{"database":"GPMDB","file_versions":[],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":26,"searchCount":3},"additional":{"omics_type":["Other"],"submitter":["Searle BC, et ak,"],"instrument_platform":["Instrument"],"disease":["Not Available"],"brenda_tissue":["Not available"],"species":["Human, Human_adenovirus_54, Human_adenovirus_a, Human_adenovirus_b, Human_adenovirus_c, Human_adenovirus_d, Human_adenovirus_e, Human_adenovirus_f, Human_adenovirus_g, Human_astrovirus, Human_bocavirus, Human_bocavirus_2, Human_bocavirus_3, Human_bocavirus_4, Human_coronavirus_229e, Human_coronavirus_hku1, Human_coronavirus_nl63, Human_coronavirus_oc43, Human_cosavirus_a, Human_cosavirus_b, Human_cosavirus_d, Human_cosavirus_e, Human_enteric_coronavirus_4408, Human_enterovirus_100, Human_enterovirus_a, Human_enterovirus_b, Human_enterovirus_c, Human_enterovirus_d, Human_erythrovirus_v9, Human_herpesvirus_1, Human_herpesvirus_2, Human_herpesvirus_3, Human_herpesvirus_4_type_1, Human_herpesvirus_4_type_2, Human_herpesvirus_5, Human_herpesvirus_6a, Human_herpesvirus_6b, Human_herpesvirus_7, Human_herpesvirus_8_type_p, Human_immunodeficiency_virus_1, Human_immunodeficiency_virus_2, Human_metapneumovirus, Human_papillomavirus_fa75_ki88_03, Human_papillomavirus_rtrx7, Human_papillomavirus_type_10, Human_papillomavirus_type_100, Human_papillomavirus_type_101, Human_papillomavirus_type_103, Human_papillomavirus_type_104, Human_papillomavirus_type_105, Human_papillomavirus_type_108, Human_papillomavirus_type_109, Human_papillomavirus_type_112, Human_papillomavirus_type_113, Human_papillomavirus_type_16, Human_papillomavirus_type_24, Human_papillomavirus_type_26, Human_papillomavirus_type_32, Human_papillomavirus_type_34, Human_papillomavirus_type_4, Human_papillomavirus_type_41, Human_papillomavirus_type_48, Human_papillomavirus_type_49, Human_papillomavirus_type_5, Human_papillomavirus_type_50, Human_papillomavirus_type_53, Human_papillomavirus_type_60, Human_papillomavirus_type_63, Human_papillomavirus_type_6b, Human_papillomavirus_type_7, Human_papillomavirus_type_71, Human_papillomavirus_type_88, Human_papillomavirus_type_9, Human_papillomavirus_type_92, Human_papillomavirus_type_96, Human_papillomavirus_type_98, Human_papillomavirus_type_99, Human_papillomavirus___1, Human_papillomavirus___18, Human_papillomavirus___2, Human_papillomavirus___54, Human_papillomavirus___61, Human_papillomavirus___cand90, Human_parainfluenza_virus_1, Human_parainfluenza_virus_2, Human_parainfluenza_virus_3, Human_parechovirus, Human_parvovirus_4, Human_parvovirus_b19, Human_picobirnavirus, Human_respiratory_syncytial_virus, Human_rhinovirus_a, Human_rhinovirus_b, Human_rhinovirus_c, Human_tmev_like_cardiovirus, Human_t_lymphotropic_virus_1, Human_t_lymphotropic_virus_2, Human_t_lymphotropic_virus_4"],"submitter_mail":["C:\\spectra\\PASS00024\\qtof\\cmn"],"publication":["15822933"],"model":["http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210015922","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210015923","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210015924"],"submitter_affiliation":["Department of Pediatrics and School of Dentistry, Oregon Health & Sciences University,"],"cell_type":["Not available"],"repository":["GPMDB"],"pubmed_abstract":["Algorithms that can robustly identify post-translational protein modifications from mass spectrometry data are needed for data-mining and furthering biological interpretations. In this study, we determined that a mass-based alignment algorithm (OpenSea) for de novo sequencing results could identify post-translationally modified peptides in a high-throughput environment. A complex digest of proteins from human cataractous lens, a tissue containing a high abundance of modified proteins, was analyzed using two-dimensional liquid chromatography, and data was collected on both high and low mass accuracy instruments. The data were analyzed using automated de novo sequencing followed by OpenSea mass-based sequence alignment. A total of 80 modifications were detected, 36 of which were previously unreported in the lens. This demonstrates the potential to identify large numbers of known and previously unknown protein modifications in a given tissue using automated data processing algorithms such as OpenSea."],"pubmed_title":["Identification of protein modifications using MS/MS de novo sequencing and the OpenSea alignment algorithm."],"pubmed_authors":["Searle Brian C BC,Dasari Surendra S,Wilmarth Phillip A PA,Turner Mark M,Reddy Ashok P AP,David Larry L LL,Nagalla Srinivasa R SR,","Searle Brian C BC, Dasari Surendra S, Wilmarth Phillip A PA, Turner Mark M, Reddy Ashok P AP, David Larry L LL, Nagalla Srinivasa R SR"],"name_synonyms":["Identifications (Psychology), Algorithm., Identification"],"description_synonyms":["AW488255, Cas1, Carnitine acetylase, human being, Slf, Somatomedin-C, D430049E23Rik, Cs-1, Gene, FPH2, Homo sapiense, electronic data file, lens crystallina, CrAT, lenses, \"Felis silvestris catus\" RELATED synonym [], Homo spaiens, Syndiostatic, Homo sapien, manganese catalase activity, Poly(methyl methacrylate), domestic cat, Hek6, Homo sapians, Polymethylmetacrylate, Gene Products, Cek6, camera-type eye lens, caperase activity, 2210418N07, bacterial catalase-peroxidase activity, Polymethyl, ENSMUSG00000074119, Implast, ERP, Erp, portion of tissue, Elkh, Homo sapients, Methacrylate, \"Felis domesticus\" RELATED synonym [], Acrylic Bone Cement, EK6, Tyrosine-protein kinase receptor EPH-2, Tissue, somatomedin-C, ocular lens, SF, crystalline lens, Superacryl, Kitl, \"cat\" EXACT common_name [], proteins, Sap-2, man, Mast cell growth factor, Isostatic, \"cats\" EXACT common_name [], haem catalase activity, 2.7.10.1, Solute carrier family 6 member 2, Surgical Simplex P, Entire lens, Catl, Homo sapience, IGF1, Etrp, Homo sampiens, Mechano growth factor, SLC6A5, NET1, Palacos R, Sol, cats, NAT1, PMMA, Simplex Opaque, Soluble KIT ligand, Sl, Home sapiens, eye lens, NET, Net, catalase-peroxidase activity, AI315345, IGF-I, Palavit, data, equilase activity, ELK, Elk, Perspex, C130099E04Rik, steel factor, lens capsule, heme catalase activity, Neuronally-expressed EPH-related tyrosine kinase, Acron, hematopoietic growth factor KL, Proteins, EPH tyrosine kinase 2, Liquid Chromatography, Kallocryl K, somatomedin, SAP2, 9330129L11, Methyl Acrylic Plastic, 2.3.1.7, Carnitine acetyltransferase, AI195249, sKITLG, A330009E03Rik, low mass., Surgical Simplex Bone Cement, polypeptide, Plexiglas, Syndiostatic Polymethyl Methacrylate, catalase reaction, Norepinephrine transporter, Homo sapian, Felis domesticus, mechano growth factor, Protein, computer data file, tissue portion, EPH-like kinase 6, Ammonium Salt, Polymethylmethacrylate, simple tissue, CAT, Homo sapeins, small mass, Igf-1, GAT, ACGNAT, optidase activity, CS1, Cas-1, SHEP7, \"domestic cat\" EXACT genbank_common_name [], mast cell growth factor, Polymethyl Methacrylate, lens, Lucite, Stem cell factor, hydrogen-peroxide:hydrogen-peroxide oxidoreductase activity, Humo sapiens, cat, hEK6, STAT5, Felis silvestris catus, Homo sapines, Plexiglass, human, CMW Bone Cement, Protein Gene Products, Gene Proteins, stem cell factor, Homo spiens, KL-1, \"human\" EXACT genbank_common_name [], EPHT2, Cat01, MGF, c-Kit ligand, KITLG, Isostatic Polymethyl Methacrylate, SCF, Syndiostatic Polymethyl"],"pubmed_title_synonyms":["Identifications (Psychology), Algorithm., Identification"],"pubmed_abstract_synonyms":["Sequence Homology Determinations, big, data, lens capsule, human being, Proteins, Liquid Chromatography, Alignment, FBN, Gene, Spectrum Analyses, Homo sapiense, low mass, Spectrum Analysis, results, lens crystallina, Determinations, ACMICD, Impact, Spectroscopy, Environmental, polypeptide, lenses, Sequence Alignments, Polypeptides, Homo spaiens, large, Homo sapien, ECTOL1, Homo sapian, Sequence, Algorithm, Homo sapians, Protein, Mass, Gene Products, tissue portion, Impacts, MFS1, simple tissue, camera-type eye lens, Analysis, Environmental Impacts, Homo sapeins, small mass, Mass Spectrum Analyses, WMS, Mass Spectroscopy, WMS2, Mass Spectrum Analysis, Mass Spectrum, study, portion of tissue, Homo sapients, Algorithm., Analyses, Determination, lens, Sequence Homology, Tissue, Spectrometry, ocular lens, Sequence Homology Determination, expanded, Humo sapiens, crystalline lens, proteins, MASS, man, Homo sapines, human, OCTD, Protein Gene Products, Environmental Impact, Gene Proteins, data analysis, Homo spiens, \"human\" EXACT genbank_common_name [], data processing, Entire lens, Homo sapience, enlarged, Homo sampiens, great, SSKS, Environments, Alignments, GPHYSD2, Home sapiens, eye lens, SGS"],"view_count":["26"],"citation_count":["0"],"search_count":["3"],"full_dataset_link":["http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210015924"],"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":["0.008019740900678593"],"download_count_scaled":["0.0"],"reanalysis_count":["0"],"normalized_connections":["1.0"],"additional_accession":[]},"is_claimable":false,"name":"Identification of protein modifications using MS/MS de novo sequencing and the OpenSea alignment algorithm.","description":"Data obtained from PASSEL: [[https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/PASS_View?datasetPassword=LN8283b&identifier=PASS00024 PASS00024]]. Data file: 93yo_sol_cat_qtof_old_runs_01_23.mgf. Published as part of  . From the Abstract: {{i}} ... A complex digest of proteins from human cataractous lens, a tissue containing a high abundance of modified proteins, was analyzed using two-dimensional liquid chromatography, and data was collected on both high and low mass accuracy instruments ... {/i}","dates":{"submission":"2013-04-20"},"accession":"GPM11210015924","cross_references":{"pubmed":["15822933"]}}