{"database":"PeptideAtlas","file_versions":[],"scores":null,"additional":{"submitter":["Michael J. Comb"],"disease":["Non-small Cell Lung Carcinoma"],"software":["TPP"],"full_dataset_link":["'https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ManageTable.cgi?TABLE_NAME=AT_sample&sample_id=6595'"],"synonyms":[""],"submitter_email":["","mcomb@cellsignal.com"],"tissue":["Lung"],"repository":["PeptideAtlas"],"sample_protocol":[""],"data_protocol":[""],"omics_type":["Proteomics"],"pubmed":[""],"instrument_platform":["LTQ Orbitrap"],"project_tag":[""],"species":["Homo Sapiens (human)"],"publication":[""],"cell_type":["H520; H838; H1437; H1563; H1568; H1792; H1944; H2170; H2172; HCC827; H2228; H2347; A549; H441; H1703; H1373; H358; H1993; Calu-3; H1648; H1975; H1666; H1869; H1650; H1734; H1793; H2023; H661; H2444; H1299; H1693; H226; H1623; H1651; H460; H2122; SKMES-1; HCC78; Cal-12T; HCC366; HCC15; HCC44; LOU-NH91."],"pubmed_abstract":["Data analysis and interpretation remain major logistical challenges when attempting to identify large numbers of protein phosphorylation sites by nanoscale reverse-phase liquid chromatography/tandem mass spectrometry (LC-MS/MS) (Supplementary Figure 1 online). In this report we address challenges that are often only addressable by laborious manual validation, including data set error, data set sensitivity and phosphorylation site localization. We provide a large-scale phosphorylation data set with a measured error rate as determined by the target-decoy approach, we demonstrate an approach to maximize data set sensitivity by efficiently distracting incorrect peptide spectral matches (PSMs), and we present a probability-based score, the Ascore, that measures the probability of correct phosphorylation site localization based on the presence and intensity of site-determining ions in MS/MS spectra. We applied our methods in a fully automated fashion to nocodazole-arrested HeLa cell lysate where we identified 1,761 nonredundant phosphorylation sites from 491 proteins with a peptide false-positive rate of 1.3%."],"pubmed_title":["A probability-based approach for high-throughput protein phosphorylation analysis and site localization."],"pubmed_authors":["Beausoleil Sean A SA, Villén Judit J, Gerber Scott A SA, Rush John J, Gygi Steven P SP"],"additional_accession":[]},"is_claimable":false,"name":"Hs_heLa_phospho_Orbi","description":"Hs_heLa_phospho_Orbi","dates":{"publication":"2006-12-31","export":"2016-03-29"},"accession":"PAe005322","cross_references":{"pubmed":["16964243"],"UniProt":["A0A024R8H9","A0A024RC46","A0A0A0MR66","A0A0A0MSA7","A0FGR8","A0FGR8-2","A0FGR8-6","A2RRP1","A5A3E0","A6NL93","A8CG34","A9IYQ1","B3KML9","B3KW93","B4DHB3","B4DKM5","B4DY08","B4E3A4","B7Z2G3","B7ZME8","E5RJU9","E7EVA0","E7EX29","E9PAV3","E9PN48","F8VRH0","F8VV04","G5E972","G8JLB6","H0Y2V6","H0YAC7","H0YBJ8","H0YFY6","H0YJH7","H0YM50","H3BS72","H7BXH2","H7BY16","H7BZ94","H7BZL0","I3L4N8","J3QR07","J9JID7","O00161","O00193","O00203","O00264","O00299","O00483","O00505","O00559","O00566","O00567","O14497","O14617","O14617-2","O14617-5","O14646","O14686","O14715","O14745","O14828","O14874","O14979","O15014","O15027","O15027-5","O15155","O15164","O15173","O15258","O15372","O15400","O15403","O15440","O43159","O43166","O43237","O43242","O43290","O43390","O43395","O43399","O43432","O43432-3","O43491","O43491-4","O43583","O43719","O43818","O43823","O43852","O43933","O60220","O60238","O60264","O60315","O60488","O60499","O60583","O60763","O60763-2","O60784","O60812","O60832","O60841","O75030","O75122","O75152","O75306","O75351","O75376","O75379","O75382","O75390","O75396","O75400","O75400-3","O75446","O75448","O75475","O75475-2","O75475-3","O75531","O75533","O75643","O75691","O75694","O75821","O75822","O75822-3","O75976","O76021","O94762","O94776","O94804","O94806","O94826","O94887","O94925","O94925-3","O95218","O95218-2","O95232","O95251","O95365","O95400","O95453","O95562","O95573","O95639","O95674","O95714","O95782","O95782-2","O95785","O95785-3","P00558","P01892","P01893","P02545","P02545-2","P02545-3","P02786","P04350","P04406","P04439","P04920","P05023","P05114","P05386","P05386-2","P05387","P05388","P05455","P06239","P06241","P06241-2","P06400","P06493","P06733","P06748","P06748-2","P06748-3","P07195","P07237","P07355","P07437","P07814","P07900","P07910","P07910-3","P07919","P07947","P08238","P08240","P08559","P08581","P08621","P08651","P08651-5","P08670","P09234","P09651","P09651-2","P0CG38","P0CG39","P0DMV8","P10321","P10412","P10606","P10636","P10644","P10809","P11021","P11142","P11171","P11388","P11717","P12270","P12694","P12931","P13010","P13051","P13051-2","P13637","P13667","P13861","P13995","P14314","P14314-2","P14406","P14625","P14854","P14866","P16070","P16188","P16401","P16403","P16949","P16989","P16989-2","P17029","P17066","P17096","P17096-2","P17275","P17535","P17661","P17812","P18124","P18583","P18583-3","P18583-6","P18887","P19338","P19532","P19634","P20020","P20336","P21127","P21359","P21796","P22059","P22087","P22234","P22626","P22626-2","P23193","P23246","P23396","P23434","P23497","P23497-4","P23588","P24534","P24928","P24941","P25440","P25705","P25788","P26358","P26358-2","P26373","P26599","P26599-3","P27635","P27816","P27816-4","P27816-5","P27824","P28290","P28370","P28370-2","P28482","P29590","P29590-14","P29590-2","P29590-3","P29590-4","P29590-9","P29692","P29692-2","P29692-3","P29692-4","P29803","P29966","P30419","P30450","P30464","P30512","P31942","P31943","P31946","P32004-3","P34931","P34932","P35222","P35232","P35251","P35268","P35269","P35579","P35580","P35580-4","P35606","P35611","P35611-4","P35658","P35659","P36578","P36871","P36871-2","P38159","P38646","P39023","P39880","P40222","P40818","P40855","P40939","P40967","P41208","P42166","P42167","P42167-2","P42566","P42694","P42695","P42696","P42704","P43007","P43243","P43243-2","P43307","P45880","P45973","P46013","P46087","P46100","P46100-6","P46379","P46379-3","P46379-4","P46783","P47712","P48634","P49006","P49736","P49756","P49792","P49810","P49840","P49841","P49916","P50402","P50502","P50548","P50993","P51116","P51149","P51397","P51531","P51532","P51608","P51608-2","P51610","P51610-4","P51858","P51858-2","P51991","P51991-2","P52292","P52701","P52756","P52948","P53621","P53985","P54098","P54105","P54198","P54652","P54727","P55081","P55197","P55199","P55265","P55265-3","P55795","P56182","P56693","P60174","P60468","P60709","P61006","P61019","P61106","P61244","P61244-2","P61978","P61978-3","P61981","P62241","P62258","P62269","P62316","P62318","P62736","P62805","P62820","P62937","P62995","P63027","P63104","P63165","P63241","P63261","P63267","P67809","P68032","P68104","P68133","P68363","P68366","P68371","P78316","P78332","P78344","P78344-2","P78527","P78536","P82094","P84098","P84103","P84157","P84157-2","P85037","P98082","P98082-3","P98175","Q00341","Q00526","Q00610","Q00610-2","Q00839","Q00839-2","Q01082","Q01082-3","Q01130","Q01167","Q01664","Q01804","Q01814","Q01850","Q02241","Q02241-3","Q02880","Q02880-2","Q03060","Q03252","Q03701","Q04671","Q05519","Q05519-2","Q05639","Q05655","Q06265","Q07000","Q07020","Q07666","Q07666-2","Q08170","Q08211","Q08945","Q09161","Q09666","Q09666-2","Q0JRZ9","Q12767","Q12769","Q12789","Q12846","Q12873","Q12888","Q12888-3","Q12906","Q12929","Q12959","Q12982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