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

School of Biological Sciences

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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).

Original language	English
Article number	140031
Number of pages	15
Journal	Scientific Data
Volume	1
DOIs	https://doi.org/10.1038/sdata.2014.31
Publication status	Published - 16 Sept 2014

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A repository of assays to quantify 10,000 human proteins by SWATH-MS
© 2014 The Authors. This is an open access article published under a Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited.
Final published version, 957 KBLicence: CC BY

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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

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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",

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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

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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

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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

M3 - Article

SN - 2052-4463

VL - 1

JO - Scientific Data

JF - Scientific Data

M1 - 140031

ER -

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

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