GPMDB00196OtherWiniewski JR, et al.InstrumentNot AvailableNot availableMus_musculus_viruses, Mousemmann@biochem.mpg.de25225357http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029871http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029850http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029851http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029874http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029852http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029875http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029853http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029876http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029854http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029855http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029877http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029834http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029856http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029878http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029835http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029879http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029836http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029837http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029859http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029838http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029839http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029870http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029860http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029861http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029840http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029862http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029841http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029863http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029842http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029864http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029843http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029866http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029844http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029845http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029867http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029846http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029868http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029847http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029869http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029848http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029849Max-Planck-Institute of Biochemistry, Germany.Not availableGPMDBAbsolute protein quantification using mass spectrometry (MS)-based proteomics delivers protein concentrations or copy numbers per cell. Existing methodologies typically require a combination of isotope-labeled spike-in references, cell counting, and protein concentration measurements. Here we present a novel method that delivers similar quantitative results directly from deep eukaryotic proteome datasets without any additional experimental steps. We show that the MS signal of histones can be used as a "proteomic ruler" because it is proportional to the amount of DNA in the sample, which in turn depends on the number of cells. As a result, our proteomic ruler approach adds an absolute scale to the MS readout and allows estimation of the copy numbers of individual proteins per cell. We compare our protein quantifications with values derived via the use of stable isotope labeling by amino acids in cell culture and protein epitope signature tags in a method that combines spike-in protein fragment standards with precise isotope label quantification. The proteomic ruler approach yields quantitative readouts that are in remarkably good agreement with results from the precision method. We attribute this surprising result to the fact that the proteomic ruler approach omits error-prone steps such as cell counting or protein concentration measurements. The proteomic ruler approach is readily applicable to any deep eukaryotic proteome dataset-even in retrospective analysis-and we demonstrate its usefulness with a series of mouse organ proteomes.A "proteomic ruler" for protein copy number and concentration estimation without spike-in standards.Wiśniewski Jacek R JR,Hein Marco Y MY,Cox Jürgen J,Mann Matthias M,Wiśniewski Jacek R JR, Hein Marco Y MY, Cox Jürgen J, Mann Matthias Mmereological quality, polypeptide, count in organism, criteria, count, concentration, has or lacks parts of type, cardinality, number, proteins, quantitative, extra or missing physical or functional parts, number of, presence, guidelines., presence or absence in organismdata, pulmo, PLXN5, DNS, experimental, (Deoxyribonucleotide)n, mol, DNAn+1, number, lung parenchyma, Nl1, Alteplase, PLEXIN-B1, Mell1, extra or missing physical or functional parts, Double-Stranded, lungs, presence, Histone, Cell, results, Deoxyribonucleic acids, SeP, (Deoxyribonucleotide)n+m, mereological quality, Histone H2b, count in organism, Histone H2a, Experiment, CEH, Tissue-type plasminogen activator chain A, count, Tissue-type plasminogen activator chain B, Deoxyribonucleic Acid, MMEL2, parenchyma of lung, T-PA, NEPII, NL1, Cell., NL2, SEH, ds-DNA, Reteplase, PATISS, desoxyribose nucleic acid, Histone H3.3, SEP, deep, AU020998, D8Ertd2e, TPA, Tpa, thymus nucleic acid, methods, t-plasminogen activator, cell, experimental section, deoxyribonucleic acid, Double Stranded, present in organism, taurine:pyruvate aminotransferase activity, number of, Histone H1(s), sample population, t-PA, sEP, experimental procedures, tPA, sample, 3.4.21.68, ds DNA, has or lacks parts of type, cardinality, SELP, Histone H5, Desoxyribonukleinsaeure, Histone H4, Histone H7, Lungs, Eph2, Double-Stranded DNA, (Deoxyribonucleotide)m, quantitative, DNA, deoxyribonucleic acids, Entire lung, DNAn, Proteomes, Histone H1, AW212668, NEP2, Histone H3, presence or absence in organismmereological quality, polypeptide, count in organism, criteria, count, concentration, has or lacks parts of type, cardinality, number, proteins, quantitative, extra or missing physical or functional parts, number of, presence, guidelines., presence or absence in organism3.4.22.-, scale tissue, criteria, DNS, Procedures, experimental, (Deoxyribonucleotide)n, determination, Laboratory, peltate hair, Aminosaeure, Mus domesticus, number, Aminocarbonsaeure, Gene, mini-ICE, CASP-14, Spectrum Analyses, guidelines, Isotope-Coded Affinity, presence, House Mouse, Deoxyribonucleic acids, element, Histone H2b, method, Histone H2a, Deoxyribonucleic Acid, House, Method, method used in an experiment, Mass, Studies, Gene Products, Mus musculus domesticus, Analysis, Isotopically-Coded Affinity, Mice, Mass Spectroscopy, Histone H3.3, Isotopically-Coded Affinity Tagging, Mass Spectrum Analysis, organ, FACT80, thymus nucleic acid, methods, amino acids, Analyses, cell, FACT, Swiss, experimental section, plant peltate hair, Double Stranded, Swiss Mice, proteins, present in organism, number of, "mouse" EXACT common_name [], Study, "Mus muscaris" RELATED misnomer [], Methodological Studies, Stable, Concentration, anatomical unit, Concentrations, sample, has or lacks parts of type, body organ, Isotope-Coded Affinity Tagging, Histone H5, Histone H4, Histone H7, "mice C57BL/6xCBA/CaJ hybrid" RELATED misspelling [], Double-Stranded DNA, (Deoxyribonucleotide)m, deoxyribonucleic acids, house mouse, DNAn, Tagging, Histone H1, Stable Isotope Labeling, Histone H3, use, Data Set, DNAn+1, Aminokarbonsaeure, Proteins, mouse, extra or missing physical or functional parts, Double-Stranded, Procedure, Spectrum Analysis, Histone, Labeling, Cell, results, mice C57BL/6xCBA/CaJ hybrid, Mus muscaris, Spectroscopy, (Deoxyribonucleotide)n+m, mereological quality, polypeptide, Isotope, count in organism, count, Mus, Stable Isotope, Protein, chemical analysis, Mini-ICE, Proteomes., ds-DNA, scales, desoxyribose nucleic acid, Mass Spectrum Analyses, Isotope Coded Affinity Tagging, Mass Spectrum, deep, Mus musculus, scale, Caspase-14 subunit p10, mice, Swiss Mouse, Spectrometry, deoxyribonucleic acid, House Mice, Caspase-14 subunit p19, Methodological, Isotope Labeling, Amino, MICE, Methodological Study, Affinity Tagging, Histone H1(s), Isotopically-Coded, sample population, experimental procedures, Laboratory Mice, domesticus, plan specification, Protein Gene Products, "house mouse" EXACT genbank_common_name [], Gene Proteins, ds DNA, cardinality, Desoxyribonukleinsaeure, Isotope-Coded, T160, Acids, Mouse, assay, quantitative, DNA, Attentions, Proteomes, Laboratory Mouse, presence or absence in organism1906http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029853dbgap_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~3lineage-covid19~0metagenomics~0pfam~0pride archive~1varsite~00Resource Reanalysis0.00.00.0058605798889574340.01.0falseA proteomic ruler for protein copy number and concentration estimation without spike-in standards.Data from ProteomeXchange, PXD ID: PXD000661. Experiment: TPA_Lung, file: 20120207_EXQ6_JRW_TPA_Lung_28_1_T.mzml. Published as part of Mol Cell Proteomics. 2014 Sep 15 . From the Abstract: {{i}} ... Here we present a novel concept that delivers similar quantitative results directly from deep eukaryotic proteome datasets without any additional experimental steps. We show that the MS-signal of histones can be used as a proteomic ruler because is proportional to the amount of DNA in the sample, which in turn depends of the number of cells ... {{/i}}2014-09-19GPM1121002985325225357PXD000661PXD000661