Options

MSMSfilter:0.0
MSMSmassrange:(180.0, 950.0)
MSMSminOccupation:0.2
MSMSresolution:16.67 ppm
MSMSresolutionDelta:-60.0
MSMSthreshold:0.001
MSMSthresholdType:relative
MSMStolerance:2.00 ppm
MSMStoleranceType:ppm
MScalibration:[388.2541, 462.1466, 529.3994, 675.6779, 753.6134, 829.7985]
MSfilter:0.0
MSmassrange:(350.0, 950.0)
MSminOccupation:0.2
MSresolution:5.56 ppm
MSresolutionDelta:-110.0
MSthreshold:0.001
MSthresholdType:relative
MStolerance:2.00 ppm
MStoleranceType:ppm
alignmentMethodMS:linear
alignmentMethodMSMS:linear
complementMasterScan:False
complementMasterScanFile:221006_Lipidomics_Plasmodium\mzml_pos-complement.csv
compress:False
dataType:mzML
dumpMasterScan:True
dumpMasterScanFile:221006_Lipidomics_Plasmodium\mzml_pos-dump.csv
importMSMS:True
ini:lpdxImportSettings_benchmark.ini
intensityCorrection:False
isotopesInMasterScan:False
isotopicCorrectionMS:True
isotopicCorrectionMSMS:True
isotopicCorrection_MSMS:False
logMemory:False
loopNr:3
masterScanFileRun:221006_Lipidomics_Plasmodium\mzml_pos.sc
masterScanInSQL:False
masterScanRun:221006_Lipidomics_Plasmodium\mzml_pos.sc
monoisotopicCorrection:False
noHead:False
noPermutations:True
optionalMSMStolerance:4.00 ppm
optionalMSMStoleranceType:ppm
optionalMStolerance:4.00 ppm
optionalMStoleranceType:ppm
pisSpectra:False
precursorMassShift:0.0
precursorMassShiftOrbi:0.0
relativeIntensity:False
removeIsotopes:True
resultFile:221006_Lipidomics_Plasmodium\mzml_pos-out.csv
scanAveragingMethod:linear
selectionWindow:0.4
setting:-1
settingsPrefix:False
spectraFormat:mzML
statistics:False
sumFattyAcids:False
tabLimited:False
timerange:(35.0, 300.0)

MFQL queries



>> filename: 210204_CE_pos_MSMS.mfql >>

# Screening for CE - MS/MS
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause 14.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = CholesterolMSMS;

DEFINE Precursor = 'C[41..49] H[30..200] O[2] N[1]' WITH DBR = (4.5,10.5), CHG = +1;
DEFINE FragmentA ='C[27] H[45]' WITH DBR = (1,8), CHG = +1;

IDENTIFY
Precursor IN MS1+ AND
FragmentA in MS2+

SUCHTHAT
Precursor.chemsc[C]/Precursor.chemsc[db] >= 4.6

REPORT
LipidSpecies = "CE %d:%d" % "((Precursor.chemsc)[C] - 27, (Precursor.chemsc)[db] - 4.5)";
LipidClass = "CE";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+NH4+";
LipidCategory = "Sterol lipid";
ScanPolarity = "positive";
Intensity = FragmentA.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "FragmentA";

PrecursorIdentifier = "[CE %d:%d +NH4]+" % "((Precursor.chemsc)[C] - 27, (Precursor.chemsc)[db] - 4.5)";
FragmentAIdentifier = "-FA %d:%d (+HO) -CE(17)" % "((Precursor.chemsc)[C] - 27, (Precursor.chemsc)[db] - 4.5)";
FragmentBIdentifier = "None";
FragmentCIdentifier = "None";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = "None";
FragmentCIntensity = "None";
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "";
FragmentCERRppm = "";
;

################ end script ##################

>> filename: 210204_DAG_pos.mfql >>

# Screening for DAG - MS/MS
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause 14.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = Diacylglycerol;

DEFINE Precursor = 'C[27..54] H[20..200] N[1] O[5]' WITH DBR = (0.5,12.5), CHG = +1;
DEFINE FragmentA = 'C[14..22] H[10..60] N[1] O[2] ' WITH DBR = (0.0,6.0), CHG = 0;
DEFINE FragmentB = 'C[14..22] H[10..60] N[1] O[2] ' WITH DBR = (0.0,6.0), CHG = 0;

IDENTIFY
Precursor IN MS1+ AND
FragmentA IN MS2+ AND
FragmentB IN MS2+

SUCHTHAT
FragmentA.chemsc + FragmentB.chemsc + 'C3 H6 O1' == Precursor.chemsc + 'N1 H4' AND
(FragmentA.chemsc[db] == 0 OR FragmentA.chemsc[C]/FragmentA.chemsc[db] >= 3.6) AND
(FragmentB.chemsc[db] == 0 OR FragmentB.chemsc[C]/FragmentB.chemsc[db] >= 3.6) AND
FragmentA.chemsc[C] <= FragmentB.chemsc[C]


REPORT
LipidSpecies = "DAG %d:%d_%d:%d" % "( (FragmentA.chemsc[C]), (FragmentA.chemsc[db]), (FragmentB.chemsc[C]), (FragmentB.chemsc[db]) )";
LipidClass = "DAG";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+NH4+";
LipidCategory = "Glycerolipid";
ScanPolarity = "positive";
Intensity = sumIntensity(FragmentA.intensity, FragmentB.intensity)/2;
IdentificationLevel = "MS2";
QuantificationIon = "FragmentA and FragmentB";

PrecursorIdentifier = "[DAG %d:%d_%d:%d +NH4]+" % "( (FragmentA.chemsc[C]), (FragmentA.chemsc[db]), (FragmentB.chemsc[C]), (FragmentB.chemsc[db]) )";
FragmentAIdentifier = "-FA %d:%d (-H) -DAG(35)" % "( (FragmentA.chemsc[C]), (FragmentA.chemsc[db]))";
FragmentBIdentifier = "-FA %d:%d (-H) -DAG(35)" % "( (FragmentB.chemsc[C]), (FragmentB.chemsc[db]))";
FragmentCIdentifier = "None";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = FragmentB.intensity;
FragmentCIntensity = "None";
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "%2.2f" % "(FragmentB.errppm)";
FragmentCERRppm = "";
;

################ end script ##################

>> filename: 210204_LPC_pos_MSMS.mfql >>

# Screening for LPC - MS/MS
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause 14.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = LysoPhosphatidylcholine;

DEFINE Precursor = 'C[20..32] H[43..67] O[7] N[1] P[1]' WITH DBR = (0.5,6.5), CHG = +1;
DEFINE FragmentA = 'C[5] H[15] O[4] N[1] P[1]' WITH DBR = (1.5,3.5), CHG = +1;

IDENTIFY
Precursor IN MS1+ AND
FragmentA IN MS2+

SUCHTHAT
isOdd(Precursor.chemsc[H])

REPORT
LipidSpecies = "LPC %d:%d" % "((Precursor.chemsc)[C] - 8, (Precursor.chemsc)[db] - 0.5)";
LipidClass = "LPC";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+H+";
LipidCategory = "Glycerolipid";
ScanPolarity = "positive";
Intensity = Precursor.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "Precursor";

PrecursorIdentifier = "[LPC %d:%d +H]+" % "((Precursor.chemsc)[C] - 8, (Precursor.chemsc)[db] - 0.5)";
FragmentAIdentifier = "PC(184)";
FragmentBIdentifier = "None";
FragmentCIdentifier = "None";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = "None";
FragmentCIntensity = "None";
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "";
FragmentCERRppm = "";
;

################ end script ##################

>> filename: 210204_MAG_pos.mfql >>

# Screening for MAG only FullMS
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause 14.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = Monoacylglycerol;

DEFINE Precursor = 'C[15..27] H[10..100] O[4] N[1]' WITH DBR = (-0.5,5.5), CHG = +1;

IDENTIFY
Precursor IN MS1+

REPORT
LipidSpecies = "MAG %d:%d" % "((Precursor.chemsc)[C] - 3, (Precursor.chemsc)[db] + 0.5)";
LipidClass = "MAG";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+NH4+";
LipidCategory = "Glycerolipid";
ScanPolarity = "positive";
Intensity = Precursor.intensity;
IdentificationLevel = "MS1";
QuantificationIon = "Precursor";

PrecursorIdentifier = "[MAG %d:%d +NH4+]+" % "((Precursor.chemsc)[C] - 3, (Precursor.chemsc)[db] + 0.5)";
FragmentAIdentifier = "None";
FragmentBIdentifier = "None";
FragmentCIdentifier = "None";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = "None";
FragmentBIntensity = "None";
FragmentCIntensity = "None";
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "";
FragmentBERRppm = "";
FragmentCERRppm = "";
;

##################

>> filename: 210204_TAG_pos_MS1_quan.mfql >>

# Screening for TAG - MS quan
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause 14.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = TriacylglycerolMSMS;

DEFINE Precursor = 'C[39..75] H[50..200] N[1] O[6]' WITH DBR = (1.5,9.5), CHG = +1;

IDENTIFY
Precursor IN MS1+

REPORT
LipidSpecies = "TAG %d:%d" % "((Precursor.chemsc[C]-3), (Precursor.chemsc[db]-1.5))";
LipidClass = "TAG";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+NH4+";
LipidCategory = "Glycerolipid";
ScanPolarity = "positive";
Intensity = Precursor.intensity;
IdentificationLevel = "MS1";
QuantificationIon = "Precursor";

PrecursorIdentifier = "[TAG %d:%d +NH4]+" % "((Precursor.chemsc[C]-3), (Precursor.chemsc[db]-1.5))";
FragmentAIdentifier = "None";
FragmentBIdentifier = "None";
FragmentCIdentifier = "None";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = "None";
FragmentBIntensity = "None";
FragmentCIntensity = "None";
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "";
FragmentBERRppm = "";
FragmentCERRppm = "";
;

################ end script ##################

>> filename: 210615_ACar_pos.mfql >>

# Screening for ACar
# modified by Daniel Krause 12.06.21
# C26 D,L-Carnitine-d9
# Fatty acid 26:0
# m/z: 607.5618
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = ACar;

DEFINE Precursor = 'C[17..35] H[36..70] O[4] N[1]' WITH DBR = (-1.5,6.5), CHG = 1;
DEFINE FragmentA = 'C[10..32] H[25..61] O[4]' WITH DBR = (-1.5,6.5), CHG = 1;
DEFINE FragmentB = 'C[3] H[9] N[1]' WITH CHG = 0;

IDENTIFY
Precursor IN MS1+ AND
FragmentA IN MS2+ AND
FragmentB IN MS2+

SUCHTHAT
FragmentA.chemsc + FragmentB.chemsc == Precursor.chemsc

REPORT
LipidSpecies = "ACar %d:%d" % "((FragmentA.chemsc)[C] - 4, (FragmentA.chemsc)[db] - 2.5)";
LipidClass = "ACar";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+H+";
LipidCategory = "Fatty acyl";
ScanPolarity = "positive";
Intensity = Precursor.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "Precursor";

PrecursorIdentifier = "[ACar(+[2]H9) 26:0 +H]+";
FragmentAIdentifier = "FA %d:%d(+C4H6O3)" % "((FragmentA.chemsc)[C] - 4, (FragmentA.chemsc)[db] - 2.5)";
FragmentBIdentifier = "None";
FragmentCIdentifier = "None";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = "None";
FragmentCIntensity = "None";
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "";
FragmentCERRppm = "";
;

################ end script ##################

>> filename: 210803_PC_pos_MS_MS184.mfql >>

# Screening for PC - MS/MS
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause 14.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = PhosphatidylcholineMSMS;

DEFINE Precursor = 'C[36..52] H[67..115] O[8] N[1] P[1]' WITH DBR = (1.5,11.5), CHG = +1;
DEFINE FragmentA = 'C[5] H[15] O[4] N[1] P[1]' WITH DBR = (1.5,3.5), CHG = +1;

IDENTIFY
Precursor IN MS1+ AND
FragmentA IN MS2+

SUCHTHAT
isOdd(Precursor.chemsc[H])

REPORT
LipidSpecies = "PC %d:%d" % "((Precursor.chemsc)[C] - 8, (Precursor.chemsc)[db] - 1.5)";
LipidClass = "PC";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+H+";
LipidCategory = "Glycerolipid";
ScanPolarity = "positive";
Intensity = FragmentA.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "FragmentA";

PrecursorIdentifier = "[PC %d:%d +H]+" % "((Precursor.chemsc)[C] - 8, (Precursor.chemsc)[db] - 1.5)";
FragmentAIdentifier = "PC(184)";
FragmentBIdentifier = "None";
FragmentCIdentifier = "None";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = "None";
FragmentCIntensity = "None";
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "";
FragmentCERRppm = "";
;
################ end script ##################

>> filename: 210803_PC-O_pos_MS_MS184.mfql >>

# Screening for PC - MS/MS
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause 21.01.13
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = PhosphatidylcholineEtherMSMS;

DEFINE Precursor = 'C[36..52] H[67..115] O[7] N[1] P[1]' WITH DBR = (0.5,11.5), CHG = +1;
DEFINE FragmentA = 'C[5] H[15] O[4] N[1] P[1]' WITH DBR = (1.5,3.5), CHG = +1;

IDENTIFY
Precursor IN MS1+ AND
FragmentA IN MS2+

SUCHTHAT
isOdd(Precursor.chemsc[H])

REPORT
LipidSpecies = "PC O-%d:%d" % "((Precursor.chemsc)[C] - 8, (Precursor.chemsc)[db] - 0.5)";
LipidClass = "PC O-";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+H+";
LipidCategory = "Glycerolipid";
ScanPolarity = "positive";
Intensity = FragmentA.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "FragmentA";

PrecursorIdentifier = "[PC O-%d:%d +H]+" % "((Precursor.chemsc)[C] - 8, (Precursor.chemsc)[db] - 0.5)";
FragmentAIdentifier = "PC O-(184)";
FragmentBIdentifier = "None";
FragmentCIdentifier = "None";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = "None";
FragmentCIntensity = "None";
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "";
FragmentCERRppm = "";
;
################ end script ##################

>> filename: 210803_PE_plasmalogen_Frags.mfql >>

# PE-Plasmalogen, Plasmenyl
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause 14.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017
# Plasmenyl with vinyl ether linkage: C-O-C=C-C-R
# Plasmanyl with ether linkage: C-O-C-C-C-R
# naming convention for plasmenyl O-FAp
# naming convention for plasmanyl O-FA

QUERYNAME = PEplasmalogen;

DEFINE Precursor = 'C[25..80] H[30..200] N[1] O[7] P[1]' WITH DBR = (0.5,10.5), CHG = 1;
DEFINE FragmentA = 'C[16..24] H[20..80] N[1] O[4] P[1]' WITH DBR = (0.5,7.5), CHG = 1; #FA-p
DEFINE FragmentB = 'C[17..25] H[20..80] O[3]' WITH DBR = (1.5,7.5), CHG = 1; #FA

IDENTIFY
Precursor IN MS1+ AND
FragmentA IN MS2+ AND
FragmentB IN MS2+

SUCHTHAT
FragmentA + FragmentB - 'H1' == Precursor

REPORT
LipidSpecies = "PE O-%d:%dp/%d:%d" % "((FragmentA.chemsc)[C] - 2, (FragmentA.chemsc)[db] - 0.5, (FragmentB.chemsc)[C] - 3, (FragmentB.chemsc)[db] - 1.5)";
LipidClass = "PE O-";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+H+";
LipidCategory = "Glycerolipid";
ScanPolarity = "positive";
Intensity = sumIntensity(FragmentA.intensity, FragmentB.intensity)/2;
IdentificationLevel = "MS2";
QuantificationIon = "FragmentA and FragmentB";

PrecursorIdentifier = "[PE O-%d:%dp/%d:%d +H]+" % "((FragmentA.chemsc)[C] - 2, (FragmentA.chemsc)[db] - 0.5, (FragmentB.chemsc)[C] - 3, (FragmentB.chemsc)[db] - 1.5)";
FragmentAIdentifier = "-FA %d:%dp (+C3H5O2)" % "((FragmentA.chemsc)[C] - 2, (FragmentA.chemsc)[db] - 0.5)";
FragmentBIdentifier = "FA %d:%d (+C3H5O2)" % "((FragmentB.chemsc)[C] - 3, (FragmentB.chemsc)[db] - 1.5)";
FragmentCIdentifier = "None";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = FragmentB.intensity;
FragmentCIntensity = "None";
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "%2.2f" % "(FragmentB.errppm)";
FragmentCERRppm = "";
;
################ end script ##################

>> filename: 210803_PE_pos_MS_MS_NL141.mfql >>

# Identify PE with checking the precursor mass, and NLS 141
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause and Dominik Schwudke
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017


QUERYNAME = PhosphatidylethanolamineNLS;
DEFINE Precursor = 'C[31..49] H[30..200] N[1] O[8] P[1]' WITH DBR = (1.5,9.5), CHG = 1; DEFINE FragmentA = 'C[23..47] H[48..96] O[4]' WITH DBR = (2.5,10.5), CHG = 1;
#DEFINE FragmentA = 'C2 H8 O4 N1 P1' WITH CHG = 0;


IDENTIFY
Precursor IN MS1+ AND
FragmentA IN MS2+ SUCHTHAT Precursor.chemsc - FragmentA.chemsc == 'C2 H8 O4 N1 P1'

REPORT
LipidSpecies = "PE %d:%d" % "((Precursor.chemsc)[C] - 5, (Precursor.chemsc)[db] - 1.5)";
LipidClass = "PE";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+H+";
LipidCategory = "Glycerolipid";
ScanPolarity = "positive";
Intensity = FragmentA.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "FragmentA";

PrecursorIdentifier = "[PE %d:%d +H]+" % "((Precursor.chemsc)[C] - 5, (Precursor.chemsc)[db] - 1.5)";
FragmentAIdentifier = "-PE(141)";
FragmentBIdentifier = "None";
FragmentCIdentifier = "None";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = "None";
FragmentCIntensity = "None";
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "";
FragmentCERRppm = "";
;
################ end script ##################

>> filename: 210803_PS_pos_MS_MS_NL185.mfql >>

# Identify PS with checking the precursor mass, and NLS 185
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause and Dominik Schwudke
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017


QUERYNAME = PhosphatidylserineNLS;
DEFINE Precursor = 'C[30..50] H[30..200] N[1] O[10] P[1]' WITH DBR = (2.5,10.5), CHG = 1; DEFINE FragmentA = 'C[23..47] H[48..96] O4' WITH DBR = (3.5,11.5), CHG = 1;
#DEFINE FragmentA = 'P1 O6 N1 C3 H8' WITH CHG = 0;


IDENTIFY
Precursor IN MS1+ AND
FragmentA IN MS2+ SUCHTHAT Precursor.chemsc - FragmentA.chemsc == 'C3 H8 O6 N1 P1'

REPORT
LipidSpecies = "PS %d:%d" % "((Precursor.chemsc)[C] - 6, (Precursor.chemsc)[db] - 2.5)";
LipidClass = "PS";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+H+";
LipidCategory = "Glycerolipid";
ScanPolarity = "positive";
Intensity = FragmentA.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "FragmentA";

PrecursorIdentifier = "[PES %d:%d +H]+" % "((Precursor.chemsc)[C] - 6, (Precursor.chemsc)[db] - 2.5)";
FragmentAIdentifier = "-PS(185)";
FragmentBIdentifier = "None";
FragmentCIdentifier = "None";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = "None";
FragmentCIntensity = "None";
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "";
FragmentCERRppm = "";
;
################ end script ##################

>> filename: 220725_Cer_pos_MSMS.mfql >>

# Screening for Cer - MSMS Check for LCB
# written 2018 - 03 - 28 by Lars F. Eggers, Dominik Schwudke, Franziska Waldow
# modified by Daniel Krause 25.07.22
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017
# Ceramides example: Cer 18:1;(OH)2/16:0 == Cer(d18:1/16:0) Lipidmaps/Swisslipids == Cer 18:1;1/16:0, sphingoid base contains 18 carbons, 1 double bond and 2 hydroxyl groups

QUERYNAME = Ceramides;

DEFINE Precursor = 'C[31..47] H[30..200] N[1] O[3..4]' WITH DBR = (0.5,2.5), CHG = 1;
DEFINE FragmentA = 'C[14..20] H[20..40] N[1]' WITH DBR = (1.5,3.5), CHG = 1;

IDENTIFY
Precursor IN MS1+ AND
FragmentA IN MS2+

SUCHTHAT
isEven(FragmentA.chemsc[C]) AND
Precursor.chemsc[db] - 0.5 >= FragmentA.chemsc[db] - 1.5 AND
(Precursor.chemsc[C]-FragmentA.chemsc[C] <= 22 AND Precursor.chemsc[C]-FragmentA.chemsc[C] >= 14) AND
Precursor.chemsc[C]/Precursor.chemsc[db] >= 5.6

REPORT
LipidSpecies = "Cer %d:%d;(OH)%d/%d:%d" % "((FragmentA.chemsc)[C], ((FragmentA.chemsc)[db] - 1.5), ((Precursor.chemsc)[O] - 1), ((Precursor.chemsc)[C] - (FragmentA.chemsc)[C]), (((Precursor.chemsc)[db] - 0.5) - ((FragmentA.chemsc)[db] - 1.5)))";
LipidClass = "Cer";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+H+";
LipidCategory = "Sphingolipid";
ScanPolarity = "positive";
Intensity = FragmentA.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "FragmentA";

PrecursorIdentifier = "[Cer %d:%d;(OH)%d/%d:%d +H]+" % "((FragmentA.chemsc)[C], ((FragmentA.chemsc)[db] - 1.5), ((Precursor.chemsc)[O] - 1), ((Precursor.chemsc)[C] - (FragmentA.chemsc)[C]), (((Precursor.chemsc)[db] - 0.5) - ((FragmentA.chemsc)[db] - 1.5)))";
FragmentAIdentifier = "LCB %d:%d;(OH)%d(-H3O2)" % "((FragmentA.chemsc)[C], ((FragmentA.chemsc)[db] - 1.5), ((Precursor.chemsc)[O] - 1))";
FragmentBIdentifier = "None";
FragmentCIdentifier = "None";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = "None";
FragmentCIntensity = "None";
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "";
FragmentCERRppm = "";
;

################ end script ##################

>> filename: 220725_SM_pos_MS_MS184.mfql >>

# Screening for SM - MSMS Check for 184
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause 25.07.22
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = SphingomyelineOne;

DEFINE Precursor = 'C[31..49] H[67..103] O[6..7] N[2] P[1]' WITH DBR = (0.5,3.5), CHG = +1;
DEFINE FragmentA = 'C[5] H[15] O[4] N[1] P[1]' WITH DBR = (1.5,3.5), CHG = +1;

IDENTIFY
Precursor IN MS1+ AND
FragmentA IN MS2+

SUCHTHAT
isEven(Precursor.chemsc[H])
# AND (avg(FragmentA.intensity)/avg(Precursor.intensity) >=1 AND avg(FragmentA.intensity)/avg(Precursor.intensity) <=100)

REPORT
LipidSpecies = "SM %d:%d;(OH)%d" % "((Precursor.chemsc)[C] - 5, (Precursor.chemsc)[db] - 0.5, (Precursor.chemsc)[O] - 4)";
LipidClass = "SM";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+H+";
LipidCategory = "Sphingolipd";
ScanPolarity = "positive";
Intensity = Precursor.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "Precursor";

PrecursorIdentifier = "[SM %d:%d;(OH)%d +H]+" % "((Precursor.chemsc)[C] - 5, (Precursor.chemsc)[db] - 0.5, (Precursor.chemsc)[O] - 4)";
FragmentAIdentifier = "SM(184)";
FragmentBIdentifier = "None";
FragmentCIdentifier = "None";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = "None";
FragmentCIntensity = "None";
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "";
FragmentCERRppm = "";
;

################ end script ##################

>> filename: 220726_HexCer_pos_MSMS.mfql >>

# Screening for HexCer - MSMS Check for Sphingosin Fragment
# written 2018 - 03 - 28 Lars F. Eggers, Dominik Schwudke
# modified by Daniel Krause 25.07.22
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = Hexosylceramide;

DEFINE Precursor = 'C[37..53] H[30..200] N[1] O[8..9]' WITH DBR = (1.5,3.5), CHG = 1;
DEFINE FragmentA = 'C[14..20] H[20..40] N[1]' WITH DBR = (1.5,3.5), CHG = 1;

IDENTIFY
Precursor IN MS1+ AND
FragmentA IN MS2+

SUCHTHAT
isEven(FragmentA.chemsc[C]) AND
Precursor.chemsc[db] - 1.5 >= FragmentA.chemsc[db] - 1.5

REPORT
LipidSpecies = "HexCer %d:%d;(OH)%d/%d:%d" % "((FragmentA.chemsc)[C], ((FragmentA.chemsc)[db] - 1.5), ((Precursor.chemsc)[O] - 6), ((Precursor.chemsc)[C] - (FragmentA.chemsc)[C] - 6), (((Precursor.chemsc)[db] - 1.5) - ((FragmentA.chemsc)[db] - 1.5)))";
LipidClass = "HexCer";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+H+";
LipidCategory = "Sphingolipid";
ScanPolarity = "positive";
Intensity = FragmentA.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "FragmentA";

PrecursorIdentifier = "[HexCer %d:%d;(OH)%d/%d:%d +H]+" % "((FragmentA.chemsc)[C], ((FragmentA.chemsc)[db] - 1.5), ((Precursor.chemsc)[O] - 6), ((Precursor.chemsc)[C] - (FragmentA.chemsc)[C] - 6), (((Precursor.chemsc)[db] - 1.5) - ((FragmentA.chemsc)[db] - 1.5)))";
FragmentAIdentifier = "LCB %d:%d;(OH)%d(-H3O2)" % "((FragmentA.chemsc)[C], ((FragmentA.chemsc)[db] - 1.5), ((Precursor.chemsc)[O] - 6))";
FragmentBIdentifier = "None";
FragmentCIdentifier = "None";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = "None";
FragmentCIntensity = "None";
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "";
FragmentCERRppm = "";
;

################ end script ##################

>> filename: 220622_CE_18-1D7-SPLASH.mfql >>

# Screening for CE - MS/MS
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause 14.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017
#
# 18:1(d7) Chol Ester, C45 H71 D7 O2, 657.64 Da
# Precursor: [M + NH4]+ C45 H75 D7 O2 N1, 675.6779 m/z
# Fragment: Cholesterol specific 369 fragment

QUERYNAME = CESplash;

DEFINE Precursor = 'C[45] H[75] D[7] O[2] N[1]' WITH DBR = (4.5,10.5), CHG = +1;
DEFINE FragmentA = 'C[27] H[45]' WITH DBR = (1,8), CHG = +1;

IDENTIFY
Precursor IN MS1+ AND
FragmentA in MS2+

REPORT
LipidSpecies = "IS CE 18:1(+[2]H7)";
LipidClass = "CE";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+NH4+";
LipidCategory = "Internal standard";
ScanPolarity = "positive";
Intensity = FragmentA.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "FragmentA";

PrecursorIdentifier = "[CE %d:%d(+[2]H7) +NH4]+" % "((Precursor.chemsc)[C] - 27, (Precursor.chemsc)[db] - 4.5)";
FragmentAIdentifier = "-FA %d:%d(+[2]H7 +HO) -CE(17)" % "((Precursor.chemsc)[C] - 27, (Precursor.chemsc)[db] - 4.5)";
FragmentBIdentifier = "None";
FragmentCIdentifier = "None";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = "None";
FragmentCIntensity = "None";
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "";
FragmentCERRppm = "";
;

################ end script ##################

>> filename: 220622_DAG_15-0-18-1D7-SPLASH.mfql >>

# Screening for DAG - MS/MS
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause 14.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017
#
# 15:0-18:1(d7) DAG, C36 H61 D7 O5, 587.55 Da
# Precursor: [M+NH4]+, C36 H65 D7 O5 N1, 605.5844 m/z
# Fragment A: lyso DAG, with 15:0 missing, deuterated fatty acid 18:1(d7) intact, 346.3344 m/z
# Fragment B: lyso DAG, with missing fatty acid 15:0 intact, 18:1d7 missing, 299.2592 m/z

QUERYNAME = DAGSplash;

DEFINE Precursor = 'C[36] H[20..200] D[7] N[1] O[5]' WITH DBR = (0.5,12.5), CHG = +1;
DEFINE FragmentA = 'C[15] H[10..60] N[1] O[2] ' WITH DBR = (0.0,6.0), CHG = 0;
DEFINE FragmentB = 'C[18] H[10..60] D[7] N[1] O[2] ' WITH DBR = (0.0,6.0), CHG = 0;

IDENTIFY
Precursor IN MS1+ AND
FragmentA IN MS2+ AND
FragmentB IN MS2+

SUCHTHAT
FragmentA.chemsc + FragmentB.chemsc + 'C3 H6 O1' == Precursor.chemsc + 'N1 H4'

REPORT
LipidSpecies = "IS DAG 15:0-18:1(+[2]H7)";
LipidClass = "DAG";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+NH4+";
LipidCategory = "Internal standard";
ScanPolarity = "positive";
Intensity = FragmentB.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "FragmentB";

PrecursorIdentifier = "[DAG %d:%d_%d:%d(+[2]H7) +NH4]+" % "( (FragmentA.chemsc[C]), (FragmentA.chemsc[db]), (FragmentB.chemsc[C]), (FragmentB.chemsc[db]) )";
FragmentAIdentifier = "-FA %d:%d(-H) -DAG(35)" % "( (FragmentA.chemsc[C]), (FragmentA.chemsc[db]))";
FragmentBIdentifier = "-FA %d:%d(+[2]H7 -H) -DAG(35)" % "( (FragmentB.chemsc[C]), (FragmentB.chemsc[db]))";
FragmentCIdentifier = "None";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = FragmentB.intensity;
FragmentCIntensity = "None";
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "%2.2f" % "(FragmentB.errppm)";
FragmentCERRppm = "";
;

################ end script ##################

>> filename: 220622_LPC_18-1D7-SPLASH.mfql >>

# Screening for LPC - MS/MS
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause 14.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

# LPC 18:1(+[2]H7)
# Precursor: [M+H]+, C26 H46 D7 O7 N1 P1, 529.3999 m/z
# Fragment A: PC(184), C5 H15 O4 N1 P1, 184.0739 m/z

QUERYNAME = LPCSplash;

DEFINE Precursor = 'C[26] H[46] D[7] O[7] N[1] P[1]' WITH DBR = (0.5,6.5), CHG = +1;
DEFINE FragmentA = 'C[5] H[15] O[4] N[1] P[1]' WITH DBR = (1.5,3.5), CHG = +1;

IDENTIFY
Precursor IN MS1+ AND
FragmentA IN MS2+

REPORT
LipidSpecies = "IS LPC 18:1(+[2]H7)";
LipidClass = "LPC";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+H+";
LipidCategory = "Internal standard";
ScanPolarity = "positive";
Intensity = Precursor.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "FragmentA";

PrecursorIdentifier = "[LPC %d:%d(+[2]H7) +H]+" % "((Precursor.chemsc)[C] - 8, (Precursor.chemsc)[db] - 0.5)";
FragmentAIdentifier = "PC(184)";
FragmentBIdentifier = "None";
FragmentCIdentifier = "None";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = "None";
FragmentCIntensity = "None";
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "";
FragmentCERRppm = "";
;

################ end script ##################

>> filename: 220622_MAG_18-1D7-SPLASH.mfql >>

# Screening for MAG only FullMS
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause 14.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

# Splash Precursors,+H+, +NH4+, +CH3COO
# MAG 18:1(+[2]H7), C21 H33 D7 O4, 363.3366 Da
# Precursor [M+H]+: C21 H34 D7 O4, 364.3444 m/z
# Precursor [M+NH4]+: C21 H37 D7 O4 N1, 381.3710 m/z
# Precursor [M+CH3COO]+: C23 H36 D7 O6, 422.3499 m/z

QUERYNAME = MAGSplash;

#DEFINE Precursor = 'C[21] H[34] D[7] O[4]' WITH DBR = (-2.5,5.5), CHG = 1; #M+H+
DEFINE Precursor = 'C[21] H[37] D[7] O[4] N[1]' WITH DBR = (-2.5,5.5), CHG = 1; #M+NH4+
#DEFINE Precursor = 'C[23] H[36] D[7] O[6]' WITH DBR = (-2.5,5.5), CHG = 1; #M+CH3COO+

IDENTIFY
Precursor IN MS1+

REPORT
LipidSpecies = "IS MAG 18:1(+[2]H7)";
LipidClass = "MAG";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+NH4+";
LipidCategory = "Internal standard";
ScanPolarity = "positive";
Intensity = Precursor.intensity;
IdentificationLevel = "MS1";
QuantificationIon = "Precursor";

PrecursorIdentifier = "[MAG %d:%d(+[2]H7) +NH4]+" % "((Precursor.chemsc)[C] - 3, (Precursor.chemsc)[db] + 0.5)";
FragmentAIdentifier = "None";
FragmentBIdentifier = "None";
FragmentCIdentifier = "None";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = "None";
FragmentBIntensity = "None";
FragmentCIntensity = "None";
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "";
FragmentBERRppm = "";
FragmentCERRppm = "";
;

##################

>> filename: 220622_PC_15-0-18-1D7-SPLASH.mfql >>

# Screening for PC - MS/MS
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause 14.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

# PC 15:0-18:1(+[2]H7), C41 H73 D7 O8 N1 P1, 752.6061 Da
# Precursor: [M+H]+, C41 H74 D7 O8 N1 P1, 753.6139 m/z
# Fragment A: PC(184), C5 H15 O4 N1 P1, 184.0739 m/z

QUERYNAME = PCSplash;

DEFINE Precursor = 'C[41] H[74] D[7] O[8] N[1] P[1]' WITH DBR = (1.5,11.5), CHG = +1;
DEFINE FragmentA = 'C[5] H[15] O[4] N[1] P[1]' WITH DBR = (1.5,3.5), CHG = +1;

IDENTIFY
Precursor IN MS1+ AND
FragmentA IN MS2+

REPORT
LipidSpecies = "IS PC 15:0-18:1(+[2]H7)";
LipidClass = "PC";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+H+";
LipidCategory = "Internal standard";
ScanPolarity = "positive";
Intensity = FragmentA.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "FragmentA";

PrecursorIdentifier = "[PC %d:%d(+[2]H7) +H]+" % "((Precursor.chemsc)[C] - 8, (Precursor.chemsc)[db] - 1.5)";
FragmentAIdentifier = "PC(184)";
FragmentBIdentifier = "None";
FragmentCIdentifier = "None";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = "None";
FragmentCIntensity = "None";
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "";
FragmentCERRppm = "";
;

################ end script ##################

>> filename: 220622_PCO_18-0p-18-1D9.mfql >>

# Screening for PC O-p - MS/MS
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause and Dominik Schwudke
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

# PC O-18:0p-18:1(+[2]H9), C44 H77 D9 O7 N1 P1, 780.6707 Da
# Precursor: [M+H]+, C44 H78 D9 O7 N1 P1, 781.6785 m/z
# Fragment A: PC(184), C5 H15 O4 N1 P1, 184.0739 m/z

QUERYNAME = PCOpSplash;

DEFINE Precursor = 'C[44] H[78] D[9] O[7] N[1] P[1]' WITH DBR = (0.5,2.5), CHG = +1;
DEFINE FragmentA = 'C[5] H[15] O[4] N[1] P[1]' WITH DBR = (1.5,3.5), CHG = +1;

IDENTIFY
Precursor IN MS1+ AND
FragmentA IN MS2+

REPORT
LipidSpecies = "IS PC O-18:0p-18:1(+[2]H9)";
LipidClass = "PC O-";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+H+";
LipidCategory = "Internal standard";
ScanPolarity = "positive";
Intensity = FragmentA.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "FragmentA";

PrecursorIdentifier = "[PC O-%d:%dp(+[2]H9) +H]+" % "((Precursor.chemsc)[C] - 8, (Precursor.chemsc)[db] - 0.5)";
FragmentAIdentifier = "PC(184)";
FragmentBIdentifier = "None";
FragmentCIdentifier = "None";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = "None";
FragmentCIntensity = "None";
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "";
FragmentCERRppm = "";
;

################ end script ##################

>> filename: 220622_PE_15-0-18-1D7-SPLASH.mfql >>

# Identify PE with checking the precursor mass, and NLS 141
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause and Dominik Schwudke
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

# PE 15:0-18:1(+[2]H7), C38 H67 D7 O8 N1 P1, 710.5591 Da
# Precursor: [M+H]+, C38 H68 D7 O8 N1 P1, 711.5670 m/z
# Fragment A: -PE(141), loss of PE specific fragment from precursor, C2 H8 O4 N1 P1, 141.0191 m/z -> 570.5479 m/z

QUERYNAME = PESplash;

DEFINE Precursor = 'C[38] H[68] D[7] N[1] O[8] P[1]' WITH DBR = (1.5,9.5), CHG = 1;
DEFINE FragmentA = 'C[2] H[8] O[4] N[1] P[1]' WITH CHG = 0;

IDENTIFY
Precursor IN MS1+ AND
FragmentA IN MS2+

REPORT
LipidSpecies = "IS PE 15:0-18:1(+[2]H7)";
LipidClass = "PE";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+H+";
LipidCategory = "Internal standard";
ScanPolarity = "positive";
Intensity = FragmentA.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "FragmentA";

PrecursorIdentifier = "[PE %d:%d(+[2]H7) +H]+" % "((Precursor.chemsc)[C] - 5, (Precursor.chemsc)[db] - 1.5)";
FragmentAIdentifier = "-PE(141)";
FragmentBIdentifier = "None";
FragmentCIdentifier = "None";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = "None";
FragmentCIntensity = "None";
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "";
FragmentCERRppm = "";
;

################ end script ##################

>> filename: 220622_PEO_18-0p-18-1D9.mfql >>

# PE-Plasmalogen Splash
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause and Dominik Schwudke
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

# PE C18(plasm)-18:1(+[2]H9), C41 H71 D9 O7 N1 P1, 738.6237 Da
# Precursor: [M+H]+, C41 H72 D9 O7 N1 P1, 739.6316 m/z
# Fragment A: [M-FA], 18:0p, loss of FA, C20 H43 O4 N1 P1, 392.2930 m/z
# Fragment B: [FA 18:1D9 + C3H5O2], C21 H30 D9 O3, 348.3464 m/z

QUERYNAME = PEOplasSplash;

DEFINE Precursor = 'C[41] H[72] D[9] N[1] O[7] P[1]' WITH DBR = (0.5,10.5), CHG = 1;
DEFINE FragmentA = 'C[20] H[43] N[1] O[4] P[1]' WITH DBR = (0.5,7.5), CHG = 1; #FA-p
DEFINE FragmentB = 'C[21] H[30] D[9] O[3]' WITH DBR = (1.5,7.5), CHG = 1; #FA

IDENTIFY
Precursor IN MS1+ AND
FragmentA IN MS2+ AND
FragmentB IN MS2+

SUCHTHAT
FragmentA + FragmentB - 'H1' == Precursor

REPORT
LipidSpecies = "IS PE C18(plasm)-18:1(+[2]H9)";
LipidClass = "PE O-";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+H+";
LipidCategory = "Internal standard";
ScanPolarity = "positive";
Intensity = sumIntensity(FragmentA.intensity, FragmentB.intensity)/2;
IdentificationLevel = "MS2";
QuantificationIon = "FragmentA and FragmentB";

PrecursorIdentifier = "[PE O-%d:%dp/%d:%d +H]+" % "((FragmentA.chemsc)[C] - 2, (FragmentA.chemsc)[db] - 0.5, (FragmentB.chemsc)[C] - 3, (FragmentB.chemsc)[db] - 1.5)";
FragmentAIdentifier = "-FA %d:%dp (+C3H5O2)" % "((FragmentA.chemsc)[C] - 2, (FragmentA.chemsc)[db] - 0.5)";
FragmentBIdentifier = "FA %d:%d (+C3H5O2)" % "((FragmentB.chemsc)[C] - 3, (FragmentB.chemsc)[db] - 1.5)";
FragmentCIdentifier = "None";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = FragmentB.intensity;
FragmentCIntensity = "None";
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "%2.2f" % "(FragmentB.errppm)";
FragmentCERRppm = "";
;
################ end script ##################

>> filename: 220622_PS_15-0-18-1D7-SPLASH.mfql >>

# Identify PS with checking the precursor mass, and NLS 185
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause and Dominik Schwudke
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017
#
# PS 15:0-18:1(+[2]H7), C39 H67 D7 N1 O10 P1, 754.5490 Da
# Precursor: [M+H]+, C39 H68 D7 N1 O10 P1, 755.5562 m/z
# Fragment A: -PS(185), loss of PS specific fragment from precursor, C36 H60 D7 O4, 570.5479 m/z

QUERYNAME = PSSplash;

DEFINE Precursor = 'C[39] H[68] D[7] N[1] O[10] P[1]' WITH DBR = (1.5,9.5), CHG = 1;
DEFINE FragmentA = 'C[36] H[60] D[7] O[4]' WITH CHG = 1;

IDENTIFY
Precursor IN MS1+ AND
FragmentA IN MS2+

REPORT
LipidSpecies = "IS PS 33:1 (+[2]H7)";
LipidClass = "PS";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+H+";
LipidCategory = "Internal standard";
ScanPolarity = "positive";
Intensity = FragmentA.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "FragmentA";

PrecursorIdentifier = "[PS %d:%d(+[2]H7) +H]+" % "((Precursor.chemsc)[C] - 5, (Precursor.chemsc)[db] - 2.5)";
FragmentAIdentifier = "-PS(185)";
FragmentBIdentifier = "None";
FragmentCIdentifier = "None";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = "None";
FragmentCIntensity = "None";
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "";
FragmentCERRppm = "";
;

################ end script ##################

>> filename: 220622_TAG_15-0-18-1D7-15-0-SPLASH.mfql >>

# Screening for TAG IS - MS1
# written 2018 - 03 -27 by Lars F. Eggers, Dominik Schwudke
# modified by Daniel Krause 14.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017
#
# TAG 15:0_18:1(+[2]H7)_15:0, C51 H89 D7 O6, 811.7646 Da
# Precursor: [M+NH4]+, C51 H93 D7 N1 O6, 829.7990 Da
# Fragment A: [M-FA(+[2]H7)-TAG], loss of fatty acid with deuteration and neutral loss of ammonia as TAG fragment,

QUERYNAME = TAGSplash;

DEFINE Precursor = 'C[51] H[93] D[7] N[1] O[6]' WITH DBR = (1.5,19.5), CHG = +1;
DEFINE FragmentA = 'C[18] H[10..76] D[7] N[1] O[2] ' WITH DBR = (0.0,6.0), CHG = 0;

IDENTIFY
Precursor IN MS1+ AND
FragmentA IN MS2+

REPORT
LipidSpecies = "IS TAG 15:0_18:1(+[2]H7)_15:0";
LipidClass = "TAG";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+NH4+";
LipidCategory = "Internal standard";
ScanPolarity = "positive";
Intensity = Precursor.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "Precursor";

PrecursorIdentifier = "[TAG %d:%d(+[2]H7) +NH4]+" % "((Precursor.chemsc[C]-3), (Precursor.chemsc[db]-1.5))";
FragmentAIdentifier = "-FA 18:1(+[2]H7 +HO -TAG(17))";
FragmentBIdentifier = "None";
FragmentCIdentifier = "None";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = "None";
FragmentCIntensity = "None";
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "";
FragmentCERRppm = "";
;

################ end script ##################

>> filename: 220712_ACar_26-0D9.mfql >>

# Screening for ACar
# modified by Daniel Krause 12.06.21
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

# C26 D,L-Carnitine-d9
# Precursor: [ACar+H]+, C33 H57 D9 O4 N1, 549.5557 m/z
# Fragment A: FA 26:0(+C4H6O3), C30 H57 O4, 481.4257 m/z

QUERYNAME = ACarStandard;

DEFINE Precursor = 'C[33] H[57] D[9] O[4] N[1]' WITH DBR = (-1.5,6.5), CHG = 1;
DEFINE FragmentA = 'C[30] H[57] O[4]' WITH DBR = (-1.5,6.5), CHG = 1;

IDENTIFY
Precursor IN MS1+ AND
FragmentA IN MS2+

SUCHTHAT
FragmentA.chemsc + 'N1 C3 D9' == Precursor.chemsc

REPORT
LipidSpecies = "IS ACar(+[2]H9) 26:0";
LipidClass = "ACar";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+H+";
LipidCategory = "Internal standard";
ScanPolarity = "positive";
Intensity = Precursor.intensity;
IdentificationLevel = "MS1";
QuantificationIon = "Precursor";

PrecursorIdentifier = "[ACar(+[2]H9) 26:0 +H]+";
FragmentAIdentifier = "FA 26:0(+C4H6O3)";
FragmentBIdentifier = "None";
FragmentCIdentifier = "None";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = "None";
FragmentCIntensity = "None";
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "";
FragmentCERRppm = "";
;

################ end script ##################

>> filename: 220726_Cer_d18-1D7-15-0.mfql >>

# Screening for CerD7 - MSMS Check for LCB
# written 2018 - 03 - 28 by Lars F. Eggers, Dominik Schwudke, Franziska Waldow
# modified by Daniel Krause 25.07.22
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017
#
# deuterated Ceramide standard
# Cer(d18:1-d7/15:0), C33 H58 D7 NO3, 530.5404 Da
# Precursor: [M+H]+, C33 H59 D7 NO3, 531.5477 m/z
# Fragment: FragmentA = Long-chain base, base chain of ceramide with length 18:1-d7, second chain 15:0, is ionized as [M+H]+, labile also [M-H2O+H]+
# Cer(d18:1-d7/15:0) == Cer 18:1;(OH)2/15:0, LCB base of 18 C with 1 DB and 2 OH groups

QUERYNAME = CeramideStandard;

DEFINE Precursor = 'C[33] H[59] D[7] N[1] O[3]' WITH DBR = (-1.5,6.5), CHG = 1;
DEFINE FragmentA = 'C[18] H[27] D[7] N[1]' WITH DBR = (-1.5,6.5), CHG = 1;
DEFINE FragmentB = 'C[17] H[27] D[7] N[1]' WITH DBR = (-1.5,6.5), CHG = 1;

IDENTIFY
Precursor IN MS1+ AND
FragmentA IN MS2+ AND
FragmentB IN MS2+

REPORT
LipidSpecies = "IS Cer 18:1;(OH)2(+[2]H7)/15:0";
LipidClass = "Cer";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+H+";
LipidCategory = "Internal standard";
ScanPolarity = "positive";
Intensity = FragmentA.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "FragmentA";

PrecursorIdentifier = "[Cer %d:%d;(OH)%d(+[2]H7)/%d:%d +H]+" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5, (Precursor.chemsc)[O] - 1, (Precursor.chemsc)[C] - (FragmentA.chemsc)[C], (((Precursor.chemsc)[db] - 0.5) - ((FragmentA.chemsc)[db] - 1.5)))";
FragmentAIdentifier = "LCB %d:%d;(OH)%d(+[2]H7 -H3O2)" % "((FragmentA.chemsc)[C], ((FragmentA.chemsc)[db] - 1.5), ((Precursor.chemsc)[O] - 1))";
FragmentBIdentifier = "LCB %d:%d;(OH)%d(+[2]H7 -CH3O2)" % "((Precursor.chemsc)[C] - (FragmentA.chemsc)[C], (((Precursor.chemsc)[db] - 0.5) - ((FragmentA.chemsc)[db] - 1.5)), (Precursor.chemsc)[O] - 1)";
FragmentCIdentifier = "None";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = FragmentB.intensity;
FragmentCIntensity = "None";
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "%2.2f" % "(FragmentB.errppm)";
FragmentCERRppm = "";
;
################ end script ##################

>> filename: 220726_GluCer_d18-1D7-15-0.mfql >>

# Screening for GluCer D7 Standard
# written by Daniel Krause 12.06.21
# LCB, with OH removed, FA removed, sugar [+O] removed, LCB unique with D7
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017
#
# C15 Glycosyl (beta) Ceramide-D7 (d18:1-D7/15:0) == Cer 18:1;(OH)2(+[2]H7)/15:0
# Precursor: [M+H]+, C39 H69 D7 O8 N1, 693.6010 m/z
# Fragment A: LCB, C18 H27 D7 N1, d18:1(d7), 271.3131 m/z

QUERYNAME = GlucosylceramideStandard;

DEFINE Precursor = 'C[39] H[69] D[7] N[1] O[8]' WITH DBR = (1.5,3.5), CHG = 1;
DEFINE FragmentA = 'C[18] H[27] D[7] N[1]' WITH DBR = (1.5,3.5), CHG = 1;

IDENTIFY
Precursor IN MS1+ AND
FragmentA IN MS2+

SUCHTHAT
isEven(FragmentA.chemsc[C]) AND
Precursor.chemsc[db] - 1.5 >= FragmentA.chemsc[db] - 1.5

REPORT
LipidSpecies = "IS GluCer %d:%d;(OH)%d(+[2]H7)/%d:%d" % "((FragmentA.chemsc)[C], ((FragmentA.chemsc)[db] - 1.5), ((Precursor.chemsc)[O] - 6), ((Precursor.chemsc)[C] - (FragmentA.chemsc)[C] - 6), (((Precursor.chemsc)[db] - 1.5) - ((FragmentA.chemsc)[db] - 1.5)))";
LipidClass = "HexCer";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+H+";
LipidCategory = "Internal standard";
ScanPolarity = "positive";
Intensity = FragmentA.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "FragmentA";

PrecursorIdentifier = "[GluCer %d:%d;(OH)%d(+[2]H7)/%d:%d +H]+" % "((FragmentA.chemsc)[C], ((FragmentA.chemsc)[db] - 1.5), ((Precursor.chemsc)[O] - 6), ((Precursor.chemsc)[C] - (FragmentA.chemsc)[C] - 6), (((Precursor.chemsc)[db] - 1.5) - ((FragmentA.chemsc)[db] - 1.5)))";
FragmentAIdentifier = "LCB %d:%d;%d(-H3O2)" % "((FragmentA.chemsc)[C], ((FragmentA.chemsc)[db] - 1.5), (Precursor.chemsc)[O] - 6)";
FragmentBIdentifier = "None";
FragmentCIdentifier = "None";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = "None";
FragmentCIntensity = "None";
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "";
FragmentCERRppm = "";
;

################ end script ##################

>> filename: 220726_SM_d18-1-18-1D9-SPLASH.mfql >>

# Screening for SM - MSMS Check for 184
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause 14.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017
#
# SM d18:1-18:1(+[2]H9), C41 H72 D9 N2 O6 P1, 737.6397 Da
# Precursor: [M+H]+, C41 H73 D9 N2 O6 P1, 738.6470 m/z
# Fragment A: SM(184), SM specific fragment, C5 H15 O4 N1 P1, 184.0739 m/z

QUERYNAME =SMSplash;

DEFINE Precursor = 'C[41] H[73] D[9] O[6] N[2] P[1]' WITH DBR = (0.5,7.5), CHG = +1;
DEFINE FragmentA = 'C[5] H[15] O[4] N[1] P[1]' WITH DBR = (1.5,3.5), CHG = +1;

IDENTIFY
Precursor IN MS1+ AND
FragmentA IN MS2+

REPORT
LipidSpecies = "IS SM 18:1;(OH)2/18:1(+[2]H9)";
LipidClass = "SM";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+H+";
LipidCategory = "Internal standard";
ScanPolarity = "positive";
Intensity = Precursor.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "Precursor";

PrecursorIdentifier = "[SM %d:%d;(OH)%d(+[2]H9) +H]+" % "((Precursor.chemsc)[C] - 5, (Precursor.chemsc)[db] - 0.5, ((Precursor.chemsc)[O] - 4))";
FragmentAIdentifier = "SM(184)";
FragmentBIdentifier = "None";
FragmentCIdentifier = "None";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = "None";
FragmentCIntensity = "None";
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "";
FragmentCERRppm = "";
;

################ end script ##################