Defined in file omssa.asn
C++ class: CMSSearchSettings

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