MultiProtIdent: Identifying proteins using database search and protein-protein interactions

Hsien Da Huang, Tzong Yi Lee, Li Cheng Wu, Feng Mao Lin, Hsueh Fen Juan, Jorng Tzong Horng, Ann Ping Tsou

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


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 MultiProtldent is highly promising.

Original languageEnglish
Pages (from-to)690-697
Number of pages8
JournalJournal of Proteome Research
Issue number3
StatePublished - May 2005


  • Peptide mass fingerprint
  • Protein identification
  • Protein-protein interaction


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