{"database":"GPMDB","file_versions":[],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":14,"searchCount":3},"additional":{"omics_type":["Other"],"submitter":["Wang X, et al."],"instrument_platform":["Instrument"],"disease":["Not Available"],"brenda_tissue":["Not available"],"species":["Homo_sapiens_viruses, Human"],"publication":["25202125"],"submitter_mail":["junmin.peng@stjude.org"],"model":["http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003489","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003491","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003484","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003492","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003470","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003471","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003493","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003487","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003488","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003485","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003486"],"submitter_affiliation":["St. Jude Childrens Research Hospital, United States."],"cell_type":["Not available"],"repository":["GPMDB"],"pubmed_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."],"pubmed_title":["JUMP: a tag-based database search tool for peptide identification with high sensitivity and accuracy."],"pubmed_authors":["Wang Xusheng X,Li Yuxin Y,Wu Zhiping Z,Wang Hong H,Tan Haiyan H,Peng Junmin J,","Wang Xusheng X, Li Yuxin Y, Wu Zhiping Z, Wang Hong H, Tan Haiyan H, Peng Junmin J"],"name_synonyms":["sensitivity., peptide, polypeptide, Sensitivity, Specificity, Identifications (Psychology), Specificity and Sensitivity, Identification, Data Base"],"description_synonyms":["Gpi, data, PLXN5, AI461847, mol, Aminokarbonsaeure, Aminosaeure, Aminocarbonsaeure, Nl1, PLEXIN-B1, Mell1, MF, Amf, Cell, SeP, peptide, polypeptide, Experiment, CEH, mOC-X, MMEL2, Liquid Chromatography., NEPII, NL1, Pgi, NK|GPI, NL2, SEH, Gpi-1, NK, Data Base, SEP, Org, ORG, amino acids, pattern, Gpi-1r, Nlk, cell, distribution, Gpi-1s, Phi, Gpi-1t, Gpi1-r, Gpi1-s, present in organism, Gpi1-t, sEP, SELP, Eph2, Bglap-rs1, NEP2, Gpi1s"],"pubmed_title_synonyms":["sensitivity., peptide, polypeptide, Sensitivity, Specificity, Identifications (Psychology), Specificity and Sensitivity, Identification, Data Base"],"pubmed_abstract_synonyms":["use, determination, AW549739, fractured, Aminokarbonsaeure, Aminosaeure, Aminocarbonsaeure, Liquid Chromatography, split, Spectrum Analyses, Spectrum Analysis, fragmented, Spectroscopy, peptide, polypeptide, shortened, Polypeptides, chemical analysis, Mass, hemorrhaged, ruptured, Analysis, sensitivity, burst, Mass Spectrum Analyses, Data Base, Mass Spectroscopy, C79691, Mass Spectrum Analysis, torn, Mass Spectrum, amino acids, pattern, Algorithm., Analyses, distribution, cracked, Spectrometry, Specificity, stubby, present in organism, MASCOT, Lccp, mKIAA0989, Specificity and Sensitivity, Sensitivity, assay, short, Proteomes"],"view_count":["14"],"citation_count":["0"],"search_count":["3"],"full_dataset_link":["http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320003491"],"search_domains":["dbgap_ncbi~0","patentfamilies~0","rfam~0","merops~0","complex-portal~0","uniprot~0","wormbaseparasite~0","embl-covid19~0","reactome~0","emdb~0","wgs_masters~0","ebiweb_resources~0","opentargets_genetics~0","biomodels_all~0","ipd-mhc~0","ebiweb_teams~0","taxonomy~0","genome_assembly~0","sc-experiments~0","ebiweb_people~0","enzymeportal_enzymes~0","ipd-nhkir~0","cellosaurus~0","pdbe~0","chebi~0","patentproteins~0","interpro7~0","uniref~0","chembl~0","pdbekb~0","gpcrdb~0","hgnc~0","sc-genes~0","intact~0","rhea~0","ebiweb_training~0","alphafold~0","imgt-hla~0","patentnucleotides~0","ensemblroot~0","eva_studies~0","non-coding~0","europepmc~0","pubmed~1","identifiers_registry~0","pdbechem~0","hpa-covid19~0","eva-variants-covid19~0","biosamples~0","gwas_catalog~0","biotools~0","tls_masters~0","mesh~0","coding~0","sra~0","opentargets~0","efo~0","embl-pathogen~0","project~0","human_diseases~0","geo_datasets~0","embl~0","treefam~0","uniparc~0","ols~0","dgva~0","intenz~0","go~0","tsa_masters~0","biosamples-covid19~0","ebiweb_corporate~0","omim~0","lrg~0","earlycause-molecular-sequences~0","ipd-kir~0","empiar~0","rnacentral~0","orcid_data_claims~0","gpmdb~2","lineage-covid19~0","metagenomics~0","pfam~0","varsite~0"],"citation_count_scaled":["0.0"],"reanalysis_count_scaled":["0.0"],"view_count_scaled":["0.00431832202344232"],"download_count_scaled":["0.0"],"reanalysis_count":["0"],"normalized_connections":["1.0"],"additional_accession":[]},"is_claimable":false,"name":"JUMP: a tag-based database search tool for peptide identification with high sensitivity and accuracy.","description":"Data from authors [[http://stjuderesearch.org/site/lab/peng web site]]. Experiment: dataset3, file: pl08.mzXML. Published as part of Mol Cell Proteomics. 2014 Sep 8  . From the Abstract: {{i}} ... 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 ... {{/i}}","dates":{"submission":"2014-09-17"},"accession":"GPM32320003491","cross_references":{"pubmed":["25202125"]}}