title: Use of composite protein database including search result sequences for mass spectrometric analysis of cell secretome.
abstract: Mass spectrometric (MS) data of human cell secretomes are usually run through the conventional human database for identification. However, the search may result in false identifications due to contamination of the secretome with fetal bovine serum (FBS) proteins. To overcome this challenge, here we provide a composite protein database including human as well as 199 FBS protein sequences for MS data search of human cell secretomes. Searching against the human-FBS database returned more reliable results with fewer false-positive and false-negative identifications compared to using either a human only database or a human-bovine database. Furthermore, the improved results validated our strategy without complex experiments like SILAC. We expect our strategy to improve the accuracy of human secreted protein identification and to also add value for general use.
authors.affiliation: Center for Theragnosis, BRI, Korea Institute of Science and Technology, Seoul 136-791, Korea; Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea.
authors.forename: Jihye
authors.initials: J
authors.lastname: Shin
authors.affiliation: Center for Theragnosis, BRI, Korea Institute of Science and Technology, Seoul 136-791, Korea; Department of Pathology, Yonsei University College of Medicine, Seoul 120-752, Korea.
authors.forename: Gamin
authors.initials: G
authors.lastname: Kim
authors.affiliation: Center for Theragnosis, BRI, Korea Institute of Science and Technology, Seoul 136-791, Korea.
authors.forename: Mohammad Humayun
authors.initials: MH
authors.lastname: Kabir
authors.affiliation: Center for Theragnosis, BRI, Korea Institute of Science and Technology, Seoul 136-791, Korea.
authors.forename: Seong Jun
authors.initials: SJ
authors.lastname: Park
authors.affiliation: Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea.
authors.forename: Seoung Taek
authors.initials: ST
authors.lastname: Lee
authors.affiliation: Center for Theragnosis, BRI, Korea Institute of Science and Technology, Seoul 136-791, Korea; Department of Biomolecular Science, University of Science and Technology, Daejeon 305-333, Korea.
authors.forename: Cheolju
authors.initials: C
authors.lastname: Lee
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001798:Blood Proteins / Q000235:genetics / Q000302:isolation & purification; D002417:Cattle; D002460:Cell Line; D003470:Culture Media; D030562:Databases, Protein; D045325:HCT116 Cells; D006801:Humans; D020543:Proteome / Q000235:genetics / Q000302:isolation & purification; D040901:Proteomics; D057386:Search Engine; D013045:Species Specificity; D053719:Tandem Mass Spectrometry
chemical_list: D001798:Blood Proteins; D003470:Culture Media; D020543:Proteome
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