https://sage-docs.vercel.app/_next/static/chunks/pages/docs/results/search-03fd44c77429fa9a.js

1(self.webpackChunk_N_E=self.webpackChunk_N_E||[]).push([[187],{5619:function(e,d,s){(window.__NEXT_P=window.__NEXT_P||[]).push(["/docs/results/search",function(){return s(9228)}])},9228:function(e,d,s){"use strict";s.r(d),s.d(d,{__toc:function(){return n}});var r=s(5893),t=s(2673),i=s(2643);let n=[{depth:1,value:"Search Results",id:"search-results"}];function c(e){let d=Object.assign({h1:"h1",p:"p",code:"code",table:"table",thead:"thead",tr:"tr",th:"th",tbody:"tbody",td:"td"},(0,i.a)(),e.components);return(0,r.jsxs)(r.Fragment,{children:[(0,r.jsx)(d.h1,{id:"search-results",children:"Search Results"}),"\n",(0,r.jsxs)(d.p,{children:["Search results can be found in the ",(0,r.jsx)(d.code,{children:"results.sage.tsv"})," file. The table below describes the columns that are present in this file."]}),"\n",(0,r.jsxs)(d.table,{children:[(0,r.jsx)(d.thead,{children:(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.th,{children:"Header"}),(0,r.jsx)(d.th,{children:"Description"})]})}),(0,r.jsxs)(d.tbody,{children:[(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"peptide"})}),(0,r.jsx)(d.td,{children:"Peptide sequence, including modifications in ProForma format (e.g., NC[+57.021]HKGSFK)."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"proteins"})}),(0,r.jsx)(d.td,{children:"Semicolon-delimited list of proteins matching the peptide sequence."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"num_proteins"})}),(0,r.jsx)(d.td,{children:"Number of proteins matching the peptide sequence."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"filename"})}),(0,r.jsx)(d.td,{children:"File containing this PSM"})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"scannr"})}),(0,r.jsx)(d.td,{children:"Spectrum identifier from mzML file."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"rank"})}),(0,r.jsxs)(d.td,{children:["Rank of the PSM. If ",(0,r.jsx)(d.code,{children:"report_psms > 1"}),", then the best match will have rank = 1, the second best match will have rank = 2, etc."]})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"label"})}),(0,r.jsx)(d.td,{children:"Target/Decoy label (-1: decoy, 1: target)."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"expmass"})}),(0,r.jsx)(d.td,{children:"Experimental mass of the peptide."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"calcmass"})}),(0,r.jsx)(d.td,{children:"Calculated mass of the peptide."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"charge"})}),(0,r.jsx)(d.td,{children:"Reported precursor charge."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"pepide_len"})}),(0,r.jsx)(d.td,{children:"Length of the peptide sequence."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"missed_cleavages"})}),(0,r.jsx)(d.td,{children:"Number of missed cleavages."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"isotope_error"})}),(0,r.jsx)(d.td,{children:"C13 isotope error."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"precursor_ppm"})}),(0,r.jsx)(d.td,{children:"Difference between experimental mass and calculated mass, reported in parts-per-million."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"fragment_ppm"})}),(0,r.jsx)(d.td,{children:"Average parts-per-million (delta mass) for matched fragment ions compared to theoretical ions."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"hyperscore"})}),(0,r.jsx)(d.td,{children:"X!Tandem hyperscore for the PSM."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"delta_next"})}),(0,r.jsx)(d.td,{children:"Difference between the hyperscore of this candidate and the next best candidate."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"delta_bext"})}),(0,r.jsx)(d.td,{children:"Difference between the hyperscore of the best candidate (rank=1) and this candidate."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"rt"})}),(0,r.jsx)(d.td,{children:"Retention time in minutes."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"aligned_rt"})}),(0,r.jsx)(d.td,{children:"Globally aligned retention time."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"predicted_rt"})}),(0,r.jsx)(d.td,{children:"Predicted retention time, if enabled."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"delta_rt_model"})}),(0,r.jsx)(d.td,{children:"Difference between predicted and observed retention time."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"ion_mobility"})}),(0,r.jsx)(d.td,{children:"Ion mobility of the precursor, if present in mzML."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"predicted_mobility"})}),(0,r.jsx)(d.td,{children:"Predicted ion mobility of the precursor, if ion mobility measurements are present in the mzML."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"delta_mobility"})}),(0,r.jsx)(d.td,{children:"Difference between predicted and observed ion mobility."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"matched_peaks"})}),(0,r.jsx)(d.td,{children:"Number of matched theoretical fragment ions."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"longest_b"})}),(0,r.jsx)(d.td,{children:"Longest b-ion series."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"longest_y"})}),(0,r.jsx)(d.td,{children:"Longest y-ion series."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"longest_y_pct"})}),(0,r.jsx)(d.td,{children:"Longest y-ion series, divided by peptide length (as a fraction)."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"matched_intensity_pct"})}),(0,r.jsx)(d.td,{children:"Fraction of MS2 intensity explained by matched b- and y-ions (as a percentage of total MS2 intensity for this spectrum)."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"scored_candidates"})}),(0,r.jsx)(d.td,{children:"Number of scored candidates for this spectrum."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"poisson"})}),(0,r.jsx)(d.td,{children:"Probability of matching exactly N peaks across all scored candidates (Pr(x=k))."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"sage_discriminant_score"})}),(0,r.jsx)(d.td,{children:"Combined score from linear discriminant analysis, used for FDR (False Discovery Rate) calculation."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"posterior_error"})}),(0,r.jsx)(d.td,{children:"Posterior error probability for this PSM / local FDR."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"spectrum_q"})}),(0,r.jsx)(d.td,{children:"Assigned spectrum-level q-value."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"peptide_q"})}),(0,r.jsx)(d.td,{children:"Assigned peptide-level q-value."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"protein_q"})}),(0,r.jsx)(d.td,{children:"Assigned protein-level q-value."})]}),(0,r.jsxs)(d.tr,{children:[(0,r.jsx)(d.td,{children:(0,r.jsx)(d.code,{children:"ms2_intensity"})}),(0,r.jsx)(d.td,{children:"Total intensity of MS2 spectrum."})]})]})]})]})}

1d.default=(0,t.j)({MDXContent:function(){let e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:{},{wrapper:d}=Object.assign({},(0,i.a)(),e.components);return d?(0,r.jsx)(d,{...e,children:(0,r.jsx)(c,{...e})}):c(e)},pageOpts:{filePath:"pages/docs/results/search.mdx",route:"/docs/results/search",frontMatter:{title:"Search Results"},timestamp:1712161096e3,title:"Search Results",headings:n},pageNextRoute:"/docs/results/search"})}},function(e){e.O(0,[673,774,888,179],function(){return e(e.s=5619)}),_N_E=e.O()}]);