Options

MSMSfilter:1.0
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:[680.4802]
MSfilter:0.5
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:211129_Virus_Eva_Herker\211129_Virus_Eva_Herker_pos-complement.csv
compress:False
dataType:mzML
dumpMasterScan:False
dumpMasterScanFile:211129_Virus_Eva_Herker\211129_Virus_Eva_Herker_pos-dump.csv
importDir:F:\LipidXplorer-1.2.8.1\211129_Virus_Eva_Herker
importMSMS:True
ini:F:\LipidXplorer-1.2.8.1\lpdxImportSettings_Dom.ini
intensityCorrection:False
isotopesInMasterScan:False
isotopicCorrectionMS:True
isotopicCorrectionMSMS:True
isotopicCorrection_MSMS:False
logMemory:False
loopNr:3
masterScanFileImport:F:\LipidXplorer-1.2.8.1\211129_Virus_Eva_Herker\211129_Virus_Eva_Herker_pos.sc
masterScanFileRun:211129_Virus_Eva_Herker\211129_Virus_Eva_Herker_pos.sc
masterScanImport:F:\LipidXplorer-1.2.8.1\211129_Virus_Eva_Herker\211129_Virus_Eva_Herker_pos.sc
masterScanInSQL:False
masterScanRun:211129_Virus_Eva_Herker\211129_Virus_Eva_Herker_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:211129_Virus_Eva_Herker\211129_Virus_Eva_Herker_pos-out.csv
scanAveragingMethod:linear
selectionWindow:0.4
setting:108
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: 210803_PC_D7_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 = 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: 211201_PC-O_pos_MS_MS184_DB_limit6.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 = (0.5,6.5), 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
isEven(Precursor.chemsc[C])

REPORT
LipidSpecies = "PC O-%d:%d" % "((Precursor.chemsc)[C] - 8, (Precursor.chemsc)[db] - 0.5)";
LipidClass = "PCO";
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: 210204_TAG_D7.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

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 %d:%d(+[2]H7 +HO -TAG(17))" % "( (FragmentA.chemsc[C]), (FragmentA.chemsc[db]))";
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_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: 211201_PC_pos_MS_MS184_DB_limit6.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 = (1.5,7.5), 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+

SUCHTHAT
isEven(Precursor.chemsc[C])

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: 210204_LPC_D7.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 = 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: 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: 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_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_DAG_D7.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 exact mass
# Precursor: [M+NH4]+, C36 H65 D7 O5 N1, 605.5844 m/z
# Fragment: lyso DAG, with missing deuterated fatty acid 18:1(d7)
# Fragment 2: lyso DAG, with missing fatty acid 15:0

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: 210204_SM_pos_MS_MS184.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

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;%d" % "((Precursor.chemsc)[C] - 5, (Precursor.chemsc)[db] - 0.5, (Precursor.chemsc)[O] - 6)";
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;%d +H]+" % "((Precursor.chemsc)[C] - 5, (Precursor.chemsc)[db] - 0.5, (Precursor.chemsc)[O] - 6)";
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: 210204_CE_D7.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 exact mass
# 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: 210303_SM_D9.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

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 d18:1-18:1(+[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;%d(+[2]H9) +H]+" % "((Precursor.chemsc)[C] - 5, (Precursor.chemsc)[db] - 0.5, (Precursor.chemsc)[O] - 6)";
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: 210204_MAG_D7.mfql >>

# Screening for MAG only FullMS
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause 14.10.19
# Splash Precursors,+H+, +NH4+, +CH3COO
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

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 = "";
;

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