title: An informatic framework for decoding protein complexes by top-down mass spectrometry.
abstract: Efforts to map the human protein interactome have resulted in information about thousands of multi-protein assemblies housed in public repositories, but the molecular characterization and stoichiometry of their protein subunits remains largely unknown. Here, we report a computational search strategy that supports hierarchical top-down analysis for precise identification and scoring of multi-proteoform complexes by native mass spectrometry.
authors.affiliation: Department of Chemistry, Northwestern University, Evanston, Illinois, USA.
authors.forename: Owen S
authors.initials: OS
authors.lastname: Skinner
authors.affiliation: Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA.|Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA.
authors.forename: Pierre C
authors.initials: PC
authors.lastname: Havugimana
authors.affiliation: Department of Chemistry, Northwestern University, Evanston, Illinois, USA.
authors.forename: Nicole A
authors.initials: NA
authors.lastname: Haverland
authors.affiliation: Department of Chemistry, Northwestern University, Evanston, Illinois, USA.|Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA.|Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA.
authors.forename: Luca
authors.initials: L
authors.lastname: Fornelli
authors.affiliation: Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA.
authors.forename: Bryan P
authors.initials: BP
authors.lastname: Early
authors.affiliation: Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA.
authors.forename: Joseph B
authors.initials: JB
authors.lastname: Greer
authors.affiliation: Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA.
authors.forename: Ryan T
authors.initials: RT
authors.lastname: Fellers
authors.affiliation: Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA.
authors.forename: Kenneth R
authors.initials: KR
authors.lastname: Durbin
authors.affiliation: Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA.|Brazilian Center for Protein Research, University of Brasilia, Brasilia, Federal District, Brazil.
authors.forename: Luis H F
authors.initials: LH
authors.lastname: Do Vale
authors.affiliation: Department of Chemistry, Northwestern University, Evanston, Illinois, USA.
authors.forename: Rafael D
authors.initials: RD
authors.lastname: Melani
authors.affiliation: Department of Chemistry, Northwestern University, Evanston, Illinois, USA.
authors.forename: Henrique S
authors.initials: HS
authors.lastname: Seckler
authors.affiliation: Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA.
authors.forename: Micah T
authors.initials: MT
authors.lastname: Nelp
authors.affiliation: Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany.
authors.forename: Mikhail E
authors.initials: ME
authors.lastname: Belov
authors.affiliation: Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany.
authors.forename: Stevan R
authors.initials: SR
authors.lastname: Horning
authors.affiliation: Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany.
authors.forename: Alexander A
authors.initials: AA
authors.lastname: Makarov
authors.affiliation: Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA.
authors.forename: Richard D
authors.initials: RD
authors.lastname: LeDuc
authors.affiliation: Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA.
authors.forename: Vahe
authors.initials: V
authors.lastname: Bandarian
authors.affiliation: Department of Chemistry, Northwestern University, Evanston, Illinois, USA.|Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA.
authors.forename: Philip D
authors.initials: PD
authors.lastname: Compton
authors.affiliation: Department of Chemistry, Northwestern University, Evanston, Illinois, USA.|Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA.|Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA.|Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA.
authors.forename: Neil L
authors.initials: NL
authors.lastname: Kelleher
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001665:Binding Sites; D003198:Computer Simulation; D057225:Data Mining / Q000379:methods*; D030562:Databases, Protein; D013058:Mass Spectrometry / Q000379:methods*; D008956:Models, Chemical; D008969:Molecular Sequence Data; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D020543:Proteome / Q000378:metabolism*; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D020543:Proteome