[GENERAL]
AmountOfChains=2
ChainLibrary=fattyAcidChains.xlsx
CAtomsFromName=\D*(\d+):\d+
DoubleBondsFromName=\D*\d+:(\d+)
BasePeakCutoff=0.01%
AlkenylChains=1
ChainCutoff=20%
RetentionTimePostprocessing=true
SingleChainIdentification=false
SpectrumCoverage=10%


[HEAD]
!FRAGMENTS
Name=Precursor			Formula=$PRECURSOR		Charge=1	MSLevel=2	mandatory=other
Name=PChead_168			Formula=C4H11NO4P		Charge=1	MSLevel=2	mandatory=false
Name=PChead_224			Formula=C7H15O5NP		Charge=1	MSLevel=2	mandatory=false
Name=plasmalogen_fragment_403	Formula=C21H40O5P		Charge=1	MSLevel=2	mandatory=true
Name=LPC_chain  		Formula=$PRECURSOR-C9H20O7P1N1	Charge=1	MSLevel=2	mandatory=other

!INTENSITIES
Equation=LPC_chain<plasmalogen_fragment_403*2		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_head	Formula=$PRECURSOR-C2O2H4-$CHAIN	Charge=1	MSLevel=2	mandatory=false
Name=NL_Ketene_head	Formula=$PRECURSOR-C2O2H4-$CHAIN+H2O	Charge=1	MSLevel=2	mandatory=false

!INTENSITIES
Equation=Carboxy>NL_Ketene_head		mandatory=false
Equation=Carboxy>NL_Carboxy_head	mandatory=false



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