title: Ion mobility tandem mass spectrometry enhances performance of bottom-up proteomics.
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.
authors.affiliation: From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany;
authors.forename: Dominic
authors.initials: D
authors.lastname: Helm
authors.affiliation: §Waters Corporation, Manchester, UK;
authors.forename: Johannes P C
authors.initials: JP
authors.lastname: Vissers
authors.affiliation: §Waters Corporation, Manchester, UK;
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Hughes
authors.affiliation: From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany;
authors.forename: Hannes
authors.initials: H
authors.lastname: Hahne
authors.affiliation: From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany;
authors.forename: Benjamin
authors.initials: B
authors.lastname: Ruprecht
authors.affiliation: From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany;
authors.forename: Fiona
authors.initials: F
authors.lastname: Pachl
authors.affiliation: §Waters Corporation, Manchester, UK;
authors.forename: Arkadiusz
authors.initials: A
authors.lastname: Grzyb
authors.affiliation: §Waters Corporation, Manchester, UK;
authors.forename: Keith
authors.initials: K
authors.lastname: Richardson
authors.affiliation: §Waters Corporation, Manchester, UK;
authors.forename: Jason
authors.initials: J
authors.lastname: Wildgoose
authors.affiliation: From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany;
authors.forename: Stefan K
authors.initials: SK
authors.lastname: Maier
authors.affiliation: From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany;
authors.forename: Harald
authors.initials: H
authors.lastname: Marx
authors.affiliation: From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany;
authors.forename: Mathias
authors.initials: M
authors.lastname: Wilhelm
authors.affiliation: ¶Cellzome GmbH, Heidelberg, Germany;
authors.forename: Isabelle
authors.initials: I
authors.lastname: Becher
authors.affiliation: From the ‡Chair for Proteomics and Bioanalytics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany;
authors.forename: Simone
authors.initials: S
authors.lastname: Lemeer
authors.affiliation: ¶Cellzome GmbH, Heidelberg, Germany;
authors.forename: Marcus
authors.initials: M
authors.lastname: Bantscheff
authors.affiliation: §Waters Corporation, Manchester, UK;
authors.forename: James I
authors.initials: JI
authors.lastname: Langridge
authors.affiliation: 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.
authors.forename: Bernhard
authors.initials: B
authors.lastname: Kuster
mesh_terms: D017022:Flow Injection Analysis; D006367:HeLa Cells; D056572:Histone Deacetylase Inhibitors / Q000737:chemistry; D006655:Histone Deacetylases / Q000032:analysis*; D006801:Humans; D006877:Hydroxamic Acids / Q000737:chemistry; D007477:Ions; D010446:Peptide Fragments / Q000032:analysis*; D010750:Phosphoproteins / Q000032:analysis*; D010766:Phosphorylation; D040901:Proteomics / Q000295:instrumentation* / Q000379:methods; D012680:Sensitivity and Specificity; D053719:Tandem Mass Spectrometry / Q000295:instrumentation* / Q000379:methods; D013997:Time Factors; D014357:Trypsin / Q000737:chemistry
chemical_list: D056572:Histone Deacetylase Inhibitors; D006877:Hydroxamic Acids; D007477:Ions; D010446:Peptide Fragments; D010750:Phosphoproteins; C012589:trichostatin A; D014357:Trypsin; D006655:Histone Deacetylases
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