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available"],"submitter_keywords":["whole-proteome","Irradiation; whole-proteome","Irradiation"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD000402"],"sample_protocol":["Soluble protein extracts were prepared from the four samples and in solution proteolyzed with trypsin after microwave denaturation of the hyperthermophilic and trypsin recalcitrant proteins. The resulting peptides were resolved by their isoelectric point by OFFGEL electrophoresis in 12 peptide pools."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["The resulting 48 peptide samples were analyzed by nanoLC-MS/MS with a high resolution mass spectrometer. A total of 221,368 MS/MS spectra were recorded and 63,108 were assigned with confidence to peptide sequences. A total of 6,907 peptide sequences could be observed validating the detection of 852 proteins based on the “two peptides” rule."],"omics_type":["Proteomics"],"labhead":["Jean Armengaud"],"instrument_platform":[""],"labhead_affiliation":["jean.armengaud@cea.fr"],"submission_type":["COMPLETE"],"species":["Thermococcus Gammatolerans"],"publication":["25359407 Yang YS, Fernandez B, Lagorce A, Aloin V, De Guillen KM, Boyer JB, Dedieu A, Confalonieri F, Armengaud J, Roumestand C. Prioritizing targets for structural biology through the lens of proteomics: The archaeal protein TGAM_1934 from Thermococcus gammatolerans. Proteomics. 2014 Oct 31 10.1002/pmic.201300535"],"submitter_mail":["jean.armengaud@cea.fr"],"curator_keywords":["Biological"],"submitter_affiliation":["Li2D"],"submitter_country":["France"],"doi":["10.6019/PXD000402"],"pubmed_abstract":["ORFans are hypothetical proteins lacking any significant sequence similarity with other proteins. Here, we highlighted by quantitative proteomics the TGAM_1934 ORFan from the hyperradioresistant Thermococcus gammatolerans archaeon as one of the most abundant hypothetical proteins. This protein has been selected as a priority target for structure determination on the basis of its abundance in three cellular conditions. Its solution structure has been determined using multidimensional heteronuclear NMR spectroscopy. TGAM_1934 displays an original fold, although sharing some similarities with the 3D structure of the bacterial ortholog of frataxin, CyaY, a protein conserved in bacteria and eukaryotes and involved in iron-sulfur cluster biogenesis. These results highlight the potential of structural proteomics in prioritizing ORFan targets for structure determination based on quantitative proteomics data. The proteomic data and structure coordinates have been deposited to the ProteomeXchange with identifier PXD000402 (http://proteomecentral.proteomexchange.org/dataset/PXD000402) and Protein Data Bank under the accession number 2mcf, respectively."],"pubmed_title":["Prioritizing targets for structural biology through the lens of proteomics: the archaeal protein TGAM_1934 from Thermococcus gammatolerans."],"pubmed_authors":["Yang Yin-Shan YS, Fernandez Bernard B, Lagorce Arnaud A, Aloin Valérie V, De Guillen Karine Montet KM, Boyer Jean-Baptiste JB, Dedieu Alain A, Confalonieri Fabrice F, Armengaud Jean J, Roumestand Christian C"],"description_synonyms":["Taf[[II]]250, Taf200, dTAF[[II]]230, TAF[[II]]250, d230, dTAF[[II]]250, TAF[[II]]230, TFIID TAF250, cel, cell, TAF200, total expressed protein, l(3)84Ab, dTAFII250, Taf1p, TAF[II]250, BG:DS00004.13, TAFII-250, CG17603, TAF250/230, TAF[[II]], EfW1, Cell, dTAF230, dTAF250, dmTAF[[II]]230, TAFII250, DmelCG17603, TAF1., Taf250, dmTAF1, SR3-5, Taf230, p230, TAF[[II]]250/230, TFIID, TAF, Proteomes, TAF230, TAF250"],"data_synonyms":["907, XXD, peptides, Protein., Dhekelia, Eastern Sovereign Base Area, Proteins, Gene, 907 cell, Peptide, NICR1852, Protein Gene Products, polypeptide, peptide, Gene Proteins, Polypeptides, peptido, 907 细胞, XD, Protein, Gene Products, Peptid, peptidos, Polypeptide, DHEKELIA, Dhekelia Sovereign Base Area"],"pubmed_title_synonyms":["Contradens, lens capsule, Peptidomics, Protein., lens, protein complex, Proteins, ocular lens, crystalline lens, Lens <eudicots>, Gene, protein, protein-containing complex, Uniandra, lens crystallina, Protein Gene Products, lenses, Gene Proteins, native protein, Protein, Gene Products, camera-type eye lens, protein aggregate, eye lens, Lens <bivalves>"],"sample_synonyms":["PRSS, peptides, protein complex, Proteins, beta-Trypsin, Tripcellim, Points, Gene, protein, Isoelectric, pI, protein-containing complex, beta Trypsin, Peptide, Solution, Protein Gene Products, Isoelectric Points, Gene Proteins, Trypure, polypeptide, peptide, Polypeptides, Electrophoreses, native protein, peptido, soluble, Point, Protein, Gene Products, Peptid, peptidos, Polypeptide, protein aggregate, Peptide."],"pubmed_abstract_synonyms":["conformation, Peptidomics, AI461847, Ass-1, CyaY, number, Eukaryotes, Gene, Frataxin, protein, eubacteria, protein-containing complex, 3D structure|small-angle scattering assay, FARR, presence, AI451642, BANK, AA408052, Gene Products, fold, Friedreich Ataxia Protein, Pgi, Bacteriobiota, protein aggregate, Gpi-1, Friedreich, Eubacteria, Gpi-1r, Nlk, Gpi-1s, Phi, FXN Frataxin, Gpi-1t, Eucarya, Monera, Solution, eucaryotes, 3D structure|nuclear magnetic resonance (NMR), Bacteria Woese et al. 2024, ASS, Bacteria (ex Cavalier-Smith 1987), FRDA, Bacteria <bacteria>, Prokaryotae, fungi, Procaryotae, NK/GPI, Gpi, Frataxin Protein, bacteria, Archaebacteria, Archaeobacteria, Eukaryote, Data Set, protein complex, Proteins, Ataxia Protein, Eukaryotas, MF, X25, Amf, results, eukaryotes, Electron Microscopy, count in organism, native protein, 3D structure|any method, mOC-X, Protein, sequence, A530094C12Rik, prokaryotes, NK|GPI, FA, Archebacteria, FXN, Friedreich Ataxia, NK, Org, ORG, 3D structure|electron microscopy, Eukarya, Gpi1-r, Gpi1-s, Gpi1-t, cardinality., primary structure of sequence macromolecule, Protein Gene Products, Gene Proteins, Eukaryotae, 3D structure|x-ray crystallography|angstroms, AVIEF, prokaryote, Archaeon, Eucaryotae, Bglap-rs1, Prokaryota, Gpi1s"],"name_synonyms":["chemical analysis., assay, determination"],"additional_accession":[]},"is_claimable":false,"name":"Thermococcus gammatolerans shotgun analysis","description":"We monitored the Thermococcus gammatolerans proteome dynamics by nanoLC-MS/MS after a 5.0 kGy irradiation. For this, two cell samples were subjected to irradiation (samples 3 & 4) and compared to two others (samples 1 & 2) which were not irradiated.","dates":{"publication":"2014-12-04","submission":"2014-07-17"},"accession":"PXD000402","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:184922","NEWT:6703","NEWT:3555","NEWT:2","NEWT:157546","NEWT:35554","NEWT:38942","NEWT:307972","NEWT:32046","NEWT:544496","NEWT:2102","NEWT:2042546","NEWT:45351","NEWT:43179","NEWT:4513","NEWT:5722","NEWT:1247","NEWT:1129","NEWT:376741","NEWT:55153","NCBITaxon:10407","NEWT:1736309","NEWT:309800","NEWT:281395","NEWT:10360","NEWT:1211601","NEWT:876138","NEWT:47664","NEWT:557436","NEWT:317548","NEWT:3654","NEWT:237561","NEWT:5833","NEWT:6928","NEWT:10036","NEWT:36745","NEWT:498019","NEWT:1351","NEWT:1438992","NEWT:1352","NEWT:2649997","NEWT:272563","NEWT:79220","NEWT:224326","NCBITaxon:79857","NEWT:1096976","NEWT:82688","NEWT:95648","NEWT:3885","NEWT:3888","NEWT:5821","NEWT:1589","NEWT:135622","NCBITaxon:4896","NEWT:6915","NEWT:3649","NEWT:101510","NEWT:28903","NEWT:3880","NEWT:272559","NEWT:28909","NEWT:515849","NEWT:3641","NEWT:383379","NEWT:466585","NEWT:10029","NEWT:913645","NEWT:1000589","NEWT:85963","NEWT:85962","NEWT:143361","NEWT:317447","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:398580","NEWT:4442","NEWT:4565","NEWT:1264690","NEWT:515619","NEWT:31155","NEWT:192875","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:84645","NEWT:626528","NEWT:3347","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:5888","NEWT:211586","NEWT:747078","NEWT:1282","NEWT:1283","NEWT:931281","NEWT:4550","NEWT:1000561","NEWT:294381","NEWT:197","NEWT:1390363","NEWT:77133","NEWT:288705","NEWT:29176","NCBITaxon:79824","NEWT:4787","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:556182","NEWT:1270","NEWT:374990","NEWT:498217","NEWT:156471","NEWT:2242","NEWT:4784","NEWT:11320","NEWT:360106","NEWT:156476","NEWT:286","NEWT:391619","NEWT:360104","NEWT:287","NEWT:246197","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1735272","NEWT:83334","NEWT:83332","NEWT:44685","NEWT:317513","NEWT:1148","NEWT:580240","NEWT:5508","NEWT:294128","NEWT:11676","NEWT:55571","NEWT:35500","NEWT:1140","NEWT:100226","NEWT:4530","NEWT:1143","NEWT:4896","NEWT:75058","NEWT:13616","NEWT:1390","NEWT:1094343","NEWT:1336795","NEWT:172","NEWT:296543","NEWT:316435","NEWT:1773","NEWT:1895","NEWT:1182590","NEWT:3712","NEWT:82380","NEWT:105023","NEWT:866628","NEWT:935293","NEWT:64152","NEWT:4924","NEWT:749200","NEWT:375146","NEWT:990346","NEWT:145953","NEWT:257309","NEWT:100816","NEWT:263","NEWT:230741","NEWT:52283","NEWT:284812","NEWT:8175","NCBITaxon:1313","NEWT:43330","NEWT:980415","NEWT:1603293","NEWT:408169","NEWT:44544","NEWT:47946","NEWT:4911","NEWT:645463","NEWT:3702","NEWT:129249","NEWT:243277","NEWT:990119","NEWT:2850","NEWT:408172","NEWT:227321","NEWT:408170","NEWT:493760","NEWT:106590","NEWT:260710","NEWT:257313","NEWT:400772","NEWT:3708","NEWT:128161","NEWT:332648","NEWT:106592","NEWT:536231","NEWT:46704","NEWT:1436733","NEWT:460519","NEWT:1187947","NEWT:1432138","NEWT:269796","NEWT:10312","NEWT:1424507","NCBITaxon:1773","NEWT:9598","NEWT:8030","NEWT:9483","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:480","NEWT:4909","NEWT:67767","NEWT:759272","NEWT:432359","NEWT:46835","NEWT:1182263","NEWT:109757","NEWT:943146","NEWT:2711","NEWT:300852","NEWT:1502","NEWT:376686","NEWT:95486","NEWT:9103","NEWT:1883446","NEWT:29159","NEWT:253","NEWT:10306","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:8022","NEWT:145943","NCBITaxon:4932","NEWT:595536","NEWT:240906","NEWT:593117","NEWT:89920","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:180923","NEWT:108458","NEWT:272623","NEWT:272624","NEWT:2719099","NEWT:411483","NEWT:884019","NEWT:198215","NEWT:411490","NEWT:983964","NEWT:118499","NEWT:169963","NEWT:32644","NEWT:527796","NEWT:225117","NEWT:746128","NEWT:499175","NEWT:109779","NEWT:43665","NEWT:1266464","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:367830","NEWT:1255228","NEWT:178616","NEWT:649908","NEWT:410289","NEWT:373153","NEWT:375451","NEWT:352472","NEWT:357","NEWT:1071661","NEWT:360094","NEWT:470","NEWT:41364","NEWT:1313","NEWT:411469","NEWT:84023","NEWT:559292","NEWT:39491","NCBITaxon:5811","NEWT:29491","NEWT:411464","NEWT:411460","NEWT:2014887","NEWT:2762","NEWT:1174673","NEWT:1328426","NEWT:562","NEWT:411470","NEWT:33952","NEWT:2094720","NCBITaxon:2697049","NEWT:571256","NEWT:40483","NEWT:28038","NEWT:1663","NEWT:1423","NEWT:4932","NEWT:3603","NEWT:2759","NEWT:3847","NEWT:38293","NEWT:1428","NEWT:327159","NEWT:178876","NEWT:1660","NEWT:327160","NEWT:573","NEWT:9031","NEWT:1872122","NEWT:7091","NEWT:108931","NEWT:241368","NEWT:42528","NEWT:190802","NEWT:9778","NEWT:150475","NEWT:303","NEWT:9417","NEWT:7111","NEWT:347515","NEWT:1216979","NEWT:7237","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:115104","NEWT:1121114","NEWT:663","NEWT:1081927","NEWT:1238993","NEWT:67825","NEWT:185579","NEWT:941442","NEWT:220668","NEWT:13076","NEWT:1821314","NEWT:1249668","NEWT:7108","NEWT:317","NEWT:1808362","NEWT:5286","NEWT:7227","NEWT:7469","NEWT:885318",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