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


[HEAD]
!FRAGMENTS
Name=NL_H2O				Formula=$PRECURSOR-H2O		Charge=1	MSLevel=2	mandatory=true
Name=Plasmalogen_fragment_307		Formula=C21H39O			Charge=1	MSLevel=2	mandatory=false
Name=Precursor				Formula=$PRECURSOR		Charge=1	MSLevel=2	mandatory=true
Name=PEhead_WRONG			Formula=$PRECURSOR-P1O4C2N1H8	Charge=1	MSLevel=2	mandatory=other
Name=PEhead_164_WRONG			Formula=C2H8NO4PNa		Charge=1	MSLevel=2	mandatory=other
Name=PChead_WRONG			Formula=C5H15NO4P		Charge=1	MSLevel=2	mandatory=other
Name=NL_Ethanolamine_43_WRONG		Formula=$PRECURSOR-C2H5N	Charge=1	MSLevel=2	mandatory=other

!INTENSITIES
Equation=PEhead_WRONG<$BASEPEAK*0.5					mandatory=true
Equation=PEhead_WRONG<NL_H2O*3						mandatory=true
Equation=PChead_WRONG<$BASEPEAK*0.5					mandatory=true
Equation=PChead_WRONG<NL_H2O*3						mandatory=true
Equation=NL_Ethanolamine_43_WRONG+PEhead_164_WRONG<0.01*$BASEPEAK	mandatory=true
Equation=NL_Ethanolamine_43_WRONG<NL_H2O*2				mandatory=true
Equation=NL_H2O<0.5*Precursor						mandatory=true
Equation=NL_H2O<0.5*$BASEPEAK						mandatory=true

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

!INTENSITIES
Equation=plasmalogen>0.1*$BASEPEAK					mandatory=true
Equation=sn2>0.1*$BASEPEAK						mandatory=true
Equation=plasmalogen+0*$BASEPEAK>plasmalogen_H3PO4+0*$BASEPEAK		mandatory=true


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

