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

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

doi:10.1038/sdata.2014.31

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

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. MoritzStephen Tate, Ruedi Aebersold

Résultats de recherche: Contribution à un journal › Article › Revue par des pairs

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Résumé

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).

langue originale	Anglais
Numéro d'article	140031
journal	Scientific Data
Volume	1
Les DOIs	https://doi.org/10.1038/sdata.2014.31
état	Publié - 16 sept. 2014
Modification externe	Oui

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10.1038/sdata.2014.31

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Rosenberger, G., Koh, C. C., Guo, T., Röst, H. L., Kouvonen, P., Collins, B. C., Heusel, M., Liu, Y., Caron, E., Vichalkovski, A., Faini, M., Schubert, O. T., Faridi, P., Ebhardt, H. A., Matondo, M., Lam, H., Bader, S. L., Campbell, D. S., Deutsch, E. W., ... Aebersold, R. (2014). A repository of assays to quantify 10,000 human proteins by SWATH-MS. Scientific Data, 1, Article 140031. https://doi.org/10.1038/sdata.2014.31

@article{e3e16ced19f44489a5971ca3b904e9fb,

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

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).",

author = "George Rosenberger and Koh, {Ching Chiek} and Tiannan Guo and R{\"o}st, {Hannes L.} and Petri Kouvonen and Collins, {Ben C.} and Moritz Heusel and Yansheng Liu and Etienne Caron and Anton Vichalkovski and Marco Faini and Schubert, {Olga T.} and Pouya Faridi and Ebhardt, {H. Alexander} and Mariette Matondo and Henry Lam and Bader, {Samuel L.} and Campbell, {David S.} and Deutsch, {Eric W.} and Moritz, {Robert L.} and Stephen Tate and Ruedi Aebersold",

note = "Funding Information: G.R. was funded by the Swiss Federal Commission for Technology and Innovation CTI (13539.1 PFFLILS). H.L.R. was funded by ETH Zurich (ETH-30 11-2). P.K. was supported by the Finnish Cultural Foundation. E.C. was supported by a Marie Curie Intra-European Fellowship. M.F. was supported by a long-term fellowship from the European Molecular Biology Organization. M.M was funded by TRIREME. H.L. was funded by the General Research Fund (#602413) of the Research Grants Council of the Hong Kong Special Administrative Region Government. S.L.B was supported by a fellowship from the Swiss National Science Foundation (fellowship PBZHP3 143482). R.L.M., D.S.C. and E.W.D are supported in part by federal funds from the American Recovery and Reinvestment Act through Grant RC2 HG005805 from the National Human Genome Research Institute, the National Institutes of Health National Institute of General Medical Sciences under grant Nos. 2P50 GM076547/Center for Systems Biology, GM087221 and S10RR027584. R.A. was funded by the advanced European Research Council grant Proteomics v3.0 (ERC-2008-AdG_20080422), the PhosphonetX project of SystemsX.ch, and the Swiss National Science Foundation (3100A0-107679). We would like to thank Sharon Rashi-Elkeles for the generation of the CAL51 cells, the ITS Scientific IT Services of ETH Zurich for support and maintenance of the lab-internal computing infrastructure and the PRIDE Team of EBI for support of data deposition to the ProteomeXchange Consortium.",

year = "2014",

month = sep,

day = "16",

doi = "10.1038/sdata.2014.31",

language = "English",

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journal = "Scientific Data",

issn = "2052-4463",

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Rosenberger, G, Koh, CC, Guo, T, Röst, HL, Kouvonen, P, Collins, BC, Heusel, M, Liu, Y, Caron, E, Vichalkovski, A, Faini, M, Schubert, OT, Faridi, P, Ebhardt, HA, Matondo, M, Lam, H, Bader, SL, Campbell, DS, Deutsch, EW, Moritz, RL, Tate, S & Aebersold, R 2014, 'A repository of assays to quantify 10,000 human proteins by SWATH-MS', Scientific Data, VOL. 1, 140031. https://doi.org/10.1038/sdata.2014.31

TY - JOUR

T1 - A repository of assays to quantify 10,000 human proteins by SWATH-MS

AU - Rosenberger, George

AU - Koh, Ching Chiek

AU - Guo, Tiannan

AU - Röst, Hannes L.

AU - Kouvonen, Petri

AU - Collins, Ben C.

AU - Heusel, Moritz

AU - Liu, Yansheng

AU - Caron, Etienne

AU - Vichalkovski, Anton

AU - Faini, Marco

AU - Schubert, Olga T.

AU - Faridi, Pouya

AU - Ebhardt, H. Alexander

AU - Matondo, Mariette

AU - Lam, Henry

AU - Bader, Samuel L.

AU - Campbell, David S.

AU - Deutsch, Eric W.

AU - Moritz, Robert L.

AU - Tate, Stephen

AU - Aebersold, Ruedi

N1 - Funding Information: G.R. was funded by the Swiss Federal Commission for Technology and Innovation CTI (13539.1 PFFLILS). H.L.R. was funded by ETH Zurich (ETH-30 11-2). P.K. was supported by the Finnish Cultural Foundation. E.C. was supported by a Marie Curie Intra-European Fellowship. M.F. was supported by a long-term fellowship from the European Molecular Biology Organization. M.M was funded by TRIREME. H.L. was funded by the General Research Fund (#602413) of the Research Grants Council of the Hong Kong Special Administrative Region Government. S.L.B was supported by a fellowship from the Swiss National Science Foundation (fellowship PBZHP3 143482). R.L.M., D.S.C. and E.W.D are supported in part by federal funds from the American Recovery and Reinvestment Act through Grant RC2 HG005805 from the National Human Genome Research Institute, the National Institutes of Health National Institute of General Medical Sciences under grant Nos. 2P50 GM076547/Center for Systems Biology, GM087221 and S10RR027584. R.A. was funded by the advanced European Research Council grant Proteomics v3.0 (ERC-2008-AdG_20080422), the PhosphonetX project of SystemsX.ch, and the Swiss National Science Foundation (3100A0-107679). We would like to thank Sharon Rashi-Elkeles for the generation of the CAL51 cells, the ITS Scientific IT Services of ETH Zurich for support and maintenance of the lab-internal computing infrastructure and the PRIDE Team of EBI for support of data deposition to the ProteomeXchange Consortium.

PY - 2014/9/16

Y1 - 2014/9/16

N2 - 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).

AB - 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).

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DO - 10.1038/sdata.2014.31

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