title: SWATH2stats: An R/Bioconductor Package to Process and Convert Quantitative SWATH-MS Proteomics Data for Downstream Analysis Tools.
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.
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093, Zurich, Switzerland.
authors.forename: Peter
authors.initials: P
authors.lastname: Blattmann
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093, Zurich, Switzerland.|PhD program in Molecular and Translational Biomedicine, Competence Center Personalized Medicine UZH/ETH & Life Science Zurich Graduate School, ETH Zurich and University of Zurich, 8044, Zurich, Switzerland.
authors.forename: Moritz
authors.initials: M
authors.lastname: Heusel
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093, Zurich, Switzerland.|Faculty of Science, University of Zurich, 8057, Zurich, Switzerland.
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
mesh_terms: D019295:Computational Biology / Q000379:methods*; D010455:Peptides / Q000032:analysis; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software
chemical_list: D010455:Peptides