GPMDB00225OtherMarcon E, et al.InstrumentNot AvailableNot availableHomo_sapiens_viruses, Human_femalejack.greenblatt@utoronto.ca26121405Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, et 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availableGPMDBAntibodies are used in multiple cell biology applications, but there are no standardized methods to assess antibody quality-an absence that risks data integrity and reproducibility. We describe a mass spectrometry-based standard operating procedure for scoring immunoprecipitation antibody quality. We quantified the abundance of all the proteins in immunoprecipitates of 1,124 new recombinant antibodies for 152 chromatin-related human proteins by comparing normalized spectral abundance factors from the target antigen with those of all other proteins. We validated the performance of the standard operating procedure in blinded studies in five independent laboratories. Antibodies for which the target antigen or a member of its known protein complex was the most abundant protein were classified as 'IP gold standard'. This method generates quantitative outputs that can be stored and archived in public databases, and it represents a step toward a platform for community benchmarking of antibody quality.Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation.Marcon Edyta E,Jain Harshika H,Bhattacharya Anandi A,Guo Hongbo H,Phanse Sadhna S,Pu Shuye S,Byram Gregory G,Collins Ben C BC,Dowdell Evan E,Fenner Maria M,Guo Xinghua X,Hutchinson Ashley A,Kennedy Jacob J JJ,Krastins Bryan B,Larsen Brett B,Lin Zhen-Yuan ZY,Lopez Mary F MF,Loppnau Peter P,Miersch Shane S,Nguyen Tin T,Olsen Jonathan B JB,Paduch Marcin M,Ravichandran Mani M,Seitova Alma A,Vadali Gouri G,Vogelsang Maryann S MS,Whiteaker Jeffrey R JR,Zhong Guoqing G,Zhong Nan N,Zhao Lei L,Aebersold Ruedi R,Arrowsmith Cheryl H CH,Emili Andrew A,Frappier Lori L,Gingras Anne-Claude AC,Gstaiger Matthias M,Paulovich Amanda G AG,Koide Shohei S,Kossiakoff Anthony A AA,Sidhu Sachdev S SS,Wodak Shoshana J SJ,Gräslund Susanne S,Greenblatt Jack F JF,Edwards Aled M AM,Marcon Edyta E, Jain Harshika H, Bhattacharya Anandi A, Guo Hongbo H, Phanse Sadhna S, Pu Shuye S, Byram Gregory G, Collins Ben C BC, Dowdell Evan E, Fenner Maria M, Guo Xinghua X, Hutchinson Ashley A, Kennedy Jacob J JJ, Krastins Bryan B, Larsen Brett B, Lin Zhen-Yuan ZY, Lopez Mary F MF, Loppnau Peter P, Miersch Shane S, Nguyen Tin T, Olsen Jonathan B JB, Paduch Marcin M, Ravichandran Mani M, Seitova Alma A, Vadali Gouri G, Vogelsang Maryann S MS, Whiteaker Jeffrey R JR, Zhong Guoqing G, Zhong Nan N, Zhao Lei L, Aebersold Ruedi R, Arrowsmith Cheryl H CH, Emili Andrew A, Frappier Lori L, Gingras Anne-Claude AC, Gstaiger Matthias M, Paulovich Amanda G AG, Koide Shohei S, Kossiakoff Anthony A AA, Sidhu Sachdev S SS, Wodak Shoshana J SJ, Gräslund Susanne S, Greenblatt Jack F JF, Edwards Aled M AMopsonin activity, Co-Immunoprecipitations, Co-Immunoprecipitation., use, Procedures, membrane bound, Precipitation, Methodological, B-cell receptor complex, Procedure, antibodies, Methodological Study, plan specification, Co Immunoprecipitation, Study, antibody, method, immunoglobulin, BCR complex, Immune, B cell receptor accessory molecule complex, Methodological Studies, Method, method used in an experiment, B lymphocyte receptor complex, Studies, B cell receptor activity, Immune Precipitations, Precipitations, B-lymphocyte receptor complex, immunoglobulin complex, Immune Precipitation293 cell, Nat, NAT, Co-Immunoprecipitations, D17H6S113E, human being, Procedures, AP-1, cradin, Gene, B-cell receptor complex, Spectrum Analyses, Homo sapiense, FSH, Intervention or Procedure, Co Immunoprecipitation, D6S60E, antibody, Homo spaiens, BCR complex, Homo sapien, Method, Homo sapians, Studies, Mass, Immune Precipitations, Gene Products, Antigen, HEK 293, Analysis, immunoglobulin complex, Immune Precipitation, Chromatins, Mass Spectroscopy, Mass Spectrum Analysis, D6S60, Junc, Homo sapients, Analyses, interventionDescription, H-l(3)mbt-l, membrane bound, Co-Immunoprecipitation, Precipitation, Interventional, proteins, Ring3, procedures, man, SURGICAL AND MEDICAL PROCEDURES, Study, Immune, Methodological Studies, Homo sapience, Homo sampiens, chromosome scaffold, c-Jun, Precipitations, B-lymphocyte receptor complex, UNQ739, FACB, Home sapiens, 293 HEK, Gene., Intervention Strategies, data, c-jun, Proteins, Procedure, trait, antibodies, Spectrum Analysis, Fsrg1, Spectroscopy, polypeptide, G11, RING3, Homo sapian, AW228947, FSRG1, Protein, RP1, human embryonic kidney cell, mKIAA4005, techniques, Homo sapeins, HLA-RP1, A930041G11Rik, Mass Spectrum Analyses, Intervention, opsonin activity, Mass Spectrum, D6S113E, 293, M4mbt, RNF3, Rnf3, Frg-1, HEK293, Spectrometry, Humo sapiens, FA2, Methodological, HEK-293, Methodological Study, Homo sapines, human, L3MBT, Protein Gene Products, AP1, Gene Proteins, 4732493N06Rik, FAAP95, FAAP90, immunoglobulin, Homo spiens, FAB, "human" EXACT genbank_common_name [], B cell receptor accessory molecule complex, B lymphocyte receptor complex, B cell receptor activity, PSST739, Fsrg-1, methodologyopsonin activity, Co-Immunoprecipitations, Co-Immunoprecipitation., use, Procedures, membrane bound, Precipitation, Methodological, B-cell receptor complex, Procedure, antibodies, Methodological Study, plan specification, Co Immunoprecipitation, Study, antibody, method, immunoglobulin, BCR complex, Immune, B cell receptor accessory molecule complex, Methodological Studies, Method, method used in an experiment, B lymphocyte receptor complex, Studies, B cell receptor activity, Immune Precipitations, Precipitations, B-lymphocyte receptor complex, immunoglobulin complex, Immune PrecipitationCo-Immunoprecipitations, human being, Procedures, Laboratory, Health Care Benchmarking, number, Gene, B-cell receptor complex, Spectrum Analyses, Cell Biologies, Homo sapiense, Healthcare Benchmarking, presence, Intervention or Procedure, Co Immunoprecipitation, Relative, antibody, Homo spaiens, method, BCR complex, Homo sapien, Method, Homo sapians, method used in an experiment, Studies, Mass, Immune Precipitations, Gene Products, Antigen, Analysis, immunoglobulin complex, Immune Precipitation, Chromatins, Mass Spectroscopy, Mass Spectrum Analysis, Homo sapients, Biology, Analyses, interventionDescription, membrane bound, absent from organism, Co-Immunoprecipitation, PTPSTEP, Precipitation, Interventional, proteins, Cellular Biologies, procedures, man, SURGICAL AND MEDICAL PROCEDURES, Study, Immune, Neural-specific protein-tyrosine phosphatase, Methodological Studies, Benchmarks, Homo sapience, Benchmarking, Homo sampiens, chromosome scaffold, Best Practice, Precipitations, B-lymphocyte receptor complex, Healthcare, Home sapiens, Intervention Strategies, data, trait., Cellular Biology, protein complex, Biologies, Proteins, macromolecule complex, Benchmark, Procedure, trait, antibodies, Spectrum Analysis, Cell, Spectroscopy, polypeptide, count in organism, count, Homo sapian, Relative Risks, Protein, 3.1.3.48, Cellular, Health Care, techniques, Homo sapeins, Mass Spectrum Analyses, Relative Risk, opsonin activity, Intervention, Mass Spectrum, macromolecular complex, absence, Cytology, Risk, Step, Risks, protein containing complex, Spectrometry, Humo sapiens, Striatum-enriched protein-tyrosine phosphatase, Methodological, Methodological Study, Homo sapines, human, Protein Gene Products, plan specification, Gene Proteins, immunoglobulin, Homo spiens, "human" EXACT genbank_common_name [], B cell receptor accessory molecule complex, STEP, Best Practice Analysis, B lymphocyte receptor complex, B cell receptor activity, quantitative, methodology, protein-protein complex, presence or absence in organism2205http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320016573dbgap_ncbi~0patentfamilies~0rfam~0merops~0complex-portal~0uniprot~0wormbaseparasite~0embl-covid19~0reactome~0emdb~0wgs_masters~0ebiweb_resources~0opentargets_genetics~0biomodels_all~0ipd-mhc~0ebiweb_teams~0taxonomy~0genome_assembly~0sc-experiments~0ebiweb_people~0enzymeportal_enzymes~0ipd-nhkir~0cellosaurus~0pdbe~0chebi~0patentproteins~0interpro7~0uniref~0chembl~0pdbekb~0gpcrdb~0hgnc~0sc-genes~0intact~0rhea~0ebiweb_training~0alphafold~0imgt-hla~0patentnucleotides~0ensemblroot~0eva_studies~0non-coding~0europepmc~0pubmed~1identifiers_registry~0pdbechem~0hpa-covid19~0eva-variants-covid19~0biosamples~0gwas_catalog~0biotools~0tls_masters~0mesh~0coding~0sra~0opentargets~0efo~0embl-pathogen~0project~0pride~1human_diseases~0geo_datasets~0embl~0treefam~0uniparc~0ols~0dgva~0intenz~0go~0tsa_masters~0biosamples-covid19~0ebiweb_corporate~0omim~0lrg~0earlycause-molecular-sequences~0ipd-kir~0empiar~0rnacentral~0orcid_data_claims~0gpmdb~2lineage-covid19~0metagenomics~0pfam~0pride archive~1varsite~00Resource Reanalysis0.00.00.0067859346082665020.01.0falseAssessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation.Data from ProteomeXchange, PXD ID: PXD002534. File: GR_130129_20_OT3_NT_L3MBTL2_FAB_31_G11_2_HEK293.mzXML. Published as part of Nat Methods. 2015 Jun 29 . From the Abstract: {{i}} ... We describe a mass spectrometry-based standard operating procedure for scoring immunoprecipitation antibody quality. We quantified the abundance of all the proteins in immunoprecipitates of 1, 124 new recombinant antibodies for 152 chromatin-related human proteins by comparing normalized spectral abundance factors from the target antigen with those of all other proteins ... {{/i}}2015-07-20GPM3232001657326121405PXD002534PXD002534