[GENERAL]
AmountOfChains=2
ChainLibrary=fattyAcidChains.xlsx
CAtomsFromName=\D*(\d+):\d+
DoubleBondsFromName=\D*\d+:(\d+)
BasePeakCutoff=0.5%
RetentionTimePostprocessing=true
SpectrumCoverage=20%
IsobarSCExclusionRatio=0.2
IsobarSCFarExclusionRatio=0.4


[HEAD]
!FRAGMENTS
Name=phosphate_79	Formula=PO3			Charge=1	MSLevel=2	mandatory=false
Name=NL_serine_87	Formula=$PRECURSOR-C3H5NO2	Charge=1	MSLevel=2	mandatory=false
Name=PL158		Formula=C3H1D5O5P		Charge=1	MSLevel=2	mandatory=true
Name=Precursor		Formula=$PRECURSOR		Charge=1	MSLevel=2	mandatory=other
Name=NL_PChead_60_WRONG	Formula=$PRECURSOR-C2O2H4	Charge=1	MSLevel=2	mandatory=other
Name=PEhead_140_WRONG	Formula=C2H7NO4P		Charge=1	MSLevel=2	mandatory=other
Name=PEhead_201_WRONG	Formula=C5H6D5O5PN		Charge=1	MSLevel=2	mandatory=other


!INTENSITIES
Equation=PL158*0.8>Precursor						mandatory=true
Equation=phosphate_79+PL158>NL_PChead_60_WRONG*1.5			mandatory=true
Equation=phosphate_79+PL158>(PEhead_140_WRONG+PEhead_201_WRONG)*1.5	mandatory=true


[CHAINS]
!FRAGMENTS
Name=Carboxy		Formula=$CHAIN-H			Charge=1	MSLevel=2	mandatory=class
Name=NL_Carboxy_serine	Formula=$PRECURSOR-$CHAIN-C3H5NO2	Charge=1	MSLevel=2	mandatory=false
Name=NL_Ketene_serine	Formula=$PRECURSOR-$CHAIN+H2O-C3H5NO2	Charge=1	MSLevel=2	mandatory=false


!INTENSITIES
Equation=Carboxy+NL_Carboxy_serine+PL158*0>PL158*0				mandatory=true
Equation=NL_Carboxy_serine*1.5>NL_Ketene_serine					mandatory=true
Equation=Carboxy|NL_Carboxy_serine						mandatory=true
Equation=(Carboxy+NL_Carboxy_serine)*2>PEhead_140_WRONG+PEhead_201_WRONG	mandatory=true


[POSITION]
!INTENSITIES
Equation=Carboxy[1]*0.9>Carboxy[2]			mandatory=true
Equation=NL_Carboxy_serine[2]*0.9>NL_Carboxy_serine[1]	mandatory=true
Equation=NL_Ketene_serine[2]*0.9>NL_Ketene_serine[1]	mandatory=true





