{"database":"GPMDB","file_versions":[],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":47,"searchCount":5},"additional":{"omics_type":["Other"],"submitter":["Martin-Perez M, et al."],"instrument_platform":["Instrument"],"disease":["Not Available"],"brenda_tissue":["Not available"],"species":["Yeast"],"submitter_mail":["mmarper@uw.edu"],"publication":["25767917"],"model":["http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014370","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014357","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014368","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014369","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014358","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014359","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014360","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014371","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014361","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014372","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014373","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014362","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014374","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014363","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014353","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014354","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014365","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014355","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014366","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014356","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014367"],"submitter_affiliation":["Department of Genome Sciences, University of Washington"],"cell_type":["Not available"],"repository":["GPMDB"],"pubmed_abstract":["Quantitative proteomics studies of yeast that use metabolic labeling with amino acids rely on auxotrophic mutations of one or more genes on the amino acid biosynthesis pathways. These mutations affect yeast metabolism and preclude the study of some biological processes. Overcoming this limitation, it has recently been described that proteins in a yeast prototrophic strain can also be metabolically labeled with heavy amino acids. However, the temporal profiles of label incorporation under the different phases of the prototroph's growth have not been examined. Labeling trajectories are important in the study of protein turnover and dynamics, in which label incorporation into proteins is monitored across many time points. Here we monitored protein labeling trajectories for 48 h after a pulse with heavy lysine in a yeast prototrophic strain and compared them with those of a lysine auxotrophic yeast. Labeling was successful in prototroph yeast during exponential growth phase but not in stationary phase. Furthermore, we were able to determine the half-lives of more than 1700 proteins during exponential phase of growth with high accuracy and reproducibility. We found a median half-life of 2 h in both strains, which corresponds with the cellular doubling time. Nucleolar and ribosomal proteins showed short half-lives, whereas mitochondrial proteins and other energy production enzymes presented longer half-lives. Except for some proteins involved in lysine biosynthesis, we observed a high correlation in protein half-lives between prototroph and auxotroph strains. Overall, our results demonstrate the feasibility of using prototrophs for proteomic turnover studies and provide a reliable data set of protein half-lives in exponentially growing yeast."],"pubmed_title":["Feasibility of protein turnover studies in prototroph Saccharomyces cerevisiae strains."],"pubmed_authors":["Martin-Perez Miguel M,Villén Judit J,","Martin-Perez Miguel M, Villén Judit J"],"name_synonyms":["Saccharomyces oviformis, Yeasts, Saccharomyce cerevisiae, Yeast, Sprain, Bakers, Brewer's, Baker Yeasts, baker's yeast, Saccharomyes cerevisiae, proteins, Baker, Brewer, Saccharomyces uvarum var. melibiosus, Saccharomyces italicus, Saccaromyces cerevisiae, Brewers Yeast, polypeptide, Baker's Yeasts, Sccharomyces cerevisiae, Brewer's Yeasts, S cerevisiae, Candida robusta, Saccharomyces capensis, Brewers, yeast, Baker's, Strain., Strains, brewer's yeast, Baker's Yeast, Bakers Yeast, Sprains, Strains and Sprains, Brewer's Yeast, lager beer yeast, Baker Yeast, Brewer Yeast"],"description_synonyms":["biochemical pathways, projections, Metabolic Process, Materials, bioformation, Lysine Hydrochloride, Effects, Processes, lamellae, Aminosaeure, number, Aminocarbonsaeure, Metabolic Concepts, baker's yeast, Gene, high weight, biosynthesis, Metabolic Processes, presence, process of organ, Saccharomyces italicus, temporal, Long Term, protrusion, Mutations, lamella, period, Lysine Acetate, Metabolism, yeast, heavy, Gene Products, Concepts, 2, Mood, Lysine, Metabolism Concept, Phenomenon, Metabolism Phenomena, Effect, lager beer yeast, Pulses, multicellular organismal biosynthetic process, L Lysine, MAR, study, single-organism biosynthetic process, Saccharomyces italicus., amino acids, Genetic, formation, Longterm, catabolism, anabolism, Moods, epsilon-diaminocaproic acid, Saccharomyes cerevisiae, Metabolic Concept, labeling, metabolic process resulting in cell growth, proteins, ridges, Long-Term, C6H14N2O2, Saccharomyces uvarum var. melibiosus, ecotype, synthesis, Candida robusta, Saccharomyces capensis, papilla, Lysin, biotransformation, Long-Term Effect, brewer's yeast, laminae, Catabolism, Long-Term Effects, incidence, incorporation, data, use, anatomical protrusion, IRF-1, degradation, Process, Aminokarbonsaeure, Affects, anatomical process, metabolism resulting in cell growth, Proteins, lamina, Longterm Effect, flanges, Cistrons, Saccaromyces cerevisiae, Concept, Metabolic Phenomena, strain, Sccharomyces cerevisiae, polypeptide, Metabolism Concepts, count in organism, count, Acetate, Protein, Long Term Effects, Phenomena, shelf, Genetic Materials, cultivar, metabolism, L-Lysine, Genetic Material, flange, organ process, Metabolic Phenomenon, Saccharomyces oviformis, Yeast, mobilization, multicellular organism metabolic process, biodegradation, Metabolic, growth pattern, non-developmental growth, shelves, alpha, Amino, projection, ridge, turnover, Longterm Effects, Protein Gene Products, process, processes, Gene Proteins, single-organism metabolic process, Material, spine, processus, Cistron, Acids, quantitative, 6-diaminohexanoic acid, time, Enisyl, presence or absence in organism, Anabolism"],"pubmed_title_synonyms":["Saccharomyces oviformis, Yeasts, Saccharomyce cerevisiae, Yeast, Sprain, Bakers, Brewer's, Baker Yeasts, baker's yeast, Saccharomyes cerevisiae, proteins, Baker, Brewer, Saccharomyces uvarum var. melibiosus, Saccharomyces italicus, Saccaromyces cerevisiae, Brewers Yeast, polypeptide, Baker's Yeasts, Sccharomyces cerevisiae, Brewer's Yeasts, S cerevisiae, Candida robusta, Saccharomyces capensis, Brewers, yeast, Baker's, Strain., Strains, brewer's yeast, Baker's Yeast, Bakers Yeast, Sprains, Strains and Sprains, Brewer's Yeast, lager beer yeast, Baker Yeast, Brewer Yeast"],"pubmed_abstract_synonyms":["biochemical pathways, projections, Metabolic Process, Materials, bioformation, Lysine Hydrochloride, Effects, Processes, lamellae, Biocatalysts, Aminosaeure, number, Aminocarbonsaeure, Metabolic Concepts, baker's yeast, Gene, high weight, Ribosomal Protein, biosynthesis, Metabolic Processes, establishment of cell quiescence, presence, process of organ, Saccharomyces italicus, temporal, Long Term, protrusion, Mutations, lamella, period, G1/G0 transition, Lysine Acetate, Metabolism, yeast, heavy, Gene Products, Concepts, 2, Mood, Lysine, Metabolism Concept, Phenomenon, Metabolism Phenomena, Effect, Sprains, lager beer yeast, Pulses, multicellular organismal biosynthetic process, L Lysine, study, single-organism biosynthetic process, Ribosomal, Saccharomyces italicus., amino acids, Genetic, enzymes, formation, Longterm, catabolism, anabolism, Moods, epsilon-diaminocaproic acid, stubby, Saccharomyes cerevisiae, Metabolic Concept, labeling, metabolic process resulting in cell growth, proteins, ridges, Long-Term, C6H14N2O2, Saccharomyces uvarum var. melibiosus, ecotype, synthesis, Halflife, Candida robusta, Halflifes, Saccharomyces capensis, papilla, Lysin, Half Life, biotransformation, Long-Term Effect, Strains, brewer's yeast, laminae, Catabolism, Long-Term Effects, incidence, incorporation, use, anatomical protrusion, Data Set, degradation, Process, Aminokarbonsaeure, Affects, anatomical process, metabolism resulting in cell growth, Proteins, Sprain, lamina, Longterm Effect, cell cycle quiescence, flanges, Mitochondrial Protein, enzyme activity, Cistrons, Saccaromyces cerevisiae, results, Concept, Metabolic Phenomena, strain, Sccharomyces cerevisiae, polypeptide, shortened, Metabolism Concepts, count in organism, Half-Lifes, count, Acetate, Protein, Long Term Effects, Phenomena, shelf, Strain, Genetic Materials, cultivar, median, metabolism, L-Lysine, Genetic Material, flange, organ process, Metabolic Phenomenon, Saccharomyces oviformis, Yeast, mobilization, multicellular organism metabolic process, Mitochondrial, biodegradation, Metabolic, growth pattern, non-developmental growth, shelves, alpha, Amino, projection, ridge, turnover, Longterm Effects, lysine synthesis, Protein Gene Products, process, processes, Gene Proteins, stationary phase, lysine anabolism, single-organism metabolic process, Material, spine, lysine biosynthesis, processus, Cistron, Acids, quantitative, 6-diaminohexanoic acid, short, Strains and Sprains, time, Enisyl, lysine formation, presence or absence in organism, Anabolism"],"view_count":["47"],"citation_count":["0"],"search_count":["5"],"full_dataset_link":["http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320014367"],"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 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File: PRO_R2_12h.mzml. Published as part of Anal Chem. 2015 Mar 26  . From the Abstract: {{i}} ... Quantitative proteomics studies of yeast that use metabolic labeling with amino acids rely on auxotrophic mutations of one or more genes on the amino acid biosynthesis pathways. These mutations affect yeast metabolism and preclude the study of some biological processes. Overcoming this limitation, it has recently been described that proteins in a yeast prototrophic strain can also be metabolically labeled with heavy amino acids. However, the temporal profiles of label incorporation under the different phases of the prototroph\"s growth have not been examined. Labeling trajectories are important in the study of protein turnover and dynamics, in which label incorporation into proteins is monitored across many time points. Here we monitored protein labeling trajectories for 48 h after a pulse with heavy lysine in a yeast prototrophic strain and compared them with those of a lysine auxotrophic yeast ... {{/i}}","dates":{"submission":"2015-03-27"},"accession":"GPM32320014367","cross_references":{"pubmed":["25767917"],"Pride":["PXD001823"],"pride":[],"Pride Archive":["PXD001823"]}}