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

By George A. Rosenberger, C. Koh, T. Guo, Hannes L. Röst, P. Kouvonen, Ben C. Collins, M. Heusel, Yansheng Liu, E. Caron, Anton Vichalkovski and 12 more. Scientific Data, 2014

400 citations recorded by the source corpus.

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). Design Type(s) reference design • replicate design • protein expression profiling • quality control testing design Measurement Type(s) protein expression profiling Technology Type(s) mass spectrometry assay Factor Type(s) purification • Proteolysis Sample Characteristic(s) Homo sapiens • Monocyte • Neutrophil • Kidney • Muscle • Lung • Blood platelet • Gut • Blood plasma • 293 cell • THP-1 cell • U2 OS cell • HeLa cell • U2OS & HeLa • NCI60 • LNCAP cell • CAL-51 cell Design Type(s) reference design • replicate design • protein expression profiling • quality control testing design Measurement Type(s) protein expression profiling Technology Type(s) mass spectrometry assay Factor Type(s) purification • Proteolysis Sample Characteristic(s) Homo sapiens • Monocyte • Neutrophil • Kidney • Muscle • Lung • Blood platelet • Gut • Blood plasma • 293 cell • THP-1 cell • U2 OS cell • HeLa cell • U2OS & HeLa • NCI60 • LNCAP cell • CAL-51 cell Machine-accessible metadata file describing the reported data (ISA-Tab format)

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/0d2fd2a3dc691ab2632da43743a1ff44bf28051e

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

In Spectroscopy

Citations in the corpus

DIA-Umpire: comprehensive computational framework for data independent acquisition proteomics (2015, background): “…is a current limitation of this strategy: either time and sample must be consumed to generate libraries with the same samples and instrument, or libraries can be obtained independently 17 but with the caveat that fragmentation patterns and retention times may differ across experimental conditions.”
Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial (2018, positive): “The above described context-specific error estimation has been implemented in PyProphet (Rosenberger et al , 2017a), a component of the OpenSWATH work-flow, and Spectronaut (Bruderer et al , 2017).”
A proteomic atlas of senescence-associated secretomes for aging biomarker development (2019, methodology): “provides quantitative DIA assays for ~10,000 human proteins [72].”