GPMDB00153OtherFonslow BR, et al.InstrumentNot AvailableNot availableYeastNot 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mnum=GPM32320001443http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320001446http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320001445http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320001448http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320001447http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320001449http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320001440http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320001442http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320001441http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320001455http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320001454http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320001457http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320001456http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320001451http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320001450http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320001453http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320001452Department of Chemical Physiology, The Scripps Research InstituteNot availableGPMDBTwo major challenges in proteomics are the large number of proteins and their broad dynamic range in the cell. We exploited the abundance-dependent Michaelis-Menten kinetics of trypsin digestion to selectively digest and deplete abundant proteins with a method we call DigDeAPr. We validated the depletion mechanism with known yeast protein abundances, and we observed greater than threefold improvement in low-abundance human-protein identification and quantitation metrics. This methodology should be broadly applicable to many organisms, proteases and proteomic pipelines.Digestion and depletion of abundant proteins improves proteomic coverage.Fonslow Bryan R BR,Stein Benjamin D BD,Webb Kristofor J KJ,Xu Tao T,Choi Jeong J,Park Sung Kyu SK,Yates John R JR 3rd,Fonslow Bryan R BR,Stein Benjamin D BD,Webb Kristofor J KJ,Xu Tao T,Choi Jeong J,Park Sung Kyu SK,Yates John R JR,Fonslow Bryan R BR, Stein Benjamin D BD, Webb Kristofor J KJ, Xu Tao T, Choi Jeong J, Park Sung Kyu SK, Yates John R JRProtein Gene Products, Gene Products, Proteins, Gene., Gene Proteins, polypeptide, proteins, ProteinNat, NAT, data, Controlling, D17H6S113E, human being, cou, Procedures, Proteins, baker's yeast, Gene, Procedure, Homo sapiense, FSH, Tl3, Tl2, Saccaromyces cerevisiae, Saccharomyces italicus, Fsrg1, Sccharomyces cerevisiae, polypeptide, method, Homo spaiens, Experiment, RING3, Lr, Homo sapien, Method, Homo sapian, AW228947, method used in an experiment, Homo sapians, yeast, FSRG1, Protein, Studies, Gene Products, mKIAA4005, Low, techniques, Homo sapeins, lager beer yeast, Saccharomyces oviformis, Yeast, D6S113E, me75, Homo sapients, reference sample, RNF3, Rnf3, Frg-1, beta-Trypsin, Tripcellim, Humo sapiens, Saccharomyes cerevisiae, Identifications (Psychology), proteins, Ring3, Methodological, procedures, Saccharomyces uvarum var. melibiosus, Methodological Study, beta Trypsin, man, Homo sapines, D17Mit170, T1, human, Identification., Protein Gene Products, plan specification, Study, Trypure, Gene Proteins, Homo spiens, "human" EXACT genbank_common_name [], Candida robusta, Methodological Studies, Homo sapience, Saccharomyces capensis, Homo sampiens, Bra, brewer's yeast, Home sapiens, Fsrg-1, Controlled, methodologyProtein Gene Products, Gene Products, Proteins, Gene., Gene Proteins, polypeptide, proteins, Proteinbig, human being, wide/broad, cou, Procedures, Proteins, number, Gene, baker's yeast, extra or missing physical or functional parts, broad, Procedure, Homo sapiense, Tl3, Tl2, Cell, Saccaromyces cerevisiae, Saccharomyces italicus, mereological quality, polypeptide, Sccharomyces cerevisiae, large, method, Homo spaiens, Lr, Homo sapien, Method, Homo sapian, method used in an experiment, Homo sapians, Protein, yeast, Gene Products, Studies, Low, techniques, Homo sapeins, methodology., lager beer yeast, Saccharomyces oviformis, Yeast, me75, Homo sapients, Identification, cell, beta-Trypsin, expanded, Tripcellim, Humo sapiens, Saccharomyes cerevisiae, Identifications (Psychology), proteins, Methodological, procedures, number of, Saccharomyces uvarum var. melibiosus, beta Trypsin, Methodological Study, man, Homo sapines, D17Mit170, T1, human, Protein Gene Products, plan specification, Study, Gene Proteins, Trypure, wide, Homo spiens, "human" EXACT genbank_common_name [], Candida robusta, Methodological Studies, enlarged, Homo sapience, Saccharomyces capensis, Homo sampiens, great, has or lacks parts of type, cardinality, Bra, brewer's yeast, Home sapiens1503http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320001404dbgap_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~0human_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~0varsite~00.00.00.00462677359654534250.001.0falseDigestion and depletion of abundant proteins improves proteomic coverage.Data from Yates lab web site. Experiment: yeast control replicate 2, file: 120211_Yeast_Control2_Step02.mzml. Published as part of Nat Methods. 2013 Jan;10(1):54-6 9 . From the Abstract: {{i}} We exploited the abundance-dependent Michaelis-Menten kinetics of trypsin digestion to selectively digest and deplete abundant proteins with a method we call DigDeAPr. We validated the depletion mechanism with known yeast protein abundances, and we observed greater than threefold improvement in low-abundance human-protein identification and quantitation metrics. {{/i}}2014-07-02GPM3232000140423160281