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A largely unexplored feature of such protein complexes is the selective participation of specific protein isoforms and/or post-translationally modified forms. In this study, we combined native size-exclusion chromatography (SEC) with high-throughput proteomic analysis to characterize soluble protein complexes isolated from human osteosarcoma (U2OS) cells. Using this approach, we have identified over 71,500 peptides and 1,600 phosphosites, corresponding to over 8,000 proteins, distributed across 40 SEC fractions. This represents >50% of the predicted U2OS cell proteome, identified with a mean peptide sequence coverage of 27% per protein. Three biological replicates were performed, allowing statistical evaluation of the data and demonstrating a high degree of reproducibility in the SEC fractionation procedure. Specific proteins were detected interacting with multiple independent complexes, as typified by the separation of distinct complexes for the MRFAP1-MORF4L1-MRGBP interaction network. The data also revealed protein isoforms and post-translational modifications that selectively associated with distinct subsets of protein complexes. Surprisingly, there was clear enrichment for specific Gene Ontology terms associated with differential size classes of protein complexes. This study demonstrates that combined SEC/MS analysis can be used for the system-wide annotation of protein complexes and to predict potential isoform-specific interactions. All of these SEC data on the native separation of protein complexes have been integrated within the Encyclopedia of Proteome Dynamics, an online, multidimensional data-sharing resource available to the community."],"pubmed_title":["Characterization of native protein complexes and protein isoform variation using size-fractionation-based quantitative proteomics."],"pubmed_authors":["Kirkwood Kathryn J KJ,Ahmad Yasmeen Y,Larance Mark M,Lamond Angus I AI,","Kirkwood Kathryn J KJ, Ahmad Yasmeen Y, Larance Mark M, Lamond Angus I AI"],"name_synonyms":["number, polypeptide, count in organism, presence or absence in organism., proteins, quantitative, count, presence"],"description_synonyms":["Osteosarcoma of bone (disorder), Osteochondrosarcoma, Osteosarcoma of bone, data, U2OS, human being, Osteogenic Sarcomas, Osteogenic sarcoma, mol, GLM2, Osteosarcoma - disorder, Proteins, Gene, Splice Variants, function, U-2 OS, Homo sapiense, Tumor, Osteogenic, Protein Splice, Cell, polypeptide, Osteogenic Sarcoma, MHAM, Homo spaiens, Homo sapien, soluble, PTEN1, Skeletal Sarcoma, Homo sapian, [M]Osteosarcoma NOS, CWS1, Homo sapians, Protein, proteomic analysis, Gene Products, SEC, NOS, Cell., TEP1, Isoforms, Homo sapeins, Osteoblastic osteosarcoma, Osteosarcomas, study, Bone Sarcoma, Skeletal sarcoma, Sarcomas, Sarcoma of the Bone, Homo sapients, 10q23del, cell, MMAC1, Sarcoma of Bone, Selb, sec, osteoid sarcoma, Humo sapiens, Osteosarcoma, proteins, Protein Splice Variants, man, Homo sapines, Osseous Sarcoma, Osteoblastic sarcoma, human, Protein Gene Products, Gene Proteins, DEC, Sarcoma, Homo spiens, \"human\" EXACT genbank_common_name [], no ICD-O subtype, Homo sapience, no ICD-O subtype (morphologic abnormality), Homo sampiens, Variants, U2-OS, microarray, Osteosarcoma Tumors, Osteosarcoma Tumor, regulation, Chromatographies, BZS, Home sapiens, osteosarcoma, Tumors"],"pubmed_title_synonyms":["number, polypeptide, count in organism, presence or absence in organism., proteins, quantitative, count, presence"],"pubmed_abstract_synonyms":["Osteosarcoma of bone (disorder), Osteochondrosarcoma, U2OS, human being, Gene Ontology Projects, Osteogenic Sarcomas, degree (angle), Pam14, determination, HsT17725, Gene, Splice Variants, broad, Homo sapiense, Tumor, PAM14, Protein Splice, body system, Gene Ontology Project, U2 osteosarcoma cell, Gene Ontology, Intervention or Procedure, Osteogenic Sarcoma, peptide, Polypeptides, Homo spaiens, Homo sapien, Homo sapians, Gene Products, SEC, Project, system, Isoforms, Osteoblastic osteosarcoma, S863-6, study, Sarcomas, Homo sapients, anatomical systems, interventionDescription, MEAF3, Sarcoma of Bone, scattered, Selb, sec, U2OS cell, Interventional, proteins, Protein Splice Variants, man, Osseous Sarcoma, Osteoblastic sarcoma, SURGICAL AND MEDICAL PROCEDURES, C20orf20, Sarcoma, Homo sapience, Eaf3, no ICD-O subtype (morphologic abnormality), data., Homo sampiens, Eaf7, Pgr1, PGR1, RGD1308612, associated, Chromatographies, Home sapiens, 1600027N09Rik, Tumors, Intervention Strategies, Osteosarcoma of bone, data, MRG15, wide/broad, Osteogenic sarcoma, Osteosarcoma - disorder, diffuse, Proteins, Tex189, function, U-2 OS, MRG15BP, Procedure, Osteogenic, Cell, predicted, polypeptide, soluble, Skeletal Sarcoma, Homo sapian, [M]Osteosarcoma NOS, Protein, chemical analysis, proteomic analysis, mKIAA4002, NOS, Ontology Projects, Homo sapeins, connected anatomical system, AL022827, Osteosarcomas, Intervention, Ontology Project, Bone Sarcoma, Skeletal sarcoma, Gene Ontologies, URCC4, Ontology, Sarcoma of the Bone, 9130413I22Rik, RGD1306635, Ontologies, distinct, Projects, osteoid sarcoma, Humo sapiens, Osteosarcoma, arc degree, C80444, Homo sapines, MORFRG15, TEG-189, human, Protein Gene Products, organ system, Gene Proteins, wide, Homo spiens, \"human\" EXACT genbank_common_name [], AW060503, no ICD-O subtype, clear, Variants, U2-OS, microarray, Osteosarcoma Tumors, Osteosarcoma Tumor, regulation, assay, Proteomes, osteosarcoma"],"view_count":["20"],"citation_count":["0"],"search_count":["5"],"full_dataset_link":["http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32310002912"],"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":["0.006169031462060457"],"download_count_scaled":["0.0"],"normalized_connections":["1.0"],"additional_accession":[]},"is_claimable":false,"name":"Characterization of native protein complexes and protein isoform variation using size-fractionation-based quantitative proteomics.","description":"Data from ProteomeXchange, PXD ID: PXD001220. File: PT1541S1F02.mzml. Published as part of Mol Cell Proteomics. 2013 Dec;12(12):3851-73  . From the Abstract: {{i}} Proteins form a diverse array of complexes that mediate cellular function and regulation. A largely unexplored feature of such protein complexes is the selective participation of specific protein isoforms and/or post-translationally modified forms. In this study, we combined native size-exclusion chromatography (SEC) with high-throughput proteomic analysis to characterize soluble protein complexes isolated from human osteosarcoma (U2OS) cells. {{/i}}","dates":{"submission":"2014-08-14"},"accession":"GPM32310002912","cross_references":{"pubmed":["24043423"],"Pride":["PXD001220"],"pride":[],"Pride Archive":["PXD001220"]}}