searchindex.js

Search.setIndex({docnames:["analysis_results","index","tools","tutorials/clustering_basics","tutorials/proteome_discoverer","tutorials/unidentified_analysis"],envversion:53,filenames:["analysis_results.rst","index.rst","tools.rst","tutorials/clustering_basics.rst","tutorials/proteome_discoverer.rst","tutorials/unidentified_analysis.rst"],objects:{},objnames:{},objtypes:{},terms:{"10ac":5,"26947f51":5,"453f":5,"47c2":5,"4e0d":5,"4rjx":4,"65c512126868":5,"7f1f53d3":5,"981a5e9724a8":5,"case":[4,5],"default":[3,4],"export":[0,1,4],"final":4,"function":[2,4,5],"goto":4,"import":[3,4,5],"new":[2,3,4,5],Adding:5,For:[1,3,4],Its:4,The:[0,1,2,3,4,5],These:5,Use:3,Using:1,a7ca521ad257:5,a97d:5,abl:[0,3],abov:[3,4],abund:4,academi:1,accross:4,accuraci:4,actual:[2,3],adapt:[3,4],add:[3,4],added:4,adding:3,addit:4,addition:4,adjust:4,advanc:4,af18:5,after:[3,4],again:3,algorithm:[1,3,4],all:[0,2,3,4,5],allow:2,alon:4,alreadi:5,also:[0,3,4],alwai:[2,4],amanda:4,analaysi:2,analys:[1,2],analysi:[1,3,4,5],ani:[3,4,5],annot:3,api:2,approach:3,appropri:[3,4],apquant:4,around:1,assess:4,assum:3,automat:4,avail:[0,4],averag:4,avg:4,b33d:5,base:[1,2,4,5],behaviour:4,being:4,below:[4,5],benchmark:4,best:4,binari:5,bold:4,bottom:4,brim:4,build:1,built:4,call:5,can:[0,1,3,4,5],cannot:3,center:1,chang:4,character:4,characteris:5,chemistri:4,choic:3,cli:[2,3],click:[3,4,5],clone:5,cluster:1,cluster_features_cli:5,cluster_id:5,cmd:3,code:2,collect:[0,4],column:[4,5],com:[4,5],combin:3,command:[2,3,5],commerci:4,compar:2,comparison:4,compat:2,complet:4,compon:[4,5],comput:3,concis:4,condens:4,configur:3,consensu:[0,4],consid:4,consist:4,contain:[0,2,3,4,5],control:4,convert:[0,3],copi:3,core:2,correct:4,correctli:3,count:[4,5],creat:[0,3,4],current:[2,3,4,5],d5bn:4,dai:4,data:[1,2,4],dataset:[3,4],date:3,decoi:3,decoy_str:3,decreas:4,defin:4,degre:4,demo:4,depend:3,deprec:4,deriv:4,descritpt:0,design:4,detail:0,determin:4,develop:1,did:4,differ:[2,4],dir:5,directli:0,directori:3,disabl:4,discover:[0,1,2,3],document:3,doe:4,done:[3,5],doubl:3,down:4,download:[3,4,5],dure:4,each:[4,5],easiest:[3,5],easili:[0,4],effect:[2,4],empti:4,enabl:[3,4],engin:[3,4],enter:3,estim:4,everi:[3,4],exampl:[2,3,4,5],excel:0,exe:3,execut:[3,5],exist:2,expect:4,experi:4,explain:[3,5],extract:[0,3,5],f0f44a3f:5,facil:4,facilit:1,factor:4,fast:4,fdr:[3,4],featur:4,field:4,file:[0,2,3,4,5],filenam:[3,4,5],fill:5,filter:[3,4],find:4,first:[3,5],fit:5,fix:4,flexnetoper:4,focus:2,folder:[3,5],follow:[3,4,5],forget:3,format:[0,2,3],found:[0,4],four:2,fragment:[3,4],free:1,freeli:4,frequenc:4,from:[0,1,3,4],fulli:[2,4],further:4,gave:4,gener:[3,4],get:3,github:5,good:4,graphic:2,greatli:4,griss:1,group:4,gui:[2,3],had:4,hadoop:2,hardward:4,has:[3,4],have:[1,3,4],header:5,help:1,here:3,high:4,higher:4,how:[1,5],http:[0,1,4,5],icon:4,idea:4,identif:[1,4,5],identifi:4,ids:5,ignor:4,immedi:[2,4],imp:4,implement:2,importantli:0,improv:4,includ:4,incorrectli:4,increas:4,indefinit:4,independ:4,index:4,infer:4,inform:[3,4],input:[3,4,5],instal:[1,3],instead:4,instruct:[1,5],instrument:4,integr:[3,4],interfac:[2,4],invers:4,ion:[3,4],isobar:4,its:4,itself:4,j3h0:4,jar:3,java:[2,3],job:3,kei:[3,4],label:[3,4],lack:4,larg:4,larger:4,latest:[2,3],lead:4,least:4,left:[3,4],legaci:4,less:4,let:3,librari:0,licenc:4,like:3,limit:4,line:[2,3,5],link:3,list:[3,4],load:0,longer:4,look:[1,3,4],low:4,lower:4,mai:5,main:4,major:[3,4],mani:3,map:3,mark:4,master:5,match:4,max:4,maximum:4,mean:4,measur:4,memori:4,merg:1,method:[1,2],mgf:[3,5],mgf_search_result_annot:3,middl:4,million:1,minimum:4,mode:4,molecul:4,more:[3,4],most:[0,3,4],ms2:4,ms_data:3,msamanda:3,msconvert:3,msgf:3,msp:0,must:[3,5],my_clustering_result:5,my_installation_directori:5,my_result_dir:5,mz_150:4,mz_200:4,mzid:3,mzidentml:3,name:[3,5],nat:1,navig:[3,5],nearli:4,necessari:[2,4],need:[3,4,5],never:4,nevertheless:4,newli:1,next:[3,5],node:[0,1,2,3,5],non:4,note:[3,5],now:[3,5],number:[4,5],observ:4,offer:4,onc:3,one:4,onli:[2,4,5],open:[3,5],option:[3,4],org:[1,4,5],origin:4,other:[3,4,5],otherwis:3,our:[1,2,3,4,5],out:3,output:[3,5],outputfil:3,over:4,own:[1,4],p8tb:4,packag:5,parallel:4,paramet:4,paramter:4,pars:5,part:[3,4],pc1:5,pc2:5,peak:[3,4],peptid:4,per:[4,5],percol:4,perfectli:4,perform:[2,4],php:4,pick:3,pip3:5,pipelin:[3,4],pleas:3,plot:5,portal:4,possibl:4,post:1,power:4,prcomp:5,pre:[4,5],precis:4,precursor:[3,4],prepar:1,prerequesit:5,present:[3,4],press:3,pride:1,princip:5,prinicapl:5,prior:4,process:[0,1,2,4],produc:2,product:4,project:0,prompt:5,proport:4,protein:4,proteom:[0,1,2,3],proteowizard:3,provid:[1,2,4],psm:4,publish:4,puriti:4,purpos:4,pypa:5,python3:5,python:[2,5],quantit:[4,5],question:1,rather:4,raw:3,read:[2,5],reader:2,readi:2,readthedoc:0,recommend:4,refer:5,regist:4,releas:[1,3],remain:4,remov:[3,4],replic:4,report:[3,4],repositori:4,repres:4,requir:4,requisit:5,resolut:4,resourc:1,respect:4,result:[1,2,3],retriev:5,right:4,rotat:5,rough:4,round:4,row:[4,5],run:[1,4,5],same:4,sampl:[1,4],sample_1:[3,5],sample_1_annot:3,sample_2:[3,5],sample_3:[3,5],save:3,scaffold:3,scarc:4,score:4,screen:3,search:[1,4],second:4,see:[3,4],select:[3,4,5],selector:4,sep:5,sequenc:4,set:[1,5],setup:[4,5],sever:[2,4],should:[2,3,4,5],show:[4,5],shown:4,side:4,sign:4,similar:[2,3,4],similarii:4,simplest:1,simpli:[1,3,4,5],sinc:4,singl:[2,4],size:4,slow:4,small:4,smaller:4,softwar:1,some:[4,5],sp1:4,spectra:[0,1,2,3],spectral:[0,4,5],spectrum:[1,2,4],speed:4,split:4,stabl:5,stage:2,standard:0,start:4,statist:4,step:[1,3,4],still:4,store:0,subsequ:[0,4,5],summari:4,support:[0,2,3,4],system:5,tabl:[0,4,5],taken:4,tandem:3,target:4,test:2,text:5,than:4,thei:4,them:5,therebi:[0,4],therefor:[2,4],thermo:4,thermosoftwar:4,thi:[0,2,3,4,5],thread:4,through:[1,4],time:4,toler:[3,4],tool:[0,1,3,4,5],toolsuit:[0,1,2,3],total:4,tutori:[1,3,5],two:3,txt:5,type:3,under:4,unidentifi:4,unix:5,usag:1,use:[1,2,3,4,5],used:[0,1,2,3,4],user:[2,3],uses:0,using:[1,3,4],valid:4,valu:[3,4,5],varieti:[0,4],vast:[3,4],veri:4,verifi:4,version:[1,2,3,5],view:4,visibl:4,wai:[1,4,5],well:[2,4],were:4,when:4,where:[3,5],which:[1,2,3],whole:4,wide:4,window:3,within:4,without:5,work:3,workflow:4,would:3,written:5,www:[4,5],xml:3,yes:3,you:[3,4,5],your:[1,4,5],zero:5,zip:[3,5],zipbal:5},titles:["Analysing clustering results","Welcome","Clustering tools / software","How to cluster MS/MS data","Proteome Discoverer Tutorial","Analysing proteomics samples using spectrum clustering"],titleterms:{"export":5,Using:[4,5],algorithm:2,analys:[0,5],cluster:[0,2,3,4,5],content:1,data:[3,5],develop:2,discover:[4,5],featur:5,free:4,from:5,get:1,how:3,identif:3,instal:[4,5],installt:5,launch:3,manual:5,merg:3,node:4,overview:[4,5],own:2,pip:5,prepar:3,process:5,proteom:[4,5],result:[0,4,5],run:3,sampl:5,search:3,set:[3,4],softwar:2,spectra:[4,5],spectrum:5,start:1,tool:2,toolchain:5,tutori:4,using:5,version:4,welcom:1,your:3}})