title: Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data.
abstract: In mass spectrometry-based bottom-up proteomics, data-independent acquisition is an emerging technique because of its comprehensive and unbiased sampling of precursor ions. However, current data-independent acquisition methods use wide precursor isolation windows, resulting in cofragmentation and complex mixture spectra. Thus, conventional database searching tools that identify peptides by interpreting individual tandem MS spectra are inherently limited in analyzing data-independent acquisition data. Here we discuss an alternative approach, peptide-centric analysis, which tests directly for the presence and absence of query peptides. We discuss how peptide-centric analysis resolves some limitations of traditional spectrum-centric analysis, and we outline the unique characteristics of peptide-centric analysis in general.
authors.affiliation: From the ‡Department of Genome Sciences, University of Washington, Seattle, Washington;
authors.forename: Ying S
authors.initials: YS
authors.lastname: Ting
authors.affiliation: From the ‡Department of Genome Sciences, University of Washington, Seattle, Washington;
authors.forename: Jarrett D
authors.initials: JD
authors.lastname: Egertson
authors.affiliation: §Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington;
authors.forename: Samuel H
authors.initials: SH
authors.lastname: Payne
authors.affiliation: §Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington;
authors.forename: Sangtae
authors.initials: S
authors.lastname: Kim
authors.affiliation: From the ‡Department of Genome Sciences, University of Washington, Seattle, Washington;
authors.forename: Brendan
authors.initials: B
authors.lastname: MacLean
authors.affiliation: ¶Science for Life Laboratory, Royal Institute of Technology (KTH), Stockholm, Sweden;
authors.forename: Lukas
authors.initials: L
authors.lastname: Käll
authors.affiliation: ‖Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland; ‡‡Faculty of Science, University of Zurich, Zurich, Switzerland.
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
authors.affiliation: §Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington;
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
authors.affiliation: From the ‡Department of Genome Sciences, University of Washington, Seattle, Washington; **Department of Computer Science and Engineering, University of Washington, Seattle, Washington;
authors.forename: William Stafford
authors.initials: WS
authors.lastname: Noble
authors.affiliation: From the ‡Department of Genome Sciences, University of Washington, Seattle, Washington; maccoss@uw.edu.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: MacCoss
mesh_terms: D030562:Databases, Protein; D006801:Humans; D010455:Peptides / Q000302:isolation & purification*; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods
chemical_list: D010455:Peptides; D020543:Proteome