Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics

doi:10.1038/nmeth.2767

. 2014 Feb;11(2):167-70.

doi: 10.1038/nmeth.2767. Epub 2013 Dec 15.

Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics

Ute Distler¹, Jörg Kuharev², Pedro Navarro³, Yishai Levin⁴, Hansjörg Schild³, Stefan Tenzer³

Affiliations

¹ 1] Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany. [2] Focus Program Translational Neuroscience (FTN), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany. [3].
² 1] Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany. [2].
³ Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
⁴ The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel.

PMID: 24336358
DOI: 10.1038/nmeth.2767

Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics

Ute Distler et al. Nat Methods. 2014 Feb.

. 2014 Feb;11(2):167-70.

doi: 10.1038/nmeth.2767. Epub 2013 Dec 15.

Authors

Ute Distler¹, Jörg Kuharev², Pedro Navarro³, Yishai Levin⁴, Hansjörg Schild³, Stefan Tenzer³

Affiliations

¹ 1] Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany. [2] Focus Program Translational Neuroscience (FTN), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany. [3].
² 1] Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany. [2].
³ Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
⁴ The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel.

PMID: 24336358
DOI: 10.1038/nmeth.2767

Abstract

We present a data-independent acquisition mass spectrometry method, ultradefinition (UD) MS(E). This approach utilizes ion mobility drift time-specific collision-energy profiles to enhance precursor fragmentation efficiency over current MS(E) and high-definition (HD) MS(E) data-independent acquisition techniques. UDMS(E) provided high reproducibility and substantially improved proteome coverage of the HeLa cell proteome compared to previous implementations of MS(E), and it also outperformed a state-of-the-art data-dependent acquisition workflow. Additionally, we report a software tool, ISOQuant, for processing label-free quantitative UDMS(E) data.

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References

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[1] Anal Chem. 2011 Mar 15;83(6):2250-7 - PubMed

[2] Anal Chem. 2011 Mar 15;83(6):2250-7 - PubMed

[3] Nucleic Acids Res. 2013 Jan;41(Database issue):D1063-9 - PubMed

[4] Nucleic Acids Res. 2013 Jan;41(Database issue):D1063-9 - PubMed

[5] Bioinformatics. 2009 Mar 15;25(6):758-64 - PubMed

[6] Bioinformatics. 2009 Mar 15;25(6):758-64 - PubMed

[7] Anal Chem. 2010 Dec 15;82(24):10116-24 - PubMed

[8] Anal Chem. 2010 Dec 15;82(24):10116-24 - PubMed

[9] Mol Cell Proteomics. 2010 Oct;9(10):2252-61 - PubMed

[10] Mol Cell Proteomics. 2010 Oct;9(10):2252-61 - PubMed

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Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics

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Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics

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