期刊
NATURE COMMUNICATIONS
卷 8, 期 -, 页码 -出版社
NATURE PUBLISHING GROUP
DOI: 10.1038/s41467-017-00249-5
关键词
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资金
- Government of Canada through Genome Canada [OGI-088, OGI-097]
- Government of Canada through Ontario Genomics [OGI-088, OGI-097]
- Canadian Institutes of Health Research [FDN-143301]
- National Cancer Institute Clinical Proteomics Tumor Analysis Consortium (CPTAC) [U24CA160036]
- Chinese National Basic Research Programs [2014CBA02002, 2014CBA02005]
- European Union [HEALTH-F4-2013-602156]
- NIH shared instrumentation grant for the TripleTOF system at the Buck Institute [1S10 OD016281]
- Australian Government's National Collaborative Research Infrastructure Scheme
- National Institutes of Health Grant from the National Human Genome Research Institute (NHGRI) through the American Recovery and Reinvestment Act [RC2 HG005805]
- National Institutes of Health Grants from the National Institute of General Medical Sciences (NIGMS) [R01GM087221, S10RR027584, 2P50GM076547]
- National Institutes of Health Grants from National Science Foundation [MCB-1330912]
- AMED-CREST from Japan Agency for Medical Research and Development
- Funding Program for Next Generation World-Leading Researchers by the Cabinet Office
- Swiss National Science Foundation Ambizione grant [PZ00P3_161435]
- ERC Proteomics v3.0 [AdG-233226 Proteomics v.3.0, AdG-670821 Proteomics 4D]
- PhosphonetX project of SystemsX.ch
- Swiss National Science Foundation (SNSF) grant [31003A_166435]
- Swiss National Science Foundation (SNF) [31003A_166435] Funding Source: Swiss National Science Foundation (SNF)
Quantitative proteomics employing mass spectrometry is an indispensable tool in life science research. Targeted proteomics has emerged as a powerful approach for reproducible quantification but is limited in the number of proteins quantified. SWATH-mass spectrometry consists of data-independent acquisition and a targeted data analysis strategy that aims to maintain the favorable quantitative characteristics (accuracy, sensitivity, and selectivity) of targeted proteomics at large scale. While previous SWATH-mass spectrometry studies have shown high intra-lab reproducibility, this has not been evaluated between labs. In this multi-laboratory evaluation study including 11 sites worldwide, we demonstrate that using SWATH-mass spectrometry data acquisition we can consistently detect and reproducibly quantify >4000 proteins from HEK293 cells. Using synthetic peptide dilution series, we show that the sensitivity, dynamic range and reproducibility established with SWATH-mass spectrometry are uniformly achieved. This study demonstrates that the acquisition of reproducible quantitative proteomics data by multiple labs is achievable, and broadly serves to increase confidence in SWATH-mass spectrometry data acquisition as a reproducible method for large-scale protein quantification.
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