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Nature Research, Nature Methods, 2(11), p. 167-170, 2013

DOI: 10.1038/nmeth.2767

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

Journal article published in 2013 by Ute Distler, Jörg Kuharev, Pedro Navarro ORCID, Yishai Levin, Hansjörg Schild, Stefan Tenzer ORCID
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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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.