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Mol Cell Proteomics. 2014 Dec;13(12):3709-15. doi: 10.1074/mcp.M114.041038. Epub 2014 Aug 8.

Ion mobility tandem mass spectrometry enhances performance of bottom-up proteomics.

Author information

1
From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany;
2
§Waters Corporation, Manchester, UK;
3
¶Cellzome GmbH, Heidelberg, Germany;
4
From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany; ‖Center for Integrated Protein Science Munich, Germany kuster@tum.de.

Abstract

One of the limiting factors in determining the sensitivity of tandem mass spectrometry using hybrid quadrupole orthogonal acceleration time-of-flight instruments is the duty cycle of the orthogonal ion injection system. As a consequence, only a fraction of the generated fragment ion beam is collected by the time-of-flight analyzer. Here we describe a method utilizing postfragmentation ion mobility spectrometry of peptide fragment ions in conjunction with mobility time synchronized orthogonal ion injection leading to a substantially improved duty cycle and a concomitant improvement in sensitivity of up to 10-fold for bottom-up proteomic experiments. This enabled the identification of 7500 human proteins within 1 day and 8600 phosphorylation sites within 5 h of LC-MS/MS time. The method also proved powerful for multiplexed quantification experiments using tandem mass tags exemplified by the chemoproteomic interaction analysis of histone deacetylases with Trichostatin A.

PMID:
25106551
PMCID:
PMC4256517
DOI:
10.1074/mcp.M114.041038
[Indexed for MEDLINE]
Free PMC Article

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