title: MultiProtIdent: identifying proteins using database search and protein-protein interactions.
abstract: Protein identification is important in proteomics. Proteomic analyses based on mass spectra (MS) constitute innovative ways to identify the components of protein complexes. Instruments can obtain the mass spectrum to an accuracy of 0.01 Da or better, but identification errors are inevitable. This study shows a novel tool, MultiProtIdent, which can identify proteins using additional information about protein-protein interactions and protein functional associations. Both single and multiple Peptide Mass Fingerprints (PMFs) are input to MultiProtIdent, which matches the PMFs to a theoretical peptide mass database. The relationships or interactions among proteins are considered to reduce false positives in PMF matching. Experiments to identify protein complexes reveal that MultiProtIdent is highly promising. The website associated with this study is http://dbms104.csie.ncu.edu.tw/.
authors.affiliation: Department of Biological Science and Technology and Institute of Bioinformatics, National Chiao-Tung University, Hsin-Chu 300, Taiwan.
authors.forename: Hsien-Da
authors.initials: HD
authors.lastname: Huang
authors.forename: Tzong-Yi
authors.initials: TY
authors.lastname: Lee
authors.forename: Li-Cheng
authors.initials: LC
authors.lastname: Wu
authors.forename: Feng-Mao
authors.initials: FM
authors.lastname: Lin
authors.forename: Hsueh-Fen
authors.initials: HF
authors.lastname: Juan
authors.forename: Jorng-Tzong
authors.initials: JT
authors.lastname: Horng
authors.forename: Ann-Ping
authors.initials: AP
authors.lastname: Tsou
mesh_terms: D000465:Algorithms; D016208:Databases, Factual; D013058:Mass Spectrometry; D046912:Multiprotein Complexes / Q000032:analysis*; D010446:Peptide Fragments / Q000032:analysis; D025941:Protein Interaction Mapping; D011506:Proteins / Q000032:analysis*; D040901:Proteomics / Q000379:methods*
chemical_list: D046912:Multiprotein Complexes; D010446:Peptide Fragments; D011506:Proteins