MS Proteomics Data for Downstream Analysis Tools

PLoS One. 2016 Apr 7;11(4):e0153160. doi: 10.1371/journal.pone.0153160. eCollection 2016.

Abstract

SWATH-MS is an acquisition and analysis technique of targeted proteomics that enables measuring several thousand proteins with high reproducibility and accuracy across many samples. OpenSWATH is popular open-source software for peptide identification and quantification from SWATH-MS data. For downstream statistical and quantitative analysis there exist different tools such as MSstats, mapDIA and aLFQ. However, the transfer of data from OpenSWATH to the downstream statistical tools is currently technically challenging. Here we introduce the R/Bioconductor package SWATH2stats, which allows convenient processing of the data into a format directly readable by the downstream analysis tools. In addition, SWATH2stats allows annotation, analyzing the variation and the reproducibility of the measurements, FDR estimation, and advanced filtering before submitting the processed data to downstream tools. These functionalities are important to quickly analyze the quality of the SWATH-MS data. Hence, SWATH2stats is a new open-source tool that summarizes several practical functionalities for analyzing, processing, and converting SWATH-MS data and thus facilitates the efficient analysis of large-scale SWATH/DIA datasets.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods*
  • Peptides / analysis
  • Proteomics / methods*
  • Reproducibility of Results
  • Software

Substances

  • Peptides

Grants and funding

This work was supported by the Swiss SystemsX.ch initiative, evaluated by the Swiss National Science Foundation, to PB. MH was supported by grants from the European research council [233226-PROTEOMICS v3.0] and the Institut Mérieux to RA. The RA group is supported by the Swiss National Science Foundation [3100A0-130530], Advanced ERC grant [#670821], ETH Zurich and SystemsX.ch. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.