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Sci Data. 2014 Sep 16;1:140031. doi: 10.1038/sdata.2014.31. eCollection 2014.

A repository of assays to quantify 10,000 human proteins by SWATH-MS.

Author information

1
Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; PhD Program in Systems Biology, University of Zurich and ETH Zurich , CH-8093 Zurich, Switzerland.
2
Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; Ruprecht Karls University of Heidelberg , DE-69117 Heidelberg, Germany.
3
Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland.
4
Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; PhD Program in Molecular and Translational Biomedicine, Competence Centre for Systems Physiology and Metabolic Diseases (CC-SPMD), University of Zurich and ETH Zurich , CH-8093 Zurich, Switzerland.
5
Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; Department of Phytopharmaceuticals (Traditional Pharmacy), School of Pharmacy and Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, 71345-1583 Shiraz, Iran.
6
Division of Biomedical Engineering and Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Clear Water Bay , Hong Kong, China.
7
Institute for Systems Biology , Seattle, Washington 98109-5234, USA.
8
AB SCIEX , Concord, Ontario L4K 4V8, Canada.
9
Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, CH-8093 Zurich, Switzerland ; Faculty of Science, University of Zurich , CH-8057 Zurich, Switzerland.

Abstract

Mass spectrometry is the method of choice for deep and reliable exploration of the (human) proteome. Targeted mass spectrometry reliably detects and quantifies pre-determined sets of proteins in a complex biological matrix and is used in studies that rely on the quantitatively accurate and reproducible measurement of proteins across multiple samples. It requires the one-time, a priori generation of a specific measurement assay for each targeted protein. SWATH-MS is a mass spectrometric method that combines data-independent acquisition (DIA) and targeted data analysis and vastly extends the throughput of proteins that can be targeted in a sample compared to selected reaction monitoring (SRM). Here we present a compendium of highly specific assays covering more than 10,000 human proteins and enabling their targeted analysis in SWATH-MS datasets acquired from research or clinical specimens. This resource supports the confident detection and quantification of 50.9% of all human proteins annotated by UniProtKB/Swiss-Prot and is therefore expected to find wide application in basic and clinical research. Data are available via ProteomeXchange (PXD000953-954) and SWATHAtlas (SAL00016-35).

PMID:
25977788
PMCID:
PMC4322573
DOI:
10.1038/sdata.2014.31
[Indexed for MEDLINE]
Free PMC Article

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