MultiProtIdent: identifying proteins using database search and protein-protein interactions.
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/.
Huang
Hsien-Da
HD
Department of Biological Science and Technology and Institute of Bioinformatics, National Chiao-Tung University, Hsin-Chu 300, Taiwan.
Lee
Tzong-Yi
TY
Wu
Li-Cheng
LC
Lin
Feng-Mao
FM
Juan
Hsueh-Fen
HF
Horng
Jorng-Tzong
JT
Tsou
Ann-Ping
AP
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*
D046912:Multiprotein Complexes; D010446:Peptide Fragments; D011506:Proteins