76 lines
No EOL
5.3 KiB
HTML
76 lines
No EOL
5.3 KiB
HTML
<!DOCTYPE HTML>
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<title>MSSearchSettings</title>
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<script type="text/javascript" src="/core/jquery/jquery-3.6.0.min.js">
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</script>
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<script type="text/javascript">
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jQuery.getScript("/core/alerts/alerts.js", function () { galert(['pre']) });
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<h3>MSSearchSettings</h3><pre>Defined in file <a href="omssa.asn.html">omssa.asn</a>
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C++ class: <a href="../doxyhtml/classCMSSearchSettings.html">CMSSearchSettings</a>
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MSSearchSettings ::= SEQUENCE {
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precursorsearchtype <a href="MSSearchType.html">MSSearchType</a>, -- average or monoisotopic?
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productsearchtype <a href="MSSearchType.html">MSSearchType</a>, -- average or monoisotopic?
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ionstosearch SEQUENCE OF <a href="MSIonType.html">MSIonType</a>, -- which ions to search?
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peptol REAL, -- peptide mass tolerance
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msmstol REAL, -- msms mass tolerance
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zdep <a href="MSZdependence.html">MSZdependence</a>, -- what is the charge dependence of the mass tolerance?
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cutoff REAL, -- evalue cutoff
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-- next 3 fields define intensity fraction below
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-- which peaks will be discard
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cutlo REAL, -- the start of the cutoff, fraction of most intense peak
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cuthi REAL, -- the end of the cutoff
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cutinc REAL, -- the increment of the cutoff
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singlewin INTEGER, -- the size of the single charge filtering window
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doublewin INTEGER, -- the size of the double charge filtering window
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singlenum INTEGER, -- the number of peaks allowed in the single window
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doublenum INTEGER, -- the number of peaks allowed in the double window
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fixed SEQUENCE OF <a href="MSMod.html">MSMod</a>, -- fixed PTM's
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variable SEQUENCE OF <a href="MSMod.html">MSMod</a>, -- variable PTM's
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enzyme <a href="MSEnzymes.html">MSEnzymes</a>, -- digestion enzyme
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missedcleave INTEGER, -- number of missed cleaves allowed
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hitlistlen INTEGER DEFAULT 25, -- the number of hits kept in memory
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-- for a spectrum
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db VisibleString, -- sequence set to search, e.g. "nr"
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tophitnum INTEGER, -- number of m/z to consider in first pass
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minhit INTEGER DEFAULT 2, -- minimum number of m/z values for a valid hit
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minspectra INTEGER DEFAULT 4, -- minimum number of m/z for a valid spectra
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scale INTEGER DEFAULT 100, -- scale for m/z float to integer
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maxmods INTEGER DEFAULT 64, -- maximum number of mass ladders per
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-- database peptide
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taxids SEQUENCE OF INTEGER OPTIONAL, -- taxa to limit search
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chargehandling <a href="MSChargeHandle.html">MSChargeHandle</a> OPTIONAL, -- how to deal with charges
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usermods <a href="MSModSpecSet.html">MSModSpecSet</a> OPTIONAL, -- user defined modifications
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pseudocount INTEGER DEFAULT 1, -- min number of counts per precursor bin
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searchb1 INTEGER DEFAULT 0, -- should b1 product be in search (1=no, 0=yes)
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searchctermproduct INTEGER DEFAULT 0, -- should c terminus ion be searched (1=no, 0=yes)
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maxproductions INTEGER DEFAULT 0, -- max number of ions in each series (0=all)
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minnoenzyme INTEGER DEFAULT 4, -- min number of AA in peptide for noenzyme search
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maxnoenzyme INTEGER DEFAULT 0, -- max number of AA in peptide for noenzyme search (0=none)
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exactmass REAL OPTIONAL, -- the threshold in Da for adding neutron
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settingid INTEGER OPTIONAL, -- id of the search settings
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iterativesettings <a href="MSIterativeSettings.html">MSIterativeSettings</a> OPTIONAL, -- iterative search settings
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precursorcull INTEGER OPTIONAL, -- turn on aggressive precursor culling for ETD (0=none)
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infiles SEQUENCE OF <a href="MSInFile.html">MSInFile</a> OPTIONAL, -- input files
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outfiles SEQUENCE OF <a href="MSOutFile.html">MSOutFile</a> OPTIONAL, -- output files
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nocorrelationscore INTEGER OPTIONAL, -- turn on correlation score (1=nocorr)
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probfollowingion REAL OPTIONAL, -- probability of a consecutive ion (used in correlation)
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nmethionine BOOLEAN OPTIONAL, -- should nmethionine be cleaved?
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automassadjust REAL OPTIONAL, -- fraction allowable adjustment of product mass tolerance
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lomasscutoff REAL OPTIONAL, -- low mass filter in Daltons, unscaled
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libsearchsettings <a href="MSLibrarySettings.html">MSLibrarySettings</a> OPTIONAL, -- library search settings
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noprolineions SEQUENCE OF <a href="MSIonType.html">MSIonType</a> OPTIONAL, -- which ions to use no proline rule
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reversesearch BOOLEAN OPTIONAL, -- do reverse search
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othersettings SEQUENCE OF <a href="NameValue.html">NameValue</a> OPTIONAL, -- extra search settings
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numisotopes INTEGER OPTIONAL, -- number of isotopic peaks to search when using <a href="MSSearchType.html">MSSearchType</a> multiisotope
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pepppm BOOLEAN OPTIONAL, -- search precursor as ppm
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msmsppm BOOLEAN OPTIONAL, -- search product as ppm
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reportedhitcount INTEGER OPTIONAL -- the maximum number of hits to report per spectrum, 0=all
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}</pre>
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</body>
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