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

• DOI: 10.1038/sdata.2014.31
• Publication Date: 2014-09-15T14:31:58Z
• Authors: George Rosenberger; Ching Chiek Koh; Tiannan Guo; Hannes L. Röst; Petri Kouvonen; Ben C. Collins; Moritz Heusel; Yansheng Liu; Etienne Caron; Anton Vichalkovski; Marco Faini; Olga T. Schubert; Pouya Faridi; H. Alexander Ebhardt; Mariette Matondo; Henry Lam; Samuel L. Bader; David S. Campbell; Eric W. Deutsch; Robert L. Moritz; Stephen Tate; Ruedi Aebersold
• Keywords: Statistics and Probability; Proteomics; 0301 basic medicine; Data Descriptor; Proteome; [SDV]Life Sciences [q-bio]; MESH: Mass Spectrometry / methods*; Library and Information Sciences; Mass Spectrometry; 576; Education; 03 medical and health sciences; Humans; [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology; Databases, Protein; MESH: Humans; MESH: Databases, Protein*; Proteins; MESH: Proteomics / methods; Computer Science Applications; MESH: Proteins / chemistry*; MESH: Proteome* / chemistry; Statistics, Probability and Uncertainty; Systems biology; Information Systems

AbstractMass 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).