GPMDB00175OtherSelevsek N, et al.InstrumentNot AvailableNot availableYeastaebersold@imsb.biol.ethz.ch25561506http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007148http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007149http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007166http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007144http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007167http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007145http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007146http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007168http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007147http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007169http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007151http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007173http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007174http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007152http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007175http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007153http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007176http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007154http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007170http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007171http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007150http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007172http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007159http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007137http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007138http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007139http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007177http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007155http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007156http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007179http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007135http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007157http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007158http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007136http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007162http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007140http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007141http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007163http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007164http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007142http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007143http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007165http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007180http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007160http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007161ETH, Switzerland, et al..Not availableGPMDBTargeted 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.Reproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-mass spectrometry.Selevsek Nathalie N,Chang Ching-Yun CY,Gillet Ludovic C LC,Navarro Pedro P,Bernhardt Oliver M OM,Reiter Lukas L,Cheng Lin-Yang LY,Vitek Olga O,Aebersold Ruedi R,Selevsek Nathalie N, Chang Ching-Yun CY, Gillet Ludovic C LC, Navarro Pedro P, Bernhardt Oliver M OM, Reiter Lukas L, Cheng Lin-Yang LY, Vitek Olga O, Aebersold Ruedi RSaccharomyces oviformis, Yeasts, Saccharomyce cerevisiae, Yeast, Bakers, Brewer's, Baker Yeasts, baker's yeast, Saccharomyes cerevisiae, Baker, Brewer, Saccharomyces uvarum var. melibiosus, Saccharomyces italicus, Saccaromyces cerevisiae, Brewers Yeast, Baker's Yeasts, Sccharomyces cerevisiae, Brewer's Yeasts, S cerevisiae, Candida robusta, Saccharomyces capensis, Brewers, yeast, Proteomes., Baker's, brewer's yeast, Baker's Yeast, Bakers Yeast, Brewer's Yeast, lager beer yeast, Baker Yeast, Brewer YeastGene., IGF-I, data, CDF, steel factor, mol, Effects, Slf, hematopoietic growth factor KL, instrument configuration, Proteins, Somatomedin-C, Longterm Effect, somatomedin, baker's yeast, Gene, FPH2, DRF2, Saccaromyces cerevisiae, Saccharomyces italicus, Cell, sKITLG, Long Term, hardware, Sccharomyces cerevisiae, period, polypeptide, Polypeptides, POF, Injection, mechano growth factor, yeast, Long Term Effects, MLPLI, Protein, HILDA, Gene Products, Igf-1, Effect, Injectables, lager beer yeast, DiA, Saccharomyces oviformis, Yeast, SHEP7, mast cell growth factor, instrument, Longterm, cell, POF2, Stem cell factor, somatomedin-C, SF, Saccharomyes cerevisiae, HardwareType, Kitl, proteins, Long-Term, STAT5, DIASP, Saccharomyces uvarum var. melibiosus, Mast cell growth factor, DIA, Longterm Effects, Protein Gene Products, Injectable, 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, Gene Proteins, stem cell factor, reaction, KL-1, Candida robusta, Saccharomyces capensis, IGF1, MGF, c-Kit ligand, Mechano growth factor, KITLG, Long-Term Effect, Soluble KIT ligand, DIA2, brewer's yeast, SCF, Sl, Long-Term Effects, timeSaccharomyces oviformis, Mass Spectrum Analysis, Yeasts, Mass Spectrum, Saccharomyce cerevisiae, Yeast, Analyses, Bakers, Brewer's, Spectrometry, Baker Yeasts, baker's yeast, Saccharomyes cerevisiae, Baker, Spectrum Analyses, Brewer, Saccharomyces uvarum var. melibiosus, Spectrum Analysis, Saccharomyces italicus, Saccaromyces cerevisiae, Brewers Yeast, Spectroscopy, Baker's Yeasts, Sccharomyces cerevisiae, Brewer's Yeasts, S cerevisiae, Candida robusta, Saccharomyces capensis, Brewers, yeast, Mass, Mass., Baker's, Analysis, brewer's yeast, Baker's Yeast, Bakers Yeast, Brewer's Yeast, Proteomes, Mass Spectrum Analyses, lager beer yeast, Baker Yeast, Mass Spectroscopy, Brewer Yeastosmotic stress response, biochemical pathways, big, Metabolic Process, Procedures, determination, Effects, Circulatory, Processes, Aminosaeure, instrument configuration, number, Aminocarbonsaeure, Metabolic Concepts, Brewer's, saccharide, Gene, Baker Yeasts, baker's yeast, hydrates de carbone, Spectrum Analyses, broad, Metabolic Processes, glucide, Saccharomyces italicus, Long Term, Brewers Yeast, Failure, Biomedical, osmotic response, hardware, Circulatory Collapse, carbohydrates, period, Polypeptides, method, large, Investigative, Method, Injection, Metabolism, method used in an experiment, glucido, yeast, Medical Research, Mass, Gene Products, Studies, Concepts, Analysis, Metabolism Concept, Phenomenon, Medical, Effect, Injectables, Metabolism Phenomena, Mass Spectroscopy, lager beer yeast, Mass Spectrum Analysis, Shock, study, Saccharomyce cerevisiae, Kohlenhydrate, amino acids, MRM, Analyses, Biology, Research, Longterm, cell, catabolism, Saccharomyes cerevisiae, HardwareType, Metabolic Concept, proteins, Baker, metabolic process resulting in cell growth, number of, Long-Term, Brewer, Saccharomyces uvarum var. melibiosus, Hypovolemic Shock, Study, Injectable, reaction, Hypovolemic, S cerevisiae, Candida robusta, Methodological Studies, Saccharomyces capensis, sample, great, has or lacks parts of type, Investigational Medicine, Medicine, Baker's, biotransformation, Long-Term Effect, brewer's yeast, Catabolism, Long-Term Effects, incorporation, data, wide/broad, degradation, Process, Aminokarbonsaeure, metabolism resulting in cell growth, Proteins, Longterm Effect, saccharides, extra or missing physical or functional parts, Circulatory Failure, Procedure, Spectrum Analysis, Saccaromyces cerevisiae, Cell, Multiple Reaction Monitoring, Concept, Metabolic Phenomena, Spectroscopy, mereological quality, polypeptide, Baker's Yeasts, Sccharomyces cerevisiae, Investigative Medicine, Metabolism Concepts, Experimental, Protein, Systems, chemical analysis, Long Term Effects, Brewers, Proteomes., Phenomena, Bakers Yeast, glucides, metabolism, Mass Spectrum Analyses, Investigational, Kohlenhydrat, Brewer Yeast, Metabolic Phenomenon, saccharidum, Saccharomyces oviformis, Yeasts, Mass Spectrum, Yeast, mobilization, multicellular organism metabolic process, biodegradation, instrument, Metabolic, SRM, Experimental Medicine, Spectrometry, expanded, Bakers, Methodological, Carbohydrate, carbohidratos, Methodological Study, sample population, turnover, Longterm Effects, Protein Gene Products, plan specification, Collapse, Gene Proteins, Brewer's Yeasts, carbohidrato, wide, single-organism metabolic process, enlarged, cardinality, assay, Baker's Yeast, glucidos, time, Proteomes, Brewer's Yeast, Baker Yeast, Anabolism1705http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320007153dbgap_ncbi~0patentfamilies~0rfam~0merops~0complex-portal~0uniprot~0wormbaseparasite~0embl-covid19~0reactome~0emdb~0wgs_masters~0ebiweb_resources~0opentargets_genetics~0biomodels_all~0ipd-mhc~0ebiweb_teams~0taxonomy~0genome_assembly~0sc-experiments~0ebiweb_people~0enzymeportal_enzymes~0ipd-nhkir~0cellosaurus~0pdbe~0chebi~0patentproteins~0interpro7~0uniref~0chembl~0pdbekb~0gpcrdb~0hgnc~0sc-genes~0intact~0rhea~0ebiweb_training~0alphafold~0imgt-hla~0patentnucleotides~0ensemblroot~0eva_studies~0non-coding~0europepmc~0pubmed~1identifiers_registry~0pdbechem~0hpa-covid19~0eva-variants-covid19~0biosamples~0gwas_catalog~0biotools~0tls_masters~0mesh~0coding~0sra~0opentargets~0efo~0embl-pathogen~0project~0pride~1human_diseases~0geo_datasets~0embl~0treefam~0uniparc~0ols~0dgva~0intenz~0go~0tsa_masters~0biosamples-covid19~0ebiweb_corporate~0omim~0lrg~0earlycause-molecular-sequences~0ipd-kir~0empiar~0rnacentral~0orcid_data_claims~0gpmdb~2lineage-covid19~0metagenomics~0pfam~0pride archive~1varsite~00Resource Reanalysis0.00.00.0052436767427513880.01.0falseReproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-MS.Data from ProteomeXchange, PXD ID: PXD001010. File: nselevse_L120203_020-Yeast OGE 11- 4 ul - IDA20-150ms.mgf. Published as part of Mol Cell Proteomics. 2015 Jan 5 . From the Abstract: {{i}} ... We sampled cell cultures in biological triplicates at six time points following the application of osmotic stress and acquired single injection DIA datasets 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 ... {{/i}}2015-01-23GPM3232000715325561506PXD001010PXD001010