GPMDB00175OtherHaiyan Tan, et al.InstrumentNot AvailableNot availableHomo_sapiens_viruses, Humanjunmin.peng@stjude.org25307156http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210034774http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210034775St. Jude Proteomics Facility, St. Jude Children"s Research Hospital, Memphis, TNNot availableGPMDBAlzheimer's disease (AD) is the most common form of dementia, characterized by progressive loss of cognitive function. One of the pathological hallmarks of AD is the formation of neurofibrillary tangles composed of abnormally hyperphosphorylated tau protein, but global deregulation of protein phosphorylation in AD is not well analyzed. Here, we report a pilot investigation of AD phosphoproteome by titanium dioxide enrichment coupled with high resolution LC-MS/MS. During the optimization of the enrichment method, we found that phosphate ion at a low concentration (e.g. 1 mM) worked efficiently as a nonphosphopeptide competitor to reduce background. The procedure was further tuned with respect to peptide-to-bead ratio, phosphopeptide recovery, and purity. Using this refined method and 9 h LC-MS/MS, we analyzed phosphoproteome in one milligram of digested AD brain lysate, identifying 5243 phosphopeptides containing 3715 nonredundant phosphosites on 1455 proteins, including 31 phosphosites on the tau protein. This modified enrichment method is simple and highly efficient. The AD case study demonstrates its feasibility of dissecting phosphoproteome in a limited amount of postmortem human brain. All MS data have been deposited in the ProteomeXchange with identifier PXD001180 (http://proteomecentral.proteomexchange.org/dataset/PXD001180).Refined phosphopeptide enrichment by phosphate additive and the analysis of human brain phosphoproteome.Tan Haiyan H,Wu Zhiping Z,Wang Hong H,Bai Bing B,Li Yuxin Y,Wang Xusheng X,Zhai Bo B,Beach Thomas G TG,Peng Junmin J,Tan Haiyan H, Wu Zhiping Z, Wang Hong H, Bai Bing B, Li Yuxin Y, Wang Xusheng X, Zhai Bo B, Beach Thomas G TG, Peng Junmin Jthe brain, Brain, brain structure., Nervous System, Homo sapients, suprasegmental structures, human being, Entire brain, CNS, Brains, determination, Encephalon, Humo sapiens, Homo sapiense, suprasegmental levels of nervous system, Encephalons, man, Homo sapines, encephalon, human, Homo spaiens, Homo spiens, "human" EXACT genbank_common_name [], Homo sapien, Homo sapience, Homo sapian, Homo sampiens, Homo sapians, chemical analysis, central nervous system, synganglion, assay, phosphates, Homo sapeins, Home sapiensPilot, LC-MS2, liquid chromatography tandem mass spectroscopy, study, data, low concentration, LCMSMS, Procedures, Titania, brookite, anatase titanium dioxide, PILOT, LC-MS/MS, introduction., titanium oxide, Methodological, Procedure, Methodological Study, rutile, LC-MS-MS, plan specification, Study, nano-TiO2, method, LC/MS/MS, Methodological Studies, liquid chromatography-tandem mass spectroscopy, Method, anatase, method used in an experiment, LC-MSMS, Studies, nano-anatase, liquid chromatography tandem mass spectrometry, titanium white, background, EGR-3the brain, Brain, brain structure., Nervous System, Homo sapients, suprasegmental structures, human being, Entire brain, CNS, Brains, determination, Encephalon, Humo sapiens, Homo sapiense, suprasegmental levels of nervous system, Encephalons, man, Homo sapines, encephalon, human, Homo spaiens, Homo spiens, "human" EXACT genbank_common_name [], Homo sapien, Homo sapience, Homo sapian, Homo sampiens, Homo sapians, chemical analysis, central nervous system, synganglion, assay, phosphates, Homo sapeins, Home sapiensPilot, liquid chromatography tandem mass spectroscopy, Cognitive Function, Presenile Alzheimer Dementia, Tangles, ALZHEIMERS DIS, Entire brain, progressive dementia, Early Onset, Amentias, brookite, PILOT, Homo sapiense, composed of, Alzheimer's disease, Tangle, peptide, AD, nano-TiO2, unspecified, Homo sapien, Method, Homo sapians, titanium white, synganglion, Gpi-1, Paranoid Dementia, multicellular organismal biosynthetic process, Presenile Alzheimer, LATE ONSET ALZHEIMER DIS, single-organism biosynthetic process, Homo sapients, LCMSMS, DAT - Dementia Alzheimer's type, Neurofibrillary, Titania, Nlk, anabolism, Amentia, composition, Familial, proteins, suprasegmental levels of nervous system, SURGICAL AND MEDICAL PROCEDURES, rutile, Cognitions, Methodological Studies, Homo sapience, AD - Alzheimer's disease, Functions, Alzheimer Type Dementia, Case Histories, nano-anatase, ALZHEIMER DIS EARLY ONSET, Presenile, Familial Dementias, SIMPLE, Home sapiens, EGR-3, Alzheimers disease, ratio, LC-MS2, Data Set., Gpi, Senile, low concentration, suprasegmental structures, sporadic Alzheimer's disease, Acute Confusional Senile Dementia, LC-MS/MS, Procedure, Alzheimer's Dementia, brain structure, Alzheimer Type, mOC-X, Homo sapian, PIG7, NOS, NK|GPI, Case Studies, Dementia, Senile Paranoid Dementia, Org, ORG, Alzheimers, Alzheimer, content, anatase titanium dioxide, Encephalon, Neurofibrillary Tangle, proportionality, Gpi1-r, Dementias, rate, Gpi1-s, Methodological, lysed material, Gpi1-t, Methodological Study, Homo sapines, human, Alzheimer's, loss of, Senile Dementia, liquid chromatography-tandem mass spectroscopy, Alzheimer's Disease, Bglap-rs1, hyperphosphorylated, Gpi1s, Dementia of the Alzheimer's type, the brain, Brain, human being, Procedures, AI461847, Gene, biosynthesis, Focal Onset, Encephalons, unspecified (disorder), LC-MS-MS, Intervention or Procedure, ALZHEIMER DIS, protein amino acid phosphorylation, method, Homo spaiens, [X]Dementia in Alzheimer's disease, anatase, method used in an experiment, LC-MSMS, central nervous system, Studies, Gene Products, Pgi, Senile Paranoid Dementias, study, proportion, Nervous System, tau Protein, CNS, Brains, formation, interventionDescription, Gpi-1r, Gpi-1s, Phi, Gpi-1t, Interventional, man, FOCAL ONSET ALZHEIMERS DIS, Case Study, Cognitive Functions, synthesis, Study, lysate, Alzheimer Disease, Homo sampiens, Alzheimer's disease (disorder), Alzheimers Dementia, TP53I7, Alzheimer Senile Dementia, Intervention Strategies, Disease, data, bead, Proteins, titanium oxide, compositionality, MF, mg, Amf, encephalon, Primary Senile Degenerative Dementia, cognitive function, [X]Dementia in Alzheimer's disease (disorder), polypeptide, LC/MS/MS, tau, Protein, background, Homo sapeins, NK, Intervention, Paranoid Dementias, Dementia in Alzheimer's disease, Function, Alzheimer's Disease Pathway, Humo sapiens, Cognitive, Alzheimer Dementia, introduction, plan specification, Protein Gene Products, Familial Dementia, Gene Proteins, Homo spiens, "human" EXACT genbank_common_name [], Late Onset, Senile Paranoid, Dementia in Alzheimer's disease (disorder), structure, quotient, liquid chromatography tandem mass spectrometry1705http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210034774dbgap_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~2lineage-covid19~0metagenomics~0pfam~0pride archive~1varsite~00Resource Reanalysis0.00.00.0052436767427513880.01.0falseRefined phosphopeptide enrichment by phosphate additive and the analysis of human brain phosphoproteome.Data from ProteomeXchange, PXD ID: PXD001180. File: tio2_250ug.mzml. Published as part of Proteomics. 2015 Jan;15(2-3):500-7 . From the Abstract: {{i}} Here, we report a pilot investigation of AD phosphoproteome by titanium dioxide enrichment coupled with high resolution LC-MS/MS. During the optimization of the enrichment method, we found that phosphate ion at a low concentration (e.g. 1 mM) worked efficiently as a nonphosphopeptide competitor to reduce background. {{/i}}2015-02-03GPM1121003477425307156PXD001180PXD001180