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::SYMBOL:Ccm;MODIFIED:C;MASS:160.03065
#################
#Modifications selected as variable
modification:variable::SYMBOLEXT:phl-hyd;MODIFIED:L;DELTAMASS:1.97926456
modification:variable::SYMBOLEXT:me;MODIFIED:E;DELTAMASS:14.015650
modification:variable::SYMBOL:Mox;MODIFIED:M;MASS:147.035395
modification:variable::SYMBOLEXT:phl-loop;MODIFIED:L;DELTAMASS:-16.0313
modification:variable::SYMBOL:Nda;MODIFIED:N;MASS:115.026397
#################
#cross-linker selected for the search
crosslinker:AsymetricSingleAminoAcidRestrictedCrossLinker:Name:Photo-Leucine;MASS:-16.0313;FIRSTLINKEDAMINOACIDS:Ccm,Mox,R,H,K,D,E,S,T,N,Q,C,U,G,P,A,V,I,L,M,F,Y,W,Nda;SECONDLINKEDAMINOACIDS:L,Mleu;id:39
crosslinker:NonCovalentBound:Name:NonCovalent;id:117
#################
#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:3ppm
#################
#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:3
#################
#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
MAX_MODIFICATION_PER_PEPTIDE:2
missing_isotope_peaks:2
MAXPEPTIDEMASS:7000
TOPMATCHESONLY:true
