[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=false

Name=Plasmalogen_fragment_307		Formula=C21H39O			Charge=1	MSLevel=2	mandatory=false

Name=Precursor_WRONG			Formula=$PRECURSOR		Charge=1	MSLevel=2	mandatory=other

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<0.4*$BASEPEAK		mandatory=true

Equation=NL_Ethanolamine_43_WRONG<NL_H2O*2		mandatory=true

Equation=Precursor_WRONG<$BASEPEAK*0.5			mandatory=true

Equation=Precursor_WRONG<NL_H2O*2			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



