GPMDB00174OtherKeshishian H, et al.InstrumentNot AvailableNot availableHomo_sapiens_viruses, Humanscarr@broad.mit.edu25724909Broad Institute of MIT and 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availableGPMDBWe have developed a novel plasma protein analysis platform with optimized sample preparation, chromatography, and MS analysis protocols. The workflow, which utilizes chemical isobaric mass tag labeling for relative quantification of plasma proteins, achieves far greater depth of proteome detection and quantification while simultaneously having increased sample throughput than prior methods. We applied the new workflow to a time series of plasma samples from patients undergoing a therapeutic, "planned" myocardial infarction for hypertrophic cardiomyopathy, a unique human model in which each person serves as their own biologic control. Over 5300 proteins were confidently identified in our experiments with an average of 4600 proteins identified per sample (with two or more distinct peptides identified per protein) using iTRAQ four-plex labeling. Nearly 3400 proteins were quantified in common across all 16 patient samples. Compared with a previously published label-free approach, the new method quantified almost fivefold more proteins/sample and provided a six- to nine-fold increase in sample analysis throughput. Moreover, this study provides the largest high-confidence plasma proteome dataset available to date. The reliability of relative quantification was also greatly improved relative to the label-free approach, with measured iTRAQ ratios and temporal trends correlating well with results from a 23-plex immunoMRM (iMRM) assay containing a subset of the candidate proteins applied to the same patient samples. The functional importance of improved detection and quantification was reflected in a markedly expanded list of significantly regulated proteins that provided many new candidate biomarker proteins. Preliminary evaluation of plasma sample labeling with TMT six-plex and ten-plex reagents suggests that even further increases in multiplexing of plasma analysis are practically achievable without significant losses in depth of detection relative to iTRAQ four-plex. These results obtained with our novel platform provide clear demonstration of the value of using isobaric mass tag reagents in plasma-based biomarker discovery experiments.Multiplexed, Quantitative Workflow for Sensitive Biomarker Discovery in Plasma Yields Novel Candidates for Early Myocardial Injury.Keshishian Hasmik H,Burgess Michael W MW,Gillette Michael A MA,Mertins Philipp P,Clauser Karl R KR,Mani D R DR,Kuhn Eric W EW,Farrell Laurie A LA,Gerszten Robert E RE,Carr Steven A SA,Keshishian Hasmik H, Burgess Michael W MW, Gillette Michael A MA, Mertins Philipp P, Clauser Karl R KR, Mani D R DR, Kuhn Eric W EW, Farrell Laurie A LA, Gerszten Robert E RE, Carr Steven A SAPlasma, Fresh, Fresh Frozen Plasmas, Fresh Frozen, Blood Plasma, portion of blood plasma, advanced, Frozen Plasma, Fresh Frozen Plasma, Blood, number, Wound., portion of plasma, Plasmas, presence, early, Frozen Plasmas, count in organism, blood plasm, Workflows, count, sensitive, Blood Plasmas, Trauma, precocious, biological marker, quantitative, Work Flow, Work Flows, plasma, presence or absence in organismdetermination, Strokes, HYPERTR OBSTR CARDIOMYOP, Blood, Cahp, Homo sapiense, Hypertrophic Cardiomyopathies, HOCM - Hypertrophic obstructive cardiomyopathy, Hypertrophic cardiomyopathy (disorder), Long Term, CYPIIB20, Homo sapien, Method, p25-alpha, Homo sapians, Work Flow, Effect, WMS, Fresh Frozen Plasmas, Fresh Frozen, increased, Cardiac infarction, Homo sapients, reference sample, MRP-1, SUBVALV STENOSIS, C17orf35, IDIOPATHIC HYPERTROPHIC SUBVALV STENOSIS, proteins, procedures, primary hypertrophic cardiomyopathy (disorder) [Ambiguous], Stroke, Methodological Studies, Homo sapience, sample, Asymmetric Septal Hypertrophy, VMP, GPHYSD2, Heart Attacks, Home sapiens, Long-Term Effects, PGs5, plasma, RNP24, SGS, Myocardial infarction, Asymmetric Septal Hypertrophies, hypertrophic, Infarct, Cardiomyopathy, Frozen Plasma, Asymmetric, PMM 2, Chp, CHP, Myocardial Infarcts, Infarcts, Longterm Effect, P24, Myocardial Infarct, Procedure, Cardiomyopathies, p24 family protein beta-1, Plasmas, 5H9 antigen, Idiopathic Hypertrophic Subvalvular Stenosis, ACMICD, Cytochrome P450 2B20, Workflows, Idiopathic Hypertrophic Subaortic Stenosis, Obstructive cardiomyopathy, Cell growth-inhibiting gene 2 protein, Idiopathic Hypertrophic, tspan-29, Cardiovascular Stroke, Homo sapian, Myocardial infarction NOS, p22, p25, IHSSs, p24, NOS, HCM, Leukocyte antigen MIC3, Calcineurin B-like protein, SLC9A1BP, Hypertrophies, Asymmetric Septal, Hypertrophy, CD9 antigen, heart attack, CYPIIB10, portion of blood plasma, MIC3, TPPP|p25, hyper. obst. cardiomyopathy, Obstructive Cardiomyopathy, Hypertrophic, MASS, Methodological, Sid470p, Methodological Study, Homo sapines, MYOCARDIAL INFARCTION, Primary hypertrophic cardiomyopathy, human, blood plasm, SUBVALV STENOSIS IDIOPATHIC HYPERTROPHIC, Patient, Infarction of heart, Heart attack, TPPP1, CDG1, (MI), AI046351, Sid 470, Infarction, Tubulin polyglutamylase complex subunit 5, Proteomes, time, Work Flows, accessory, Fresh, Hypertrophic Obstructive Cardiomyopathies, p24beta1, CDG1a, human being, Fresh Frozen Plasma, Procedures, mol, Effects, CDGS, FBN, motility-related protein, Gene, Obstructive Cardiomyopathies, vac, tetraspanin-29, supernumerary, Tspan-29, period, Attack - heart, Homo spaiens, Hypertrophic obstructive cardiomyopathy (disorder), ECTOL1, Gene Products, Studies, Inpatient, Calcium-binding protein p22, Person, Blood Plasma, Longterm, cell, labeling, Long-Term, TPPP, Calcium-binding protein CHP, man, OCTD, Study, CDG1B, Septal Hypertrophies, Clients, Homo sampiens, Blood Plasmas, Heart Attack, Long-Term Effect, Controlled., Chromatographies, Cytochrome P450 clone PF3|46, Tetraspanin-29, cell growth-inhibiting gene 2 protein, data, Controlling, MI - Myocardial infarction, AA960066, 1500003O03Rik, 5.3.1.8, MYOCARDIAL, Proteins, HCM - Hypertrophic cardiomyopathy, Client, MI, Cell, IHSS, Hypertrophic Obstructive, Subvalvular Stenosis, Frozen Plasmas, polypeptide, Experiment, EF-hand calcium-binding domain-containing protein p22, Septal Hypertrophy, leukocyte antigen MIC3, chemical analysis, Protein, Long Term Effects, 1.14.14.1, hypertrophic myocardiopathy, MFS1, techniques, Phosphohexomutase, Homo sapeins, WMS2, Plasma, Cardiovascular, Hypertrophic Obstructive Cardiomyopathy, P24A, Myocardial Infarctions, increased number, Phosphomannose isomerase, Humo sapiens, portion of plasma, PM1, TSPAN29, Testosterone 16-alpha hydroxylase, Myocardial, sample population, Longterm Effects, PMI1, Protein Gene Products, Gene Proteins, present in greater numbers in organism, 25 kDa brain-specific protein, Homo spiens, Motility-related protein, "human" EXACT genbank_common_name [], Infarctions, PMI, Cytochrome P450-16-alpha, SSKS, Membrane protein p24A, INFARCTION (MI), assay, CD9, Cardiovascular Strokes, p25alpha, methodology, Myocardial infarction (disorder)Plasma, Fresh, Fresh Frozen Plasmas, Fresh Frozen, Blood Plasma, portion of blood plasma, advanced, Frozen Plasma, Fresh Frozen Plasma, Blood, number, Wound., portion of plasma, Plasmas, presence, early, Frozen Plasmas, count in organism, blood plasm, Workflows, count, sensitive, Blood Plasmas, Trauma, precocious, biological marker, quantitative, Work Flow, Work Flows, plasma, presence or absence in organismdetermination, Strokes, HYPERTR OBSTR CARDIOMYOP, Ass-1, Blood, Homo sapiense, Hypertrophic Cardiomyopathies, HOCM - Hypertrophic obstructive cardiomyopathy, Hypertrophic cardiomyopathy (disorder), Long Term, temporal, Polypeptides, Homo sapien, Method, Homo sapians, AA408052, fold, Work Flow, Effect, WMS, average, Fresh Frozen Plasmas, Fresh Frozen, increased, Cardiac infarction, Homo sapients, reference sample, SUBVALV STENOSIS, IDIOPATHIC HYPERTROPHIC SUBVALV STENOSIS, proteins, procedures, free, primary hypertrophic cardiomyopathy (disorder) [Ambiguous], ASS, Stroke, forecasting, Methodological Studies, Homo sapience, scientific observation, sample, Asymmetric Septal Hypertrophy, GPHYSD2, Heart Attacks, Home sapiens, Long-Term Effects, plasma, SGS, Myocardial infarction, Asymmetric Septal Hypertrophies, hypertrophic, Infarct, Cardiomyopathy, Frozen Plasma, Asymmetric, Data Set, Myocardial Infarcts, Infarcts, Longterm Effect, Myocardial Infarct, Normalcy, Procedure, Cardiomyopathies, Plasmas, Idiopathic Hypertrophic Subvalvular Stenosis, results, ACMICD, any method, Workflows, Idiopathic Hypertrophic Subaortic Stenosis, S-adenosyl-L-methionine:thiol S-methyltransferase activity, Obstructive cardiomyopathy, Idiopathic Hypertrophic, Cardiovascular Stroke, Homo sapian, Myocardial infarction NOS, IHSSs, NOS, HCM, Hypertrophies, Asymmetric Septal, Hypertrophy, heart attack, portion of blood plasma, hyper. obst. cardiomyopathy, Obstructive Cardiomyopathy, expanded, Hypertrophic, MASS, Methodological, Methodological Study, Homo sapines, MYOCARDIAL INFARCTION, Primary hypertrophic cardiomyopathy, human, blood plasm, Health, SUBVALV STENOSIS IDIOPATHIC HYPERTROPHIC, Patient, enlarged, Infarction of heart, Heart attack, (MI), Infarction, TMT, Proteomes, time, Work Flows, accessory, Fresh, big, Hypertrophic Obstructive Cardiomyopathies, human being, Fresh Frozen Plasma, Procedures, Effects, FBN, Gene, Obstructive Cardiomyopathies, supernumerary, period, Attack - heart, Homo spaiens, method, large, Hypertrophic obstructive cardiomyopathy (disorder), ECTOL1, method used in an experiment, Gene Products, Studies, Person, Normalities, study, Blood Plasma, Longterm, labeling, Long-Term, man, study assay, OCTD, Study, Septal Hypertrophies, Clients, Homo sampiens, Blood Plasmas, great, Heart Attack, Long-Term Effect, biological marker, biological marker., Chromatographies, incidence, thiol methyltransferase activity, Controlled, measuring, Controlling, MI - Myocardial infarction, MYOCARDIAL, Proteins, HCM - Hypertrophic cardiomyopathy, Client, MI, IHSS, Hypertrophic Obstructive, futurology, Subvalvular Stenosis, Frozen Plasmas, polypeptide, Septal Hypertrophy, chemical analysis, Protein, Long Term Effects, hypertrophic myocardiopathy, MFS1, techniques, Homo sapeins, WMS2, Plasma, Cardiovascular, Hypertrophic Obstructive Cardiomyopathy, distinct, Myocardial Infarctions, Normality, increased number, Humo sapiens, portion of plasma, patient, Myocardial, sample population, Longterm Effects, Protein Gene Products, plan specification, Gene Proteins, present in greater numbers in organism, Homo spiens, "human" EXACT genbank_common_name [], Infarctions, clear, SSKS, INFARCTION (MI), assay, Cardiovascular Strokes, methodology, Myocardial infarction (disorder)1704http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210037151dbgap_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~0massive~1hpa-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~00.00.00.0052436767427513880.001.0falseMultiplexed, Quantitative Workflow for Sensitive Biomarker Discovery in Plasma Yields Novel Candidates for Early Myocardial Injury.Data from Massive, ID: MSV000078918. Experiment: Discovery_inPatient_IgY14_Supermix_depletion, PMI_Patient1, file: G20121012_PMI_P24_SMdepl_iTRAQ_basicRP_fr23.mzml. Published as part of Mol Cell Proteomics. 2015 Feb 27 . From the Abstract: {{i}} We have developed a novel plasma protein analysis platform with optimized sample preparation, chromatography and MS analysis protocols. The workflow, which utilizes chemical isobaric mass tag labeling for relative quantification of plasma proteins, achieves far greater depth of proteome detection and quantification while simultaneously having increased sample throughput than prior methods. We applied the new workflow to a time series of plasma samples from patients undergoing a therapeutic, planned myocardial infarction (PMI) for hypertrophic cardiomyopathy, a unique human model in which each person serves as their own biologic control ... {{/i}}2015-04-10GPM1121003715125724909MSV000078918