title: Reproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-mass spectrometry.
abstract: Targeted mass spectrometry by selected reaction monitoring (S/MRM) has proven to be a suitable technique for the consistent and reproducible quantification of proteins across multiple biological samples and a wide dynamic range. This performance profile is an important prerequisite for systems biology and biomedical research. However, the method is limited to the measurements of a few hundred peptides per LC-MS analysis. Recently, we introduced SWATH-MS, a combination of data independent acquisition and targeted data analysis that vastly extends the number of peptides/proteins quantified per sample, while maintaining the favorable performance profile of S/MRM. Here we applied the SWATH-MS technique to quantify changes over time in a large fraction of the proteome expressed in Saccharomyces cerevisiae in response to osmotic stress. We sampled cell cultures in biological triplicates at six time points following the application of osmotic stress and acquired single injection data independent acquisition data sets on a high-resolution 5600 tripleTOF instrument operated in SWATH mode. Proteins were quantified by the targeted extraction and integration of transition signal groups from the SWATH-MS datasets for peptides that are proteotypic for specific yeast proteins. We consistently identified and quantified more than 15,000 peptides and 2500 proteins across the 18 samples. We demonstrate high reproducibility between technical and biological replicates across all time points and protein abundances. In addition, we show that the abundance of hundreds of proteins was significantly regulated upon osmotic shock, and pathway enrichment analysis revealed that the proteins reacting to osmotic shock are mainly involved in the carbohydrate and amino acid metabolism. Overall, this study demonstrates the ability of SWATH-MS to efficiently generate reproducible, consistent, and quantitatively accurate measurements of a large fraction of a proteome across multiple samples.
authors.affiliation: From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland;
authors.forename: Nathalie
authors.initials: N
authors.lastname: Selevsek
authors.affiliation: §Department of Statistics, Purdue University, West Lafayette IN, USA;
authors.forename: Ching-Yun
authors.initials: CY
authors.lastname: Chang
authors.affiliation: From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland;
authors.forename: Ludovic C
authors.initials: LC
authors.lastname: Gillet
authors.affiliation: ‖‖Institute for Immunology, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany.
authors.forename: Pedro
authors.initials: P
authors.lastname: Navarro
authors.affiliation: ¶Biognosys, 8952 Zürich, Switzerland;
authors.forename: Oliver M
authors.initials: OM
authors.lastname: Bernhardt
authors.affiliation: ¶Biognosys, 8952 Zürich, Switzerland;
authors.forename: Lukas
authors.initials: L
authors.lastname: Reiter
authors.affiliation: §Department of Statistics, Purdue University, West Lafayette IN, USA;
authors.forename: Lin-Yang
authors.initials: LY
authors.lastname: Cheng
authors.affiliation: ‖College of Science, Northeastern University, 02115 Boston Massachusetts;
authors.forename: Olga
authors.initials: O
authors.lastname: Vitek
authors.affiliation: From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland; ‡‡Faculty of Science, University of Zürich, Switzerland; aebersold@imsb.biol.ethz.ch.
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
mesh_terms: D050260:Carbohydrate Metabolism; D013058:Mass Spectrometry / Q000379:methods*; D009995:Osmosis; D010455:Peptides / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000032:analysis*
chemical_list: D010455:Peptides; D029701:Saccharomyces cerevisiae Proteins