{"database":"MassIVE","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://massive-ftp.ucsd.edu/x01/MSV000083965/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"submitter":["Lo�c Dayon"],"full_dataset_link":["https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=56003ddb60724bfb811d35b775a7ab80"],"submitter_email":["Loic.Dayon@rd.nestle.com"],"sample_protocol":[""],"repository":["MassIVE"],"file_size":["31"],"ptm_modification":["UNIMOD:4 - \"Iodoacetamide derivative.\"","UNIMOD:7 - \"Deamidation.\"","UNIMOD:23 - \"Dehydration.\"","UNIMOD:737 - \"Sixplex Tandem Mass Tag.\"","UNIMOD:1 - \"Acetylation.\"","UNIMOD:35 - \"Oxidation or Hydroxylation.\"","UNIMOD:385 - \"Loss of ammonia.\""],"data_protocol":[""],"omics_type":["Proteomics"],"instrument_platform":["LTQ Orbitrap Elite"],"species":["Homo Sapiens (ncbitaxon:9606)"],"submitter_affiliation":["Proteomics Team Leader, Nestl� Institute of Health Sciences SA"],"pubmed_abstract":["Cerebrospinal fluid (CSF) is a body fluid of choice for biomarker studies of brain disorders but remains relatively under-studied compared with other biological fluids such as plasma, partly due to the more invasive means of its sample collection. The present study establishes an in-depth CSF proteome through the analysis of a unique CSF sample from a pool of donors. After immunoaffinity depletion, the CSF sample was fractionated using off-gel electrophoresis and analyzed with liquid chromatography tandem mass spectrometry (MS) using the latest generation of hybrid Orbitrap mass spectrometers. The shotgun proteomic analysis allowed the identification of 20 689 peptides mapping on 3379 proteins. To the best of our knowledge, the obtained data set constitutes the largest CSF proteome published so far. Among the CSF proteins identified, 34% correspond to genes whose transcripts are highly expressed in brain according to the Human Protein Atlas. The principal Alzheimer's disease biomarkers (e.g., tau protein, amyloid-β, apolipoprotein E, and neurogranin) were detected. Importantly, our data set significantly contributes to the Chromosome-centric Human Proteome Project (C-HPP), and 12 proteins considered as missing are proposed for validation in accordance with the HPP guidelines. Of these 12 proteins, 8 proteins are based on 2 to 6 uniquely mapping peptides from this CSF analysis, and 4 match a new peptide with a \"stranded\" single peptide in PeptideAtlas from previous CSF studies. The MS proteomic data are available to the ProteomeXchange Consortium ( http://www.proteomexchange.org/ ) with the data set identifier PXD009646."],"pubmed_title":["Deep Dive on the Proteome of Human Cerebrospinal Fluid: A Valuable Data Resource for Biomarker Discovery and Missing Protein Identification."],"pubmed_authors":["Macron Charlotte C, Lane Lydie L, Núñez Galindo Antonio A, Dayon Loïc L"],"name_synonyms":["Gene., Cerebro Spinal Fluid, Biological Markers, Viral Marker, human being, Viral, Surrogate Endpoints, Surrogate Endpoint, Clinical Markers, Laboratory, protein complex, Clinical Marker, Modern, Serum Markers, Proteins, Fluids, Biochemical, total expressed protein, End Point, Cerebrospinal Fluids, Endpoint, Biochemical Markers, spinal fluid, protein, Serum, protein-containing complex, Biologic Marker, Spinal Fluid, Immune Marker, Human, Cerebrospinal, Surrogate End Points, Cerebro Spinal Fluids, Spinal Fluids, Surrogate Markers, Laboratory Markers, protein polypeptide chains, Fluid, cerebral spinal fluid, native protein, Homo sapiens, natural protein, polypeptide chain, Marker, Biological, Surrogate End Point, Protein, Gene Products, Cerebro Spinal, liquor cerebrospinalis, protein aggregate, Man, Biologic Markers, Biomarker, Serum Marker, Man (Taxonomy), Clinical, End Points, Surrogate, Biological Marker, Endpoints, proteins, CSF, Immunologic, Laboratory Marker, Cerebro, human, Surrogate Marker, Protein Gene Products, Gene Proteins, Immunologic Markers, Immune, Markers, Biochemical Marker, Viral Markers, Modern Man, biological marker, Immunologic Marker, Proteomes, humans, Biologic, Immune Markers"],"description_synonyms":["liquid chromatography tandem mass spectroscopy, Presenile Alzheimer Dementia, Biological Markers, Viral Marker, dmBest1, ALZHEIMERS DIS, Materials, Surrogate Endpoints, determination, Laboratory, Early Onset, Blood, Biochemical, Endpoint, Serum, fluid, Early Onset Alzheimer Disease, DmelCG6264, Alzheimer's disease, DmelCG6383, P17 Protein Kinase C Substrate, Primary Senile Degenerative, Polypeptides, AD, B2T, Laboratory Markers, systemic amyloidosis, cerebral spinal fluid, sampling, peptido, diseases, Biological, SPH3, DGS, ARB, 1, liquor cerebrospinalis, diseases and disorders, synganglion, with cerebral amyloid angiopathy, WMS, Presenile Alzheimer, Fresh Frozen Plasmas, Fresh Frozen, amyloidosis, human disease, LCMSMS, Familial Alzheimer Disease (FAD), Alzheimer Diseases, Man (Taxonomy), peptides, HPP, DAT - Dementia Alzheimer's type, early-onset, C1, Tissue, human protein, crumb, chromatid, elevated, suprasegmental levels of nervous system, Focal Onset Alzheimer's Disease, Substance, Amyloid, Late Onset Alzheimer Disease, childhood, Immune, Markers, AD - Alzheimer's disease, EL2, DmelCG1106, Viral Markers, sample, Alzheimer Type Dementia, AD1, Homo sapiens disease, Tissue Donor, Presenile, GPHYSD2, plasma, Alzheimers disease, SGS, LC-MS2, Cerebro Spinal Fluid, apolipoprotein, Senile, Alzheimer disease, suprasegmental structures, Frozen Plasma, Transplant Donor, Viral, sporadic Alzheimer's disease, CG6264, Surrogate Endpoint, Data Set, HS3, CG6383, Acute Confusional Senile Dementia, phosphoethanol-aminuria, Transplant, Modern, LC-MS/MS, familial, Semen Donors, Biochemical Markers, Biologic Marker, Plasmas, Alzheimer's Dementia, ACMICD, Cerebro Spinal Fluids, Alzheimer Type, Amyloid Fibrils, pyropoikilocytosis hereditary, Marker, Apolipoprotein, Genetic Materials, NOS, Donors, TU15B, Genetic Material, dBest1, Dementia, LAMB2T, Epistemology, Alzheimers, Amyloid Substance, amyloidoses, End Points, Alzheimer, Encephalon, susceptibility to, dbest1, Immunologic, MASS, Colony-stimulating factor, Csfgm, Laboratory Marker, Alzheimer-Type (ATD), Cerebro, late-onset, human, Semen Donor, CG1106, Atlases, Alzheimer's, disease, Semen, Senile Dementia, Chromosome, Biochemical Marker, Material, liquid chromatography-tandem mass spectroscopy, Acute Confusional, Alzheimer-Type Dementia (ATD), Cistron, Polypeptide, Alzheimer's Disease, Ovum, Ovum Donors, Organ Donors, Proteomes, l(3)S050920, humans, Alzheimer Type Dementia (ATD), Dementia of the Alzheimer's type, the brain, Crbs, Fresh, childhood hypophosphatasia, other disease, criteria, human being, Fresh Frozen Plasma, Alzheimers Diseases, Clinical Markers, Clinical Marker, lipophorin, Sclerosis, FBN, Gene, GM-CSF, far, Alzheimer disease 1, Amyloid Fibril, hypophospatasia, anon-WO0118547.380, Focal Onset, LC-MS-MS, unspecified (disorder), Cerebrospinal, Surrogate End Points, Human, ALZHEIMER DIS, Surrogate Markers, Electrophoreses, Crumbs, [X]Dementia in Alzheimer's disease, Homo sapiens, ECTOL1, LC-MSMS, body fluid, Gene Products, Cerebro Spinal, disease or disorder, amyloid, Man, GMCSF, RC3 Protein (Neurogranin), Biomarker, study, Blood Plasma, CT19912, presenile and senile dementia, 0509/20, tau Protein, Clinical, Genetic, VMD2, BM600, Biological Marker, gel, 1384/04, amyloidosis (disease), BMD, EBR2, Transplant Donors, non-neoplastic, OCTD, Presenile Dementia, Molgramostin, Immunologic Markers, Alzheimer Disease, Blood Plasmas, Cerebral Spinal Fluid, disorder, peptidos, biological marker, Alzheimer's disease (disorder), Ovum Donor, Alzheimers Dementia, Immunologic Marker, high elevation, Biologic, l(3)j1B5, Organ, RP50, hypophosphatasia mild, Disease, Alzheimer Syndrome, EBR2A, Serum Markers, Proteins, disorders, Fluids, End Point, total expressed protein, Cerebrospinal Fluids, spinal fluid, medical condition, Cistrons, encephalon, Peptide, Spinal Fluid, Immune Marker, Primary Senile Degenerative Dementia, l(3)07207, [X]Dementia in Alzheimer's disease (disorder), Frozen Plasmas, Alzheimer Dementias, Spinal Fluids, prophase chromosome, LC/MS/MS, Fluid, tau, Sargramostim, Surrogate End Point, SPTA, Alzheimer's Diseases, chemical analysis, Protein, proteomic analysis, condition, CRB, Crb, MFS1, Donor, l(3)S058104, specimen collection, amyloid disease, guidelines., WMS2, Biologic Markers, Fibril, Plasma, centric, Dbest, Serum Marker, Body Fluid, Organ Donor, best, Surrogate, Dementia in Alzheimer's disease, interphase chromosome, Endpoints, hereditary pyropoikilocytosis, portion of plasma, Alzheimer Type Senile Dementia, CSF, Alzheimer Dementia, Body, Surrogate Marker, sample population, Alzheimer Sclerosis, Protein Gene Products, Gene Proteins, sample collection, Fibrils, Late Onset, Familial (FAD), Modern Man, LAMNB2, SSKS, Dementia in Alzheimer's disease (disorder), liquid chromatography tandem mass spectrometry, protection against, Peptid, assay, Familial Alzheimer Diseases (FAD), BEST, Immune Markers"],"pubmed_title_synonyms":["Gene., Cerebro Spinal Fluid, Biological Markers, Viral Marker, human being, Viral, Surrogate Endpoints, Surrogate Endpoint, Health Resource, Clinical Markers, Laboratory, protein complex, Clinical Marker, Modern, Serum Markers, Proteins, Fluids, Biochemical, total expressed protein, End Point, Cerebrospinal Fluids, Endpoint, Biochemical Markers, spinal fluid, protein, Serum, protein-containing complex, Biologic Marker, Spinal Fluid, Immune Marker, Human, Cerebrospinal, Surrogate End Points, Cerebro Spinal Fluids, Spinal Fluids, Surrogate Markers, Laboratory Markers, protein polypeptide chains, Fluid, cerebral spinal fluid, Resource, native protein, Homo sapiens, natural protein, polypeptide chain, Marker, Biological, Surrogate End Point, Protein, Gene Products, Cerebro Spinal, liquor cerebrospinalis, protein aggregate, Man, Resources, Biologic Markers, Biomarker, Serum Marker, Man (Taxonomy), Clinical, End Points, Surrogate, Biological Marker, Endpoints, proteins, CSF, Immunologic, Laboratory Marker, Cerebro, human, Surrogate Marker, Protein Gene Products, Gene Proteins, Health, Immunologic Markers, Immune, Markers, Biochemical Marker, Viral Markers, Modern Man, biological marker, Immunologic Marker, Proteomes, humans, Biologic, Immune Markers"],"pubmed_abstract_synonyms":["liquid chromatography tandem mass spectroscopy, Brain Disease, Presenile Alzheimer Dementia, Biological Markers, Viral Marker, dmBest1, ALZHEIMERS DIS, Materials, Surrogate Endpoints, Product, determination, Laboratory, Early Onset, Blood, Biochemical, Endpoint, protein, Serum, fluid, Early Onset Alzheimer Disease, DmelCG6264, Alzheimer's disease, DmelCG6383, P17 Protein Kinase C Substrate, Primary Senile Degenerative, peptide, Polypeptides, AD, B2T, Laboratory Markers, protein polypeptide chains, unspecified, cerebral spinal fluid, sampling, peptido, Biological, SPH3, DGS, ARB, liquor cerebrospinalis, Central Nervous System Intracranial Disorders, synganglion, Biological Product, protein aggregate, Gpi-1, WMS, Central Nervous System Disorders, Fresh Frozen Plasmas, Fresh Frozen, LATE ONSET ALZHEIMER DIS, LCMSMS, Familial Alzheimer Disease (FAD), Biologic Drugs, Man (Taxonomy), Alzheimer Diseases, peptides, HPP, DAT - Dementia Alzheimer's type, Natural, Nlk, C1, Tissue, crumb, apo-E, proteins, chromatid, Biological Drugs, suprasegmental levels of nervous system, Focal Onset Alzheimer's Disease, Late Onset Alzheimer Disease, APOE, childhood, Immune, Biological Medicine, Markers, AD - Alzheimer's disease, EL2, DmelCG1106, Viral Markers, sample, Alzheimer Type Dementia, Medicine, Tissue Donor, ALZHEIMER DIS EARLY ONSET, Medicines, Presenile, GPHYSD2, Biologic Drug, plasma, Alzheimers disease, SGS, NK/GPI, LC-MS2, Data Set., Gpi, Cerebro Spinal Fluid, Senile, Alzheimer disease, Frozen Plasma, Transplant Donor, suprasegmental structures, Viral, CG6264, Surrogate Endpoint, Data Set, HS3, Biologic Products, CG6383, Acute Confusional Senile Dementia, phosphoethanol-aminuria, Transplant, Modern, LC-MS/MS, familial, Semen Donors, Biochemical Markers, Biologic Marker, Plasmas, Alzheimer's Dementia, ACMICD, Cerebro Spinal Fluids, Alzheimer Type, pyropoikilocytosis hereditary, mOC-X, Marker, Biopharmaceuticals, Biologic Product, Genetic Materials, NOS, Donors, NK|GPI, Intracranial CNS Disorder, TU15B, Genetic Material, Encephalon Disease, dBest1, Dementia, LAMB2T, Epistemology, Org, ORG, Alzheimers, End Points, Biological Medicines, Alzheimer, Biological Drug, Encephalon, dbest1, Gpi1-r, Dementias, Gpi1-s, Encephalopathy, Biologics, Immunologic, MASS, Colony-stimulating factor, Csfgm, Laboratory Marker, Alzheimer-Type (ATD), Cerebro, Gpi1-t, human, Semen Donor, CG1106, Atlases, Intracranial, Semen, Senile Dementia, Chromosome, Biochemical Marker, Material, liquid chromatography-tandem mass spectroscopy, Acute Confusional, Alzheimer-Type Dementia (ATD), Cistron, Polypeptide, Alzheimer's Disease, Ovum, Ovum Donors, Organ Donors, Proteomes, l(3)S050920, Bglap-rs1, humans, Gpi1s, Alzheimer Type Dementia (ATD), Dementia of the Alzheimer's type, Crbs, the brain, Fresh, childhood hypophosphatasia, Hybrids, criteria, human being, Encephalopathies, Fresh Frozen Plasma, Alzheimers Diseases, Biologic Pharmaceuticals, Clinical Markers, AI461847, Clinical Marker, Sclerosis, Intracranial Central Nervous System Disorders, FBN, Gene, GM-CSF, Brain Disorders, far, hypophospatasia, guidelines, anon-WO0118547.380, protein-containing complex, Focal Onset, LC-MS-MS, unspecified (disorder), Cerebrospinal, Surrogate End Points, Human, ALZHEIMER DIS, Surrogate Markers, Intracranial CNS Disorders, Electrophoreses, Brain Disorder, Crumbs, Homo sapiens, polypeptide chain, [X]Dementia in Alzheimer's disease, ECTOL1, LC-MSMS, CNS Disorder, body fluid, Gene Products, Cerebro Spinal, Pgi, Man, GMCSF, Biologicals, RC3 Protein (Neurogranin), Drugs, Biomarker, study, Blood Plasma, CT19912, 0509/20, tau Protein, Clinical, Genetic, Gpi-1r, VMD2, Gpi-1s, BM600, Biological Marker, gel, 1384/04, Phi, Natural Product, Gpi-1t, BMD, Chimeras, EBR2, Transplant Donors, FOCAL ONSET ALZHEIMERS DIS, OCTD, Presenile Dementia, Molgramostin, Immunologic Markers, Alzheimer Disease, Encephalon Diseases, Blood Plasmas, Cerebral Spinal Fluid, CNS Disorders, peptidos, biological marker, Alzheimer's disease (disorder), Ovum Donor, Alzheimers Dementia, Immunologic Marker, Biologic, l(3)j1B5, Pharmaceuticals, Organ, RP50, Alzheimer Senile Dementia, hypophosphatasia mild, Products, Disease, Biologic Medicines, protein complex, Alzheimer Syndrome, EBR2A, Serum Markers, Proteins, Fluids, End Point, total expressed protein, Cerebrospinal Fluids, spinal fluid, MF, Cistrons, Amf, encephalon, Peptide, Spinal Fluid, Immune Marker, Primary Senile Degenerative Dementia, l(3)07207, [X]Dementia in Alzheimer's disease (disorder), Frozen Plasmas, Alzheimer Dementias, polypeptide, Spinal Fluids, prophase chromosome, LC/MS/MS, Fluid, Hybrid, native protein, natural protein, tau, Sargramostim, Surrogate End Point, SPTA, Alzheimer's Diseases, chemical analysis, Protein, Biopharmaceutical, proteomic analysis, CRB, Crb, MFS1, Donor, l(3)S058104, specimen collection, WMS2, NK, Biologic Markers, Plasma, Dbest, Serum Marker, Body Fluid, Organ Donor, best, Surrogate, Dementia in Alzheimer's disease, interphase chromosome, Endpoints, Alzheimer's Disease Pathway, hereditary pyropoikilocytosis, portion of plasma, Alzheimer Type Senile Dementia, CSF, Alzheimer Dementia, Body, Surrogate Marker, sample population, Alzheimer Sclerosis, Drug, Protein Gene Products, Gene Proteins, sample collection, Late Onset, Familial (FAD), Modern Man, LAMNB2, SSKS, Dementia in Alzheimer's disease (disorder), Natural Products, liquid chromatography tandem mass spectrometry, Peptid, assay, Familial Alzheimer Diseases (FAD), BEST, Immune Markers"],"citation_count":["0"],"additional_accession":["PXD009646"]},"is_claimable":true,"name":"Deep Dive in the Proteome of Human Cerebrospinal Fluid: A Valuable Data Resource for Biomarker Discovery and Missing Protein Identification","description":"Cerebrospinal fluid (CSF) is a body fluid of choice for biomarker studies of brain disorders but remains relatively under-studied compared to other biological fluids such as plasma, partly due to the more invasive means of its sample collection. The present study establishes an in-depth CSF proteome through the analysis of a unique CSF sample from a pool of healthy donors. After immuno-affinity depletion, the CSF sample was fractionated using off-gel electrophoresis and analyzed with liquid chromatography tandem mass spectrometry (MS) using the latest generation of hybrid Orbitrap mass spectrometers. The shotgun proteomic analysis allowed the identification of 20689 peptides mapping on 3379 proteins. To the best of our knowledge, the obtained dataset constitutes the largest CSF proteome published so far. Among the CSF proteins identified, 34% correspond to genes defined as elevated in the brain by The Human Protein Atlas. The principal Alzheimer disease biomarkers (e.g., tau protein, amyloid-?, apolipoprotein E and neurogranin) were detected. Importantly, our dataset significantly contributes to the Chromosome-Centric Human Proteome Project (C-HPP), and 13 proteins considered as missing are proposed for validation in accordance with the HPP guidelines.","dates":{"publication":"Wed Jun 12 13:53:00 BST 2019"},"accession":"MSV000083965","cross_references":{"pubmed":["30124047"]}}