代谢组学软件：XCMS-usermanual

Allscreenshotstakenfromv.1.22.01.Page1LastUpdate:30AUG2012XCMSOnlineUsageInstructionsOverviewXCMSOnlineisaninnovativeplatformwithanintuitivegraphicalinterfacewhichallowsuserstoeasilyuploadandprocessLC/MSdataforuntargetedmetabolomicsprofiling.XCMSOnlineprovidesacompletemetabolomicsworkflowincludingfeaturedetection,retentiontimecorrection,alignment,annotationandstatisticalanalysis.Tofacilitatetheusage,predefinedparametersetsfordifferentinstrumentsetups(e.g.HPLC/QTOF,UPLC/QTOF,HPLC/Orbitrap)canbeselected.Customizedsettingscanbecreatedfromthesetemplates.Resultscanbebrowsedonlineinaninteractive,customizabletablethatshowsfeaturestatistics,EICs,boxplots,andputativeMETLINID’sforeachmetabolite.Allresultsincludingtheimagesmayalsobedownloadedasazipfileforofflineanalysis.Youwillneedauseraccounttousethesystemhoweveruseraccountsarefreeandonlyrequireavalide-mailaddresstoregister.ToprocessdatasetsusingXCMSOnlineyouwillneedtocreateajobwhichinvolvesuploadingthedatasets,definingparametersandsubmittingthejob.Youwillbenotifiedofyourjobstatus,includingerrors/warningsthatyoucancorrectpriortoresubmittingajob.Afterprocessingiscomplete,youwillbenotifiedviae-mailthatyourresultsarereadyforreview.Allscreenshotstakenfromv.1.22.01.Page2TableofContentsQuickStartGuide3UploadingDatasets5DefineParameters8ViewResults11AccountAdministration14DatasetAdministration15JobSharing17PublicShares18ResubmittingJobs19JavaWarningDialogScreenshotAppendixACustomParameterCreationAppendixBAllscreenshotstakenfromv.1.22.01.Page3QuickStart1.CreateUserAccount–Youwillinitiallyneedtoregisteryoure-mailaccounttobeabletousethesystem.Afteryouregisteryouwillreceiveane-mailattheaccountyouenteredwithvalidationinstructions.Uponvalidationyouwillhaveaccesstothesystem.Youmaythenloginusingtheusernameandpasswordcombinationyouusedtoregister.Figure1–Createuseraccountfromhomepagebyclickingonthe“Register”buttonAllscreenshotstakenfromv.1.22.01.Page42.CreateJob–Asafirst-timeuser,youwillwanttobeginbycreatinganewjob.Clickon“CreateJob”inthetopnavigationmenu(Figure2)Figure2–CreateNewJobbyclickingon“CreateJob”inthetopnavigationmenuAllscreenshotstakenfromv.1.22.01.Page53.UploadingtheDatasets-Thecreatejobpagewillopenandyouwillbeabletostartdefiningthejob(seeFigure3).Thereisastepnavigationwizarddirectlybelowthetopnavigationbarthatwillserveasaguide.Uponinitialload,adefaultjobnamewillbecreatedbasedonyourusernameandthecurrentdate.Youmayclickthejobnametoedit.UploadDataset1Initiallyyouwillneedtouploadadataset.Dataset1(left-handside)isoftendefinedasthecontroldataset.a)Clickthe“UploadDataset”buttontoinitiateanupload.Aseparatewindowwillopen.ThiswillloadtheJavamodulewhichisrequiredforlargeuploads.Evenifyoureceiveawarning(seeAppendix–FigureA1),click“Run”.Aftertheappletruns,youwillbepresentedwithanuploaddialogbox(seeFigure4).Figure3–InitialjobcreationpageStepNavigationWizardClickjobnametoeditUploadDatasetAllscreenshotstakenfromv.1.22.01.Page6b)Selectfiles/folderstobeincludedinthedatasetfromthefiletree(Figure4).Individualfileswillappearinthefilelistasyounavigatethefiletree.Afteryoulocatethefilesforthisdataset,dragthemtothe“DropFilesHere”area(lower-right)andtheywillimmediatelystartcompressing.Alternativelyyoucanclickthe“+”symbol(see“AddFiles”inFigure4)toselectthefilesyouwanttoinclude.Whenyouaresatisfiedallfilesareincludedinthisdataset,youmaypressthe“Upload”buttontostarttheupload.Youmayneedtomaximizewindowsizeorusescrollbarstodisplayalltext.Theanimatedlineunderafileorfolderappearsduringfilezipping.Youmayneedtowaituntilzippingfinishespriortoclickingtheuploadbutton.Note:ValidfilesthesystemcanacceptincludemzXML,mzData,mzData.XML,netCDF,wiff(ABSCIEX),CDFandfolderswith“.d”extension(Agilent)atpresent.Additionalformatsmaybeincludedinfutureversions.c)DependingonthespeedofyourInternetconnection,youmaychoosetocontinuewiththejobsetup.Atthispointyoucanminimizetheuploadinprogressandcontinue.Alternativelyyoucandragtheuploaddialogboxtoanotherpartofthescreensoyoucanaccessthemaincreatejobpage.Simplyusetheminimizebutton(singlebar)intheupperright-handcornerofthewindow(SeeFigure4).Note:minimizebuttonmaybedifferentdependingonoperatingsystem.Note:Ifyouclosethedialogbox,youwillneedtostartagain.Figure4–UploadDatasetDialogFileTreeFileListAddFiles(Dragtothisbox)Minimize“Detail”ViewAllscreenshotstakenfromv.1.22.01.Page7UploadDataset2Atthispoint,youcanrepeatstepnumber3tobegintheseconddatasetupload.TheDataset2sectioncanbefoundtotherightoftheDataset1section.Note:Youmusthaveuniquenamesforeachdataset(eveniftheidisdifferent).Youcanmodifythedatasetnamesafteranuploadhasstartedbyclickingthe“Edit”buttontotherightoftherespectivedatasetname(Figure5).Figure5–ScreenafteruploadsarecompleteModifyDatasetnameDefineParametersAllscreenshotstakenfromv.1.22.01.Page84.SelectParameterSet-Afteruploadsaredefined(stillinprogressorcomplete),youhavetodefinetheparametersthatcorrespondtothisjob.Sometemplateparametersets(e.g.HPLC/TOF,UPLC/TOF,HPLC/OrbiTrap)havebeenpredefined.Youcansimplyselectoneofthosepredefinedparametersetsorcustomizethemtoyourparticularneeds.T