{"database":"GPMDB","file_versions":[],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":24,"searchCount":5},"additional":{"omics_type":["Other"],"submitter":["Papachristou EK, et al."],"instrument_platform":["Instrument"],"disease":["Not Available"],"brenda_tissue":["Not available"],"species":["Human, Escherichia_coli_k_12_substr__dh10b, Human_adenovirus_54, Human_adenovirus_a, Human_adenovirus_b, Human_adenovirus_c, Human_adenovirus_d, Human_adenovirus_e, Human_adenovirus_f, Human_adenovirus_g, Human_astrovirus, Human_bocavirus, Human_bocavirus_2, Human_bocavirus_3, Human_bocavirus_4, Human_coronavirus_229e, Human_coronavirus_hku1, Human_coronavirus_nl63, Human_coronavirus_oc43, Human_cosavirus_a, Human_cosavirus_b, Human_cosavirus_d, Human_cosavirus_e, Human_enteric_coronavirus_4408, Human_enterovirus_100, Human_enterovirus_a, Human_enterovirus_b, Human_enterovirus_c, Human_enterovirus_d, Human_erythrovirus_v9, Human_herpesvirus_1, Human_herpesvirus_2, Human_herpesvirus_3, Human_herpesvirus_4_type_1, Human_herpesvirus_4_type_2, Human_herpesvirus_5, Human_herpesvirus_6a, Human_herpesvirus_6b, Human_herpesvirus_7, Human_herpesvirus_8_type_p, Human_immunodeficiency_virus_1, Human_immunodeficiency_virus_2, Human_metapneumovirus, Human_papillomavirus_fa75_ki88_03, Human_papillomavirus_rtrx7, Human_papillomavirus_type_10, Human_papillomavirus_type_100, Human_papillomavirus_type_101, Human_papillomavirus_type_103, Human_papillomavirus_type_104, Human_papillomavirus_type_105, Human_papillomavirus_type_108, Human_papillomavirus_type_109, Human_papillomavirus_type_112, Human_papillomavirus_type_113, Human_papillomavirus_type_16, Human_papillomavirus_type_24, Human_papillomavirus_type_26, Human_papillomavirus_type_32, Human_papillomavirus_type_34, Human_papillomavirus_type_4, Human_papillomavirus_type_41, Human_papillomavirus_type_48, Human_papillomavirus_type_49, Human_papillomavirus_type_5, Human_papillomavirus_type_50, Human_papillomavirus_type_53, Human_papillomavirus_type_60, Human_papillomavirus_type_63, Human_papillomavirus_type_6b, Human_papillomavirus_type_7, Human_papillomavirus_type_71, Human_papillomavirus_type_88, Human_papillomavirus_type_9, Human_papillomavirus_type_92, Human_papillomavirus_type_96, Human_papillomavirus_type_98, Human_papillomavirus_type_99, Human_papillomavirus___1, Human_papillomavirus___18, Human_papillomavirus___2, Human_papillomavirus___54, Human_papillomavirus___61, Human_papillomavirus___cand90, Human_parainfluenza_virus_1, Human_parainfluenza_virus_2, Human_parainfluenza_virus_3, Human_parechovirus, Human_parvovirus_4, Human_parvovirus_b19, Human_picobirnavirus, Human_respiratory_syncytial_virus, Human_rhinovirus_a, Human_rhinovirus_b, Human_rhinovirus_c, Human_tmev_like_cardiovirus, Human_t_lymphotropic_virus_1, Human_t_lymphotropic_virus_2, Human_t_lymphotropic_virus_4"],"submitter_mail":["T.Roumeliotis@soton.ac.uk"],"publication":["23510160"],"model":["http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210017080","http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210017082"],"submitter_affiliation":["Institute for Life Sciences, Centre for Proteomic Research, University of Southampton"],"cell_type":["Not available"],"repository":["GPMDB"],"pubmed_abstract":["The ThinPrep cervical smear is widely used in clinical practice for the cytological and molecular screening against abnormal cells and Human Papillomavirus (HPV) infection. Current advancements made to LC-MS proteomics include the use of stable isotope labeling for the in-depth analysis of proteins in complex clinical specimens. Such approaches have yet to be realized for ThinPrep clinical specimens. In this study, an LC-MS method based on isobaric (iTRAQ) labeling and high-resolution FT-Orbitrap mass spectrometry was used for the proteomic analysis of 23 human ThinPrep smear specimens. Tandem mass spectrometry analysis was performed with both nitrogen high collision dissociation (HCD MS/MS) and helium collision induced dissociation (CID MS/MS) peptide fragmentation modes. The analysis of three 8-plex sample sets yielded the identification of over 3200 unique proteins at FDR < 1%, of which over 2300 proteins were quantitatively profiled in at least one of the three experiments. The interindividual variability served to define the required sample size needed to identify significant protein expression differences. The degree of in-depth proteome coverage allowed the detection of 6 HPV-derived proteins including the high-risk HPV16 type in the specimens tested. The presence of the HPV strains of origin was also confirmed with PCR-hybridization molecular methods. This proof-of-principle study constitutes the first ever report on the nontargeted analysis of HPV proteins in human ThinPrep clinical specimens with high-resolution mass spectrometry. A further testament to the sensitivity and selectivity of the proposed study method was the confident detection of a significant number of phosphopeptides in these specimens."],"pubmed_title":["The shotgun proteomic study of the human ThinPrep cervical smear using iTRAQ mass-tagging and 2D LC-FT-Orbitrap-MS: the detection of the human papillomavirus at the protein level."],"pubmed_authors":["Papachristou Evaggelia K EK,Roumeliotis Theodoros I TI,Chrysagi Argyro A,Trigoni Chrysanthi C,Charvalos Ekatherina E,Townsend Paul A PA,Pavlakis Kitty K,Garbis Spiros D SD,","Papachristou Evaggelia K EK, Roumeliotis Theodoros I TI, Chrysagi Argyro A, Trigoni Chrysanthi C, Charvalos Ekatherina E, Townsend Paul A PA, Pavlakis Kitty K, Garbis Spiros D SD"],"name_synonyms":["study, Homo sapients, human being, HPV, Human papillomavirus, Humo sapiens, FBN, human papillomavirus HPV, MASS, Homo sapiense, man, Homo sapines, human, OCTD, ACMICD, polypeptide, proteins., Homo spaiens, Homo spiens, \"human\" EXACT genbank_common_name [], Homo sapien, Homo sapience, Homo sapian, ECTOL1, Homo sampiens, Homo sapians, SSKS, MFS1, Homo sapeins, GPHYSD2, Home sapiens, Human Papilloma Virus, WMS, WMS2, SGS"],"description_synonyms":["human being, Procedures, JCAP, Slf, Slpa, Eseptin, Somatomedin-C, FPH2, Spectrum Analyses, Homo sapiense, electronic data file, method, Homo spaiens, Homo sapien, Method, method used in an experiment, Homo sapians, Studies, Mass, Sint1, Analysis, MBNL, AF17q25, Mass Spectroscopy, Mass Spectrum Analysis, study, Homo sapients, Analyses, somatomedin-C, SF, CACP, Kitl, labeling, man, Mast cell growth factor, MSF, Msf, Study, Methodological Studies, Homo sapience, IGF1, Homo sampiens, Mechano growth factor, Soluble KIT ligand, Sl, Home sapiens, IGF-I, data, SeptD1, steel factor, hematopoietic growth factor KL, FNZ, somatomedin, FINC, HAPO, Procedure, LETS, Spectrum Analysis, sKITLG, CIG, Spectroscopy, SINT1, HCD, Homo sapian, mechano growth factor, proteomic analysis, computer data file, PNUTL4, ED-B, Homo sapeins, Igf-1, human., Mass Spectrum Analyses, NAPB, Mass Spectrum, SHEP7, SZP, FN, mast cell growth factor, EXP40, EXP42, Stem cell factor, Spectrometry, Humo sapiens, Methodological, STAT5, Methodological Study, Homo sapines, plan specification, stem cell factor, Homo spiens, KL-1, \"human\" EXACT genbank_common_name [], EXP35, MGF, c-Kit ligand, KITLG, GFND2, GFND, MSF1, SCF, Proteomes, EXP"],"pubmed_title_synonyms":["study, Homo sapients, human being, HPV, Human papillomavirus, Humo sapiens, FBN, human papillomavirus HPV, MASS, Homo sapiense, man, Homo sapines, human, OCTD, ACMICD, polypeptide, proteins., Homo spaiens, Homo spiens, \"human\" EXACT genbank_common_name [], Homo sapien, Homo sapience, Homo sapian, ECTOL1, Homo sampiens, Homo sapians, SSKS, MFS1, Homo sapeins, GPHYSD2, Home sapiens, Human Papilloma Virus, WMS, WMS2, SGS"],"pubmed_abstract_synonyms":["atypia, Size, human being, degree (angle), Procedures, determination, Tandem, number, A4, Gene, Spectrum Analyses, Homo sapiense, Isotope-Coded Affinity, Mass Spectrometry Mass Spectrometry, presence, TYPE, DAGA4, peptide, Relative, method, Homo spaiens, Homo sapien, Method, method used in an experiment, Homo sapians, Gene Products, Studies, Mass, Sample Sizes, atypical, Analysis, Isotopically-Coded Affinity, MAM, SCG3, Sprains, sensitivity, Isotopically-Coded Affinity Tagging, Mass Spectroscopy, Mass Spectrum Analysis, study, Homo sapients, Infections, Analyses, Identification, N, HPV, Human papillomavirus, proteins, labeling, Mass Spectrometry, procedures, number of, man, Study, Methodological Studies, Stable, Homo sapience, Homo sampiens, sample, has or lacks parts of type, Isotope-Coded Affinity Tagging, Sensitivity, variability of a physical quality, Helium 4, Strains, Tagging, Home sapiens, Stable Isotope Labeling, close to, use, aberrant, Proteins, Sprain, defective, extra or missing physical or functional parts, Procedure, Labeling, Spectrum Analysis, Cell, collisionally activated dissociation, CID, LGMD2C, near to, Spectroscopy, mereological quality, polypeptide, Isotope, count in organism, CAD, HCD, count, Human Papilloma Virus Infection, Stickstoff, Stable Isotope, Homo sapian, chemical analysis, Protein, Relative Risks, proteomic analysis, Strain, Sizes, techniques, Homo sapeins, Human Papilloma Virus, Isotope Coded Affinity Tagging, Mass Spectrum Analyses, Relative Risk, PCR, Mass Spectrum, Risk, DMDA1, Risks, Spectrometry, Specificity, Humo sapiens, Identifications (Psychology), human papillomavirus HPV, Methodological, Mass Spectrometry-Mass Spectrometry, azote, arc degree, Isotope Labeling, Affinity Tagging, Methodological Study, Homo sapines, Isotopically-Coded, cardinality., human, sample population, polymerase chain reaction, nitrogeno, Protein Gene Products, plan specification, Gene Proteins, Human Papillomavirus Infection, Homo spiens, \"human\" EXACT genbank_common_name [], nitrogen, Sample, DMDA, Specificity and Sensitivity, Helium-4, approaches, vicinity of, SCARMD2, Isotope-Coded, assay, quantitative, 7N, Strains and Sprains, Proteomes, methodology, presence or absence in organism"],"view_count":["24"],"citation_count":["0"],"search_count":["5"],"full_dataset_link":["http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210017082"],"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 archive~1","varsite~0"],"reanalysis_count":["0"],"submitter_keywords":["Resource Reanalysis"],"citation_count_scaled":["0.0"],"reanalysis_count_scaled":["0.0"],"view_count_scaled":["0.007402837754472548"],"download_count_scaled":["0.0"],"normalized_connections":["1.0"],"additional_accession":[]},"is_claimable":false,"name":"The Shotgun Proteomic Study of the Human ThinPrep Cervical Smear Using iTRAQ Mass-Tagging and 2D LC-FT-Orbitrap-MS: The Detection of the Human Papillomavirus at the Protein Level.","description":"Data from ProteomeXchante, PXD ID: PXD000109. Data file: 29SEP12_cervical_smear_1st_exp_HCD.msf.mgf. Published as part of J Proteome Res. 2013 May 3;12(5):2078-89  . From the Abstract: {{i}}{{/i}} ... In this study, an LC-MS method based on isobaric (iTRAQ) labeling and high-resolution FT-Orbitrap mass spectrometry was used for the proteomic analysis of 23 human ThinPrep smear specimens ...{{i}}","dates":{"submission":"2013-05-12"},"accession":"GPM11210017082","cross_references":{"pubmed":["23510160"],"Pride":["PXD000109"],"pride":[],"Pride Archive":["PXD000109"]}}