[GENERAL]
AmountOfChains=2
ChainLibrary=fattyAcidChains.xlsx
CAtomsFromName=\D*(\d+):\d+
DoubleBondsFromName=\D*\d+:(\d+)
BasePeakCutoff=1%
ChainCutoff=10%
AlkenylChains=1
SpectrumCoverage=10%
RetentionTimePostprocessing=false
RetentionTimePostprocessing=true
IsobarSCExclusionRatio=0.2
IsobarSCFarExclusionRatio=0.4


[HEAD]
!FRAGMENTS
Name=Precursor		Formula=$PRECURSOR		Charge=1	MSLevel=2	mandatory=other
Name=NL_H2O		Formula=$PRECURSOR-H2O		Charge=1	MSLevel=2	mandatory=false
Name=PEhead_wrong	Formula=$PRECURSOR-P1O4C2N1H8	Charge=1	MSLevel=2	mandatory=other
Name=PChead_wrong	Formula=C5H15NO4P		Charge=1	MSLevel=2	mandatory=other
Name=Plasmalogen_fragment_307	Formula=C21H39O		Charge=1	MSLevel=2	mandatory=other

!INTENSITIES
Equation=PChead_wrong<0.6*$BASEPEAK			mandatory=true
Equation=Plasmalogen_fragment_307<0.25*$BASEPEAK	mandatory=true
Equation=Plasmalogen_fragment_307<PEhead_wrong		mandatory=true
Equation=PEhead_wrong+PChead_wrong<10*NL_H2O		mandatory=true

[CHAINS]
!FRAGMENTS
Name=plasmalogen	Formula=$ALKENYLCHAIN+C2H7O3PN		Charge=1	MSLevel=2	mandatory=false
Name=plasmalogen_H3PO4	Formula=$ALKENYLCHAIN+C2H7O3PN-H3PO4	Charge=1	MSLevel=2	mandatory=true
Name=sn2		Formula=$CHAIN+C3H5O			Charge=1	MSLevel=2	mandatory=true

!INTENSITIES
Equation=plasmalogen+plasmalogen_H3PO4>0.25*$BASEPEAK	mandatory=true
Equation=sn2>0.25*$BASEPEAK				mandatory=false
Equation=plasmalogen>0.5*Plasmalogen_fragment_307	mandatory=true
Equation=sn2>0.5*Plasmalogen_fragment_307		mandatory=true


[POSITION]
!INTENSITIES
Equation=sn2[2]>0*$BASEPEAK	mandatory=true
Equation=plasmalogen[1]>0*$BASEPEAK	mandatory=true

