{"database":"GPMDB","file_versions":[],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":22,"searchCount":5},"additional":{"omics_type":["Other"],"submitter":["Chen Y, et al."],"instrument_platform":["Instrument"],"disease":["Not Available"],"brenda_tissue":["Not available"],"species":["Homo_sapiens_viruses, Human"],"publication":["26108252"],"submitter_mail":["tongwang@jnu.edu.cn"],"model":["http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016161","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016160","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016163","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016162","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016154","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016176","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016153","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016175","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016156","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016178","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016155","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016177","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016158","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016179","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016157","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016159","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016170","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016150","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016172","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016171","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016152","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016174","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016151","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016173","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016143","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016165","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016164","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016145","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016167","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016166","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016144","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016147","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016169","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016146","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016149","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016148"],"submitter_affiliation":["Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University"],"cell_type":["Not available"],"repository":["GPMDB"],"pubmed_abstract":["Finding protein evidence (PE) for protein coding genes is a primary task of the Phase I Chromosome-Centric Human Proteome Project (C-HPP). Currently, there are 2948 PE level 2-4 coding genes per neXtProt, which are deemed missing proteins in the human proteome. As most samples prepared and analyzed in the C-HPP framework were focusing on detergent soluble proteins, we posit that as a natural composition the cytoplasmic detergent-insoluble proteins (DIPs) represent a source of finding missing proteins. We optimized a workflow and separated cytoplasmic DIPs from three human lung and three human hepatoma cell lines via differential speed centrifugation. We verified that the detergent-soluble proteins (DSPs) could be sufficiently depleted and the cytoplasmic DIP isolation was partially reproducible with Spearman r > 0.70 according to two independent SILAC MS experiments. Through label-free MS, we identified 4524 and 4156 DIPs from lung and liver cells, respectively. Among them, a total of 23 missing proteins (22 PE2 and 1 PE4) were identified by MS, and 18 of them had translation evidence; in addition, six PE5 proteins were identified by MS, three with translation evidence. We showed that cytoplasmic DIPs were not an enrichment of transmembrane proteins and were chromosome-, cell type-, and tissue-specific. Furthermore, we demonstrated that DIPs were distinct from DSPs in terms of structural and physical-chemical features. In conclusion, we have found 23 missing proteins and 6 PE5 proteins from the cytoplasmic insoluble proteome that is biologically and physical-chemically different from the soluble proteome, suggesting that cytoplasmic DIPs carry comprehensive and valuable information for finding PE of missing proteins. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD001694."],"pubmed_title":["Identification of Missing Proteins Defined by Chromosome-Centric Proteome Project in the Cytoplasmic Detergent-Insoluble Proteins."],"pubmed_authors":["Chen Yang Y,Li Yaxing Y,Zhong Jiayong J,Zhang Jing J,Chen Zhipeng Z,Yang Lijuan L,Cao Xin X,He Qing-Yu QY,Zhang Gong G,Wang Tong T,","Chen Yang Y, Li Yaxing Y, Zhong Jiayong J, Zhang Jing J, Chen Zhipeng Z, Yang Lijuan L, Cao Xin X, He Qing-Yu QY, Zhang Gong G, Wang Tong T"],"name_synonyms":["Protein Gene Products, insoluble, Gene., Gene Proteins, polypeptide, centric, prophase chromosome, Chromosome, Identification, interphase chromosome, Protein, Gene Products, Proteins, Identifications (Psychology), Gene, proteins, chromatid, Proteomes"],"description_synonyms":["SIGNS SYMPTOMS, data, human being, pulmo, Meth, HS3, AP-1, DESC, c-jun, Proteins, lung parenchyma, Cell Lines, Gene, cell_line, compositionality, Homo sapiense, lungs, composed of, Chalk, Cell, Symptoms and Signs, polypeptide, Crystal., Signs and Symptoms, Homo spaiens, Workflows, Homo sapien, soluble, Homo sapian, parenchyma of lung, SPTA, Homo sapians, SPH3, Protein, Tina, Gene Products, Line, Finding, Homo sapeins, Work Flow, Separated, Lines, insoluble, Junc, Separation, Divorced, Homo sapients, Glass, HPP, content, Separations, Rathburn disease, Humo sapiens, cell line cell, composition, proteins, Divorces, Phosphoethanolaminuria, man, Homo sapines, human, cell line, Protein Gene Products, Speed, AP1, Gene Proteins, Homo spiens, \"human\" EXACT genbank_common_name [], Homo sapience, EL2, Ice, velocity, Homo sampiens, structure, c-Jun, Lungs, Entire lung, Clinical Finding, Home sapiens, Proteomes, Work Flows, Diagnostic Findings"],"pubmed_title_synonyms":["Protein Gene Products, insoluble, Gene., Gene Proteins, polypeptide, centric, prophase chromosome, Chromosome, Identification, interphase chromosome, Protein, Gene Products, Proteins, Identifications (Psychology), Gene, proteins, chromatid, Proteomes"],"pubmed_abstract_synonyms":["WASLBP, protein translation, DIP1, Materials, human being, Meth, ZMIZ4, Msx-interacting-zinc finger protein, Gene, Spectrum Analyses, Homo sapiense, composed of, Chalk, Symptoms and Signs, jecur, Homo spaiens, Homo sapien, isolation, parenchyma of lung, Homo sapians, SPH3, Tina, Dsip1, Gene Products, Line, Mass, Gilz, hDIP, Analysis, Finding, Work Flow, Separated, Androgen receptor-interacting protein 3, Mass Spectroscopy, MIZ, insoluble, Mass Spectrum Analysis, portion of tissue, PIASX, Divorced, Homo sapients, Glass, Genetic, HPP, Analyses, PIASX-ALPHA, Rathburn disease, mGcl-1, Tissue, iecur, cell line cell, composition, proteins, chromatid, Divorces, purification, man, free, cell line, Tilz3, isolation and purification, K2p3.1, fully spanning plasma membrane, Homo sapience, EL2, Ice, DIP, Homo sampiens, Entire lung, Home sapiens, Diagnostic Findings, PE-2, Data Set., distinct from, SIGNS SYMPTOMS, VIP54, DAB2-interacting protein, protein anabolism, data, protein biosynthetic process, pulmo, dJ439F8.1, HS3, OAT1, 6.3.2.-, DESC, Entire liver, WISH, Proteins, lung parenchyma, Cell Lines, integral to membrane, PIAS-NY protein, cell_line, MIZ1, Miz1, compositionality, lungs, TSC-22R, Cistrons, Spectrum Analysis, Cell, ARIP3, Spectroscopy, polypeptide, TASK, Signs and Symptoms, prophase chromosome, Workflows, TBAK1, soluble, Homo sapian, SPTA, Protein, protein formation, tissue portion, Genetic Materials, dA59H18.1, protein biosynthesis, simple tissue, Homo sapeins, Genetic Material, Mass Spectrum Analyses, Lines, Crystal, centric, Mass Spectrum, Separation, transmembrane, SIZ2, PPH4, interphase chromosome, content, Separations, GILZ, Spectrometry, Humo sapiens, Phosphoethanolaminuria, Homo sapines, PE2, cell_type, human, Protein Gene Products, Speed, Gene Proteins, Livers, Homo spiens, \"human\" EXACT genbank_common_name [], SNAT, Protein inhibitor of activated STAT x, Chromosome, protein synthesis, Material, velocity, ORF1, DP-interacting protein, structure, CRS4, DSPS, SPIN90, Cistron, Lungs, Protein inhibitor of activated STAT2, DSIPI, Msx-interacting zinc finger protein, TASK-1, Clinical Finding, Proteomes, Work Flows, PIASX-BETA, AF3P21"],"view_count":["22"],"citation_count":["0"],"search_count":["5"],"full_dataset_link":["http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016148"],"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","pride~1","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","pride archive~1","varsite~0"],"reanalysis_count":["0"],"submitter_keywords":["Resource Reanalysis"],"citation_count_scaled":["0.0"],"reanalysis_count_scaled":["0.0"],"view_count_scaled":["0.006785934608266502"],"download_count_scaled":["0.0"],"normalized_connections":["1.0"],"additional_accession":[]},"is_claimable":false,"name":"Identification of missing proteins defined by chromosome-centric proteome project in the cytoplasmic detergent-insoluble proteins","description":"Data from ProteomeXchange, PXD ID: PXD001694. File: lungSILAC_first_14.mzml. Published as part of J Proteome Res. 2015 Jun 25  . From the Abstract: {{i}} ... As most samples prepared and analyzed in the C-HPP framework were focusing on detergent soluble proteins, we posit that as a natural composition, the cytoplasmic detergent-insoluble proteins (DIPs) represent a source of finding missing proteins. We optimized a workflow and separated cytoplasmic DIPs from 3 human lung and 3 human hepatoma cell lines via differential speed centrifugation ... {{/i}}","dates":{"submission":"2015-06-29"},"accession":"GPM32320016148","cross_references":{"pubmed":["26108252"],"Pride":["PXD001694"],"pride":[],"Pride Archive":["PXD001694"]}}