PeptideAtlasapplication/xmlftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Yeast/PAe000093/PAe000093_428_searchdatabase_tandem.fastaftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Yeast/PAe000093/PAe000093_mzXML_201104201631.tar.gzftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Yeast/PAe000093/PAe000093_428_searchdatabase_spectrast.splibftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Yeast/PAe000093/PAe000093_prot_428_201104201641.propertiesftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Yeast/PAe000093/PAe000093_428_tandem.paramsftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Yeast/PAe000093/PAe000093_READMEftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Yeast/PAe000093/PAe000093_428_search.params.tar.gzftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Yeast/PAe000093/PAe000093_prot_428_201104201641.tar.gzftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Yeast/PAe000093/PAe000093_Search_Results_428_201104201639.propertiesftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Yeast/PAe000093/PAe000093_428_spectrast.paramsftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Yeast/PAe000093/PAe000093_mzXML_201104201631.propertiesftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Yeast/PAe000093/PAe000093_Search_Results_428_201104201639.tar.gzprimaryOK200Mark FloryTPP'https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ManageTable.cgi?TABLE_NAME=AT_sample&sample_id=100'mflory@wesleyan.eduPeptideAtlasProteomicsLTQSaccharomyces Cerevisiae (yeast)Understanding how proteins and their complex interaction networks convert the genomic information into a dynamic living organism is a fundamental challenge in biological sciences. As an important step towards understanding the systems biology of a complex eukaryote, we cataloged 63% of the predicted Drosophila melanogaster proteome by detecting 9,124 proteins from 498,000 redundant and 72,281 distinct peptide identifications. This unprecedented high proteome coverage for a complex eukaryote was achieved by combining sample diversity, multidimensional biochemical fractionation and analysis-driven experimentation feedback loops, whereby data collection is guided by statistical analysis of prior data. We show that high-quality proteomics data provide crucial information to amend genome annotation and to confirm many predicted gene models. We also present experimentally identified proteotypic peptides matching approximately 50% of D. melanogaster gene models. This library of proteotypic peptides should enable fast, targeted and quantitative proteomic studies to elucidate the systems biology of this model organism.A high-quality catalog of the Drosophila melanogaster proteome.Brunner Erich E, Ahrens Christian H CH, Mohanty Sonali S, Baetschmann Hansruedi H, Loevenich Sandra S, Potthast Frank F, Deutsch Eric W EW, Panse Christian C, de Lichtenberg Ulrik U, Rinner Oliver O, Lee Hookeun H, Pedrioli Patrick G A PG, Malmstrom Johan J, Koehler Katja K, Schrimpf Sabine S, Krijgsveld Jeroen J, Kregenow Floyd F, Heck Albert J R AJ, Hafen Ernst E, Schlapbach Ralph R, Aebersold Ruedi RfalseT00yeast cell-cycle experiment2007-12-312016-03-29PAe000093YAL003WYAL005CYAL007CYAL012WYAL023CYAL035WYAL036CYAL038WYAR002C-AYBL004WYBL007CYBL015WYBL016WYBL023CYBL024WYBL030CYBL039CYBL045CYBL047CYBL050WYBL059C-AYBL072CYBL076CYBL087CYBR015CYBR017CYBR025CYBR031WYBR034CYBR048WYBR078WYBR082CYBR084WYBR088CYBR092CYBR096WYBR101CYBR115CYBR118WYBR121CYBR126CYBR127CYBR143CYBR149WYBR159WYBR162CYBR169CYBR196CYBR198CYBR218CYBR234CYBR244WYBR245CYBR247CYBR248CYBR249CYBR263WYBR265WYBR283CYBR286WYCL009CYCL017CYCL030CYCL040WYCL050CYCL059CYCL064CYCR012WYCR020W-BYCR051WYDL014WYDL022WYDL029WYDL040CYDL055CYDL061CYDL063CYDL084WYDL097CYDL100CYDL108WYDL126CYDL134CYDL136WYDL140CYDL143WYDL144CYDL145CYDL164CYDL170WYDL171CYDL185WYDL188CYDL190CYDL195WYDL201WYDL229WYDR002WYDR023WYDR037WYDR038CYDR045CYDR050CYDR064WYDR074WYDR091CYDR101CYDR119WYDR121WYDR127WYDR129CYDR158WYDR170CYDR172WYDR188WYDR190CYDR211WYDR226WYDR233CYDR238CYDR243CYDR251WYDR294CYDR324CYDR333CYDR341CYDR346CYDR353WYDR361CYDR368WYDR380WYDR385WYDR399WYDR418WYDR429CYDR447CYDR450WYDR454CYDR476CYDR483WYDR496CYDR502CYDR508CYDR529CYEL020W-AYEL026WYEL031WYEL034WYEL037CYEL040WYEL046CYEL047CYEL053CYEL071WYER001WYER006WYER009WYER023WYER025WYER036CYER043CYER052CYER055CYER056C-AYER057CYER062CYER070WYER089CYER091CYER103WYER110CYER133WYER155CYER156CYER165WYER178WYFL007WYFL037WYFL039CYFL045CYFR006WYFR010WYFR028CYFR037CYGL001CYGL008CYGL009CYGL011CYGL026CYGL031CYGL049CYGL062WYGL070CYGL097WYGL099WYGL105WYGL120CYGL122CYGL133WYGL135WYGL137WYGL147CYGL148WYGL150CYGL155WYGL167CYGL173CYGL195WYGL200CYGL202WYGL206CYGL207WYGL211WYGL234WYGL244WYGL245WYGL252CYGL253WYGR032WYGR040WYGR054WYGR060WYGR061CYGR090WYGR094WYGR103WYGR109W-AYGR116WYGR118WYGR124WYGR128CYGR145WYGR148CYGR158CYGR162WYGR173WYGR175CYGR180CYGR184CYGR192CYGR204WYGR207CYGR211WYGR214WYGR234WYGR240CYGR253CYGR254WYGR256WYGR264CYGR279CYGR285CYHL034CYHL039WYHR003CYHR005C-AYHR008CYHR019CYHR020WYHR025WYHR027CYHR030CYHR039CYHR042WYHR049WYHR051WYHR052WYHR064CYHR065CYHR068WYHR072WYHR089CYHR106WYHR112CYHR128WYHR137WYHR174WYHR183WYHR190WYHR196WYHR197WYHR208WYIL021WYIL030CYIL053WYIL075CYIL078WYIL094CYIL109CYIL125WYIL142WYIR012WYJL008CYJL014WYJL026WYJL034WYJL052WYJL080CYJL109CYJL111WYJL121CYJL130CYJL136CYJL138CYJL140WYJL145WYJL166WYJL167WYJL186WYJL190CYJL200CYJR007WYJR009CYJR016CYJR063WYJR064WYJR070CYJR077CYJR104CYJR109CYJR123WYJR144WYJR148WYKL006WYKL009WYKL018WYKL021CYKL029CYKL033W-AYKL035WYKL056CYKL060CYKL081WYKL113CYKL114CYKL127WYKL130CYKL135CYKL145WYKL150WYKL181WYKL182WYKL210WYKL216WYKR002WYKR014CYKR042WYKR048CYKR081CYKR082WYLL010CYLL018CYLL024CYLL050CYLR019WYLR022CYLR027CYLR028CYLR038CYLR044CYLR050CYLR060WYLR075WYLR089CYLR090WYLR109WYLR113WYLR134WYLR153CYLR167WYLR175WYLR179CYLR180WYLR186WYLR197WYLR199CYLR216CYLR243WYLR244CYLR249WYLR293CYLR300WYLR303WYLR304CYLR314CYLR342WYLR347CYLR355CYLR384CYLR388WYLR390W-AYLR398CYLR401CYLR413WYLR420WYLR432WYLR440CYLR441CYLR447CYML008CYML028WYML052WYML056CYML070WYML072CYML085CYML086CYML105CYML123CYML124CYML125CYML126CYMR012WYMR015CYMR038CYMR058WYMR079WYMR080CYMR083WYMR092CYMR093WYMR099CYMR105CYMR116CYMR120CYMR146CYMR186WYMR202WYMR203WYMR205CYMR208WYMR212CYMR215WYMR217WYMR220WYMR229CYMR235CYMR242CYMR246WYMR290CYMR295CYMR297WYMR307WYMR314WYMR315WYNL010WYNL035CYNL036WYNL055CYNL061WYNL064CYNL096CYNL112WYNL113WYNL131WYNL132WYNL134CYNL135CYNL137CYNL138WYNL141WYNL156CYNL175CYNL178WYNL182CYNL189WYNL232WYNL236WYNL244CYNL247WYNL255CYNL280CYNL287WYNL288WYNL292WYNL301CYNL302CYNR016CYNR043WYNR046WYOL022CYOL040CYOL049WYOL058WYOL061WYOL064CYOL077CYOL086CYOL097CYOL140WYOL151WYOR007CYOR027WYOR039WYOR046CYOR063WYOR065WYOR074CYOR095CYOR096WYOR099WYOR108WYOR116CYOR128CYOR136WYOR142WYOR151CYOR153WYOR157CYOR202WYOR204WYOR209CYOR221CYOR230WYOR239WYOR243CYOR259CYOR261CYOR267CYOR271CYOR272WYOR276WYOR293WYOR303WYOR304WYOR323CYOR335CYOR341WYOR347CYOR356WYOR361CYOR362CYOR374WYOR375CYPL001WYPL012WYPL028WYPL032CYPL061WYPL091WYPL093WYPL106CYPL111WYPL119CYPL131WYPL145CYPL154CYPL160WYPL169CYPL208WYPL212CYPL226WYPL231WYPL237WYPL239WYPL243WYPL260WYPL262WYPL263CYPR010CYPR020WYPR024WYPR035WYPR036WYPR062WYPR063CYPR081CYPR086WYPR108WYPR110CYPR145WYPR165WYPR181CYPR183W17450130P06208-2P07263-2P38431-2R0020C4932