title: JUMP: a tag-based database search tool for peptide identification with high sensitivity and accuracy.
abstract: Database search programs are essential tools for identifying peptides via mass spectrometry (MS) in shotgun proteomics. Simultaneously achieving high sensitivity and high specificity during a database search is crucial for improving proteome coverage. Here we present JUMP, a new hybrid database search program that generates amino acid tags and ranks peptide spectrum matches (PSMs) by an integrated score from the tags and pattern matching. In a typical run of liquid chromatography coupled with high-resolution tandem MS, more than 95% of MS/MS spectra can generate at least one tag, whereas the remaining spectra are usually too poor to derive genuine PSMs. To enhance search sensitivity, the JUMP program enables the use of tags as short as one amino acid. Using a target-decoy strategy, we compared JUMP with other programs (e.g. SEQUEST, Mascot, PEAKS DB, and InsPecT) in the analysis of multiple datasets and found that JUMP outperformed these preexisting programs. JUMP also permitted the analysis of multiple co-fragmented peptides from "mixture spectra" to further increase PSMs. In addition, JUMP-derived tags allowed partial de novo sequencing and facilitated the unambiguous assignment of modified residues. In summary, JUMP is an effective database search algorithm complementary to current search programs.
authors.affiliation: From the ‡St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, Tennessee 38105;
authors.forename: Xusheng
authors.initials: X
authors.lastname: Wang
authors.affiliation: §Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105;
authors.forename: Yuxin
authors.initials: Y
authors.lastname: Li
authors.affiliation: §Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105;
authors.forename: Zhiping
authors.initials: Z
authors.lastname: Wu
authors.affiliation: §Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105; ‡‡Integrated Biomedical Sciences Program, The University of Tennessee Health Science Center, Memphis, Tennessee 38163.
authors.forename: Hong
authors.initials: H
authors.lastname: Wang
authors.affiliation: From the ‡St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, Tennessee 38105;
authors.forename: Haiyan
authors.initials: H
authors.lastname: Tan
authors.affiliation: From the ‡St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, Tennessee 38105; §Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105; junmin.peng@stjude.org.
authors.forename: Junmin
authors.initials: J
authors.lastname: Peng
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D002853:Chromatography, Liquid; D030562:Databases, Protein; D006801:Humans; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods* / Q000706:statistics & numerical data*; D010455:Peptides / Q000302:isolation & purification*; D040901:Proteomics / Q000295:instrumentation / Q000379:methods*; D053719:Tandem Mass Spectrometry
chemical_list: D010455:Peptides