title: Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics.
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.
authors: 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].
authors: Ute
authors: U
authors: Distler
authors: 1] Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany. [2].
authors: Jörg
authors: J
authors: Kuharev
authors: Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
authors: Pedro
authors: P
authors: Navarro
authors: The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel.
authors: Yishai
authors: Y
authors: Levin
authors: Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
authors: Hansjörg
authors: H
authors: Schild
authors: Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
authors: Stefan
authors: 0000000330340017
authors: S
authors: Tenzer
mesh_terms: D002853:Chromatography, Liquid; D006367:HeLa Cells; D006801:Humans; D007477:Ions / Q000737:chemistry*; D010446:Peptide Fragments / Q000032:analysis*; D020543:Proteome / Q000032:analysis*; D040901:Proteomics; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D007477:Ions; D010446:Peptide Fragments; D020543:Proteome