[GENERAL]
AmountOfChains=2
ChainLibrary=fattyAcidChains.xlsx
CAtomsFromName=\D*(\d+):\d+
DoubleBondsFromName=\D*\d+:(\d+)
BasePeakCutoff=0.01%
AlkenylChains=1
ChainCutoff=10%
SpectrumCoverage=25%
RetentionTimePostprocessing=true
SingleChainIdentification=true
IsobarSCExclusionRatio=0.2


[HEAD]
!FRAGMENTS
Name=Precursor			Formula=$PRECURSOR		Charge=1	MSLevel=2	mandatory=false
Name=NL_PChead_60		Formula=$PRECURSOR-C2O2H4	Charge=1	MSLevel=2	mandatory=true
Name=PChead_168			Formula=C4H11NO4P		Charge=1	MSLevel=2	mandatory=false
Name=PChead_224			Formula=C7H15O5NP		Charge=1	MSLevel=2	mandatory=false
Name=PChead_242			Formula=C7H17O6NP		Charge=1	MSLevel=2	mandatory=false
Name=plasmalogen_fragment_403	Formula=C21H40O5P		Charge=1	MSLevel=2	mandatory=true


!INTENSITIES
Equation=NL_PChead_60*0.8>Precursor			mandatory=true
Equation=NL_PChead_60>$BASEPEAK*0.55			mandatory=true
Equation=NL_PChead_60*0.05>PChead_168			mandatory=true
Equation=NL_PChead_60*0.1>PChead_224			mandatory=true
Equation=NL_PChead_60*0.05>PChead_242			mandatory=true
Equation=plasmalogen_fragment_403>0.002*$BASEPEAK	mandatory=true


[CHAINS]
!FRAGMENTS
Name=Carboxy		Formula=$CHAIN-H			Charge=1	MSLevel=2	mandatory=true
Name=Alkenyl		Formula=$ALKENYLCHAIN-H			Charge=1	MSLevel=2	mandatory=false
Name=NL_Carboxy		Formula=$PRECURSOR-$CHAIN		Charge=1	MSLevel=2	mandatory=false
Name=NL_Carboxy_head	Formula=NL_PChead_60-$CHAIN		Charge=1	MSLevel=2	mandatory=false
Name=NL_Ketene_head	Formula=NL_PChead_60-$CHAIN+H2O		Charge=1	MSLevel=2	mandatory=true

!INTENSITIES
Equation=Carboxy>NL_Ketene_head*0.8		mandatory=true
Equation=NL_Ketene_head*0.8>NL_Carboxy_head	mandatory=true
Equation=Alkenyl<0.2*$BASEPEAK			mandatory=true
Equation=Carboxy*0.2>Alkenyl			mandatory=true


[POSITION]
!INTENSITIES
Equation=Carboxy[2]>0.1*NL_Ketene_head[2]+0*$BASEPEAK	mandatory=true
Equation=Alkenyl[1]>0*$BASEPEAK		mandatory=true
