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Nat Methods. 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.

Author information

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.

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.

PMID:
24336358
DOI:
10.1038/nmeth.2767
[Indexed for MEDLINE]

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