base_directory_path:/Users/salman/xi_data/
BufferInput:1000
BufferOutput:4000
EVALUATELINEARS:true
FRAGMENTTREE:FU
IsotopPattern:Averagin
mgcpeaks:10
minCharge:3
MINIMUM_TOP_SCORE:0
sqlbuffer:100
# ignored : TOPMATCHESONLY:false
topmgxhits:10
UseCPUs:-2
#################
#Modifications selected as fixed
modification:fixed::SYMBOLEXT:ce;MODIFIED:C;DELTAMASS:71.037113805
#################
#Modifications selected as variable
modification:variable::SYMBOL:Mox;MODIFIED:M;MASS:147.035395
#################
#cross-linker selected for the search
crosslinker:NonCovalentBound:Name:NonCovalent;id:117
crosslinker:SymetricSingleAminoAcidRestrictedCrossLinker:Name:DSSO;MASS:158.0037648;LINKEDAMINOACIDS:K(0),S(0.2),T(0.2),Y(0.2),nterm(0);id:139
#################
#Ions to considere
fragment:BIon;id:1
fragment:PeptideIon;id:3
fragment:YIon;id:2
#################
#losses to be considered
loss:AminoAcidRestrictedLoss:NAME:CH3SOH;aminoacids:Mox;MASS:63.99828547;id:4
loss:AminoAcidRestrictedLoss:NAME:H20;aminoacids:S,T,D,E;MASS:18.01056027;cterm;id:1
loss:AminoAcidRestrictedLoss:NAME:NH3;aminoacids:R,K,N,Q;MASS:17.02654493;nterm;id:2
#################
#Tolerance for matching the precursor mass
tolerance:precursor:2ppm
#################
#Tolerance for matching the fragment masses
tolerance:fragment:5ppm
#################
#How many missed cleavages are to be considered.
# Be aware that variable modification or linked aminoacids are not known at the time of digest
missedcleavages:2
#################
#How many alpha-peptide candidates to considere
topmgchits:10
#################
#enzyme defined for digestion
digestion:PostAAConstrainedDigestion:DIGESTED:K,R,K8,R10;ConstrainingAminoAcids:P;NAME=Trypsin
#################
#deprecated
synthetic:false
#################
#manually defined settings for the search
loss:CleavableCrossLinkerPeptide:MASS:54.0105647;NAME:A
loss:CleavableCrossLinkerPeptide:MASS:103.9932001;NAME:S
loss:CleavableCrossLinkerPeptide:MASS:85.9826354;NAME:T
modification:linear::SYMBOLEXT:dssonh;MODIFIED:K,S,T,Y;DELTAMASS:175.030313905
modification:linear::SYMBOLEXT:dssooh;MODIFIED:K,S,T,Y;DELTAMASS:176.0143295
modification:linear::SYMBOLEXT:dssonh;MODIFIED:X;PROTEINPOSITION:nterm;DELTAMASS:175.030313905
modification:linear::SYMBOLEXT:dssooh;MODIFIED:X;PROTEINPOSITION:nterm;DELTAMASS:176.0143295
modification:linear::SYMBOLEXT:met;MODIFIED:E;DELTAMASS:14.015650
MAX_MODIFICATION_PER_PEPTIDE:2

missing_isotope_peaks:3

TOPMATCHESONLY:true