MSSearchSettings
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
}