Options

MSMSfilter:1.0
MSMSmassrange:(180.0, 950.0)
MSMSminOccupation:0.2
MSMSresolution:14.29 ppm
MSMSresolutionDelta:-70.0
MSMSthreshold:0.001
MSMSthresholdType:relative
MSMStolerance:2.00 ppm
MSMStoleranceType:ppm
MScalibration:[485.3378, 529.4626, 587.4059, 709.5519, 811.6199, 828.5625]
MSfilter:0.5
MSmassrange:(400.0, 950.0)
MSminOccupation:0.2
MSresolution:5.88 ppm
MSresolutionDelta:-100.0
MSthreshold:0.001
MSthresholdType:relative
MStolerance:2.00 ppm
MStoleranceType:ppm
alignmentMethodMS:linear
alignmentMethodMSMS:linear
complementMasterScan:False
complementMasterScanFile:211129_Virus_Eva_Herker\211022_Virus_EH_Batch1_Batch2_Batch3_neg-complement.csv
compress:False
dataType:mzML
dumpMasterScan:True
dumpMasterScanFile:211129_Virus_Eva_Herker\211022_Virus_EH_Batch1_Batch2_Batch3_neg-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_neg.sc
masterScanFileRun:211129_Virus_Eva_Herker\211022_Virus_EH_Batch1_Batch2_Batch3_neg.sc
masterScanImport:F:\LipidXplorer-1.2.8.1\211129_Virus_Eva_Herker\211129_Virus_Eva_Herker_neg.sc
masterScanInSQL:False
masterScanRun:211129_Virus_Eva_Herker\211022_Virus_EH_Batch1_Batch2_Batch3_neg.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\220720_Virus_EH_Batch1_Batch2_Batch3_neg-out.csv
scanAveragingMethod:linear
selectionWindow:0.6
setting:108
settingsPrefix:False
spectraFormat:mzML
statistics:False
sumFattyAcids:False
tabLimited:False
timerange:(336.0, 600.0)

MFQL queries



>> filename: 210204_PI_FA_D7.mfql >>

# Screening for PI
# modified by Daniel Krause 01.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = PISplash;

DEFINE Precursor = 'C[42] H[71] D[7] O[13] P[1]' WITH DBR = (3.5,10.5), CHG = -1;
DEFINE FragmentA = 'C[15] H[20..50] O[2]' WITH DBR = (1.5,7.5), CHG = -1;
DEFINE FragmentB = 'C[18] H[20..49] D[7] O[2]' WITH DBR = (1.5,7.5), CHG = -1;
DEFINE FragmentC = 'C[6] H[10] O[8] P[1]' WITH DBR = (1.5,4.5), CHG = -1; #Headgroup-PI

IDENTIFY
Precursor IN MS1- AND
FragmentA IN MS2- AND
FragmentB IN MS2- AND
FragmentC IN MS2-

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

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

PrecursorIdentifier = "[PI %d:%d_%d:%d(+[2]H7) -H]-" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5, (FragmentB.chemsc)[C], (FragmentB.chemsc)[db] - 1.5)";
FragmentAIdentifier = "FA %d:%d (+O)" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
FragmentBIdentifier = "FA %d:%d(+[2]H7) (+O)" % "((FragmentB.chemsc)[C], (FragmentB.chemsc)[db] - 1.5)";
FragmentCIdentifier = "PI(241)";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = FragmentB.intensity;
FragmentCIntensity = FragmentC.intensity;
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "%2.2f" % "(FragmentB.errppm)";
FragmentCERRppm = "%2.2f" % "(FragmentC.errppm)";
;

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

>> filename: 201215_LCL.mfql >>

# Screening for LysoCardiolipin
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause 01.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = LysoCardiolipin;

DEFINE Precursor = 'Ci[1] C[44..80] H[50..250] O[16] P[2]' WITH DBR = (4,18), CHG = -2;

IDENTIFY
Precursor IN MS1-

SUCHTHAT
isEven(Precursor.chemsc[H])

REPORT
LipidSpecies = "LCL %d:%d" % "((Precursor.chemsc)[C] - 8, (Precursor.chemsc)[db] - 4)";
LipidClass = "LCL";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "-H+";
LipidCategory = "Glycerophospholipid";
ScanPolarity = "negative";
Intensity = Precursor.intensity;
IdentificationLevel = "MS1";
QuantificationIon = "Precursor";

PrecursorIdentifier = "[LCL %d:%d -H]-" % "((Precursor.chemsc)[C] - 8, (Precursor.chemsc)[db] - 4)";
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: 210806_neg_TAG_D7_Ac_MS.mfql >>

# Screening for in negative mode TAG IS - MS1 as acetate adduct
# written 2018 - 03 -27 by Lars F. Eggers, Dominik Schwudke
# modified by Daniel Krause
# 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[53] H[91] D[7] O[8]' WITH DBR = (1.5,19.5), CHG = -1;


IDENTIFY
Precursor IN MS1-

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 = "+CH3COO-";
LipidCategory = "Internal standard";
ScanPolarity = "negative";
Intensity = Precursor.intensity;
IdentificationLevel = "MS1";
QuantificationIon = "Precursor";

PrecursorIdentifier = "[TAG %d:%d(+[2]H7) +CH3COO]-" % "((Precursor.chemsc[C]-5), (Precursor.chemsc[db]-3.5))";
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: 210804_neg_Cer_Ac_MS.mfql >>

# Screening for CerD7 - acetate adduct in negative ione mode
# written 2018 - 03 - 28 by Lars F. Eggers, Dominik Schwudke, Franziska Waldow
# 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
#
# deuterated Ceramide standard
# Cer(d18:1-d7/15:0), C33 H58 D7 NO3, 530.5404 exact mass
# 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]+

QUERYNAME = Ceramides;

DEFINE Precursor = 'C[30..46] H[30..200]N[1] O[5..6]' WITH DBR = (1.5,4.5), CHG = -1;


IDENTIFY
Precursor IN MS1-
REPORT
LipidSpecies = "Cer %d:%d;%d" % "((Precursor.chemsc)[C] - 2, (Precursor.chemsc)[db] - 1.5, (Precursor.chemsc)[O] - 5)";
LipidClass = "Cer";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+CH3COO-";
LipidCategory = "Sphingolipid";
ScanPolarity = "negative";
Intensity = Precursor.intensity;
IdentificationLevel = "MS1";
QuantificationIon = "Precursor";

PrecursorIdentifier = "[Cer %d:%d;%d(+CH3COO)-]" % "((Precursor.chemsc)[C] - 2, (Precursor.chemsc)[db] - 1.5, (Precursor.chemsc)[O] - 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_PE_FA_D7.mfql >>

# Screening for PE
# modified by Daniel Krause 01.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = PESplash;

DEFINE Precursor = 'C[38] H[66] D[7] O[8] N[1] P[1]' WITH DBR = (2.5,9.5), CHG = -1;
DEFINE FragmentA = 'C[15] H[20..50] O[2]' WITH DBR = (1.5,7.5), CHG = -1;
DEFINE FragmentB = 'C[18] H[20..49] D[7] O[2]' WITH DBR = (1.5,7.5), CHG = -1;

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

SUCHTHAT
FragmentA.chemsc + FragmentB.chemsc + 'C5 H11 O4 N1 P1' == Precursor.chemsc

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 = "negative";
Intensity = FragmentB.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "FragmentB";

PrecursorIdentifier = "[PE %d:%d_%d:%d(+[2]H7) -H]-" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5, (FragmentB.chemsc)[C], (FragmentB.chemsc)[db] - 1.5)";
FragmentAIdentifier = "FA %d:%d (+O)" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
FragmentBIdentifier = "FA %d:%d(+[2]H7) (+O)" % "((FragmentB.chemsc)[C], (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: 201215_LPI_MSMS.mfql >>

# Screening for LysoPI - MS/MS
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause 01.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = LysoPhosphatidylinositol;

DEFINE Precursor = 'C[21..33] H[10..140] O[12] P[1]' WITH DBR = (2.5,8.5), CHG = -1;
DEFINE FragmentA = 'C[14..22] H[20..49] O[2]' WITH DBR = (1.5,7.5), CHG = -1;
DEFINE FragmentB = 'C6 H10 O8 P1' WITH CHG = -1;

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

SUCHTHAT
FragmentA.chemsc + FragmentB.chemsc + 'C3 H7 O2' == Precursor.chemsc AND
(FragmentA.chemsc[C]/FragmentA.chemsc[db] >= 2.9)

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

PrecursorIdentifier = "[LPI %d:%d -H]-" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
FragmentAIdentifier = "None";
FragmentBIdentifier = "None";
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_PE_MSMS.mfql >>

# Screening for PE - MS/MS
# modified by Daniel Krause 01.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = Phosphatidylethanolamine;

DEFINE Precursor = 'C[29..53] H[57..105] O[8] N[1] P[1]' WITH DBR = (2.5,12.5), CHG = -1;
DEFINE FragmentA = 'C[14..22] H[20..49] O[2]' WITH DBR = (1.5,7.5), CHG = -1;
DEFINE FragmentB = 'C[14..22] H[20..49] O[2]' WITH DBR = (1.5,7.5), CHG = -1;

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

SUCHTHAT
FragmentA.chemsc + FragmentB.chemsc + 'C5 H11 O4 N1 P1' == Precursor.chemsc AND
(FragmentA.chemsc[C]/FragmentA.chemsc[db] >= 2.9) AND
(FragmentB.chemsc[C]/FragmentB.chemsc[db] >= 2.9)

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

PrecursorIdentifier = "[PE %d:%d_%d:%d -H]-" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5, (FragmentB.chemsc)[C], (FragmentB.chemsc)[db] - 1.5)";
FragmentAIdentifier = "FA %d:%d (+O)" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
FragmentBIdentifier = "FA %d:%d (+O)" % "((FragmentB.chemsc)[C], (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: 201215_LPS_MSMS.mfql >>

# Screening for LysoPS - MS/MS
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause 01.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = LysoPhosphatidylethanolserineMSMS;

DEFINE Precursor = 'C[18..30] H[10..200] O[9] N[1] P[1]' WITH DBR = (2.5,8.5), CHG = -1;
DEFINE FragmentA = 'C[14..22] H[20..49] O[2]' WITH DBR = (1.5,7.5), CHG = -1;
DEFINE FragmentB = 'C3 H5 O2 N1' WITH CHG = 0;

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

SUCHTHAT
FragmentA.chemsc + FragmentB.chemsc + 'C3 H7 P1 O5' == Precursor.chemsc AND
(FragmentA.chemsc[C]/FragmentA.chemsc[db] >= 2.9)

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

PrecursorIdentifier = "[LPS %d:%d -H]-" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
FragmentAIdentifier = "FA %d:%d (+O)" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
FragmentBIdentifier = "-PS(87)";
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_FA_D7.mfql >>

# Screening for LPC
# written 2017 - 01 - 24 by Lars F. Eggers
# modified by Daniel Krause, Dominik Schwudke 01.11.19
# 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[28] H[48] D[7] O[9] N[1] P[1]' WITH CHG = -1;
DEFINE FragmentA = 'C[18] H[26] D[7] O[2]' WITH CHG = -1;
DEFINE FragmentB = 'C[25] H[42] D[7] O[7] N[1] P[1]' WITH CHG = -1;

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

SUCHTHAT
FragmentA.chemsc + FragmentB.nlsc + 'C7 H16 P1 O5 N1' == Precursor.chemsc

REPORT
LipidSpecies = "IS LPC 18:1(+[2]H7)";
LipidClass = "LPC";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+CH3COO-";
LipidCategory = "Internal standard";
ScanPolarity = "negative";
Intensity = FragmentA.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "FragmentA";

PrecursorIdentifier = "[LPC %d:%d +CH3COO-]-" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
FragmentAIdentifier = "FA %d:%d(+[2]H7) (+O)" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)"; # correct "FA %d:%d(+[2]H7)-H"
FragmentBIdentifier = "-PC(74)";
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_O-p_D9.mfql >>

# Screening for PE O-p
# modified by Daniel Krause 01.10.19
# C18(plasm)-18:1(d9) PE
# Fatty acid 18:1 R-O-C(=O)-C-C-C-C-C-C-C-C=C-C-C-C-C-C(D2)-C(D2)-C(D2)-C(D3)
# Vinyl ether, plasmenyl, fatty acid R-O-C=C-C-C-C-C-C-C-C-C-C-C-C-C-C-C-C-C
# m/z: 737.6159
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = PEOpStandard;

DEFINE Precursor = 'C[41] H[70] D[9] O[7] N[1] P[1]' WITH DBR = (2.5,9.5), CHG = -1;
DEFINE FragmentA = 'C[23] H[47] O[6] N[1] P[1]' WITH DBR = (-1.5,7.5), CHG = -1;
DEFINE FragmentB = 'C[18] H[24] D[9] O[2]' WITH DBR = (1.5,7.5), CHG = -1;

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

SUCHTHAT
FragmentA.chemsc + FragmentB.chemsc == Precursor.chemsc + 'H1 O1'

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

PrecursorIdentifier = "[PE O-18:0p-18:1(+[2]H9) -H]-";
FragmentAIdentifier = "FA O-18:0p (+O)";
FragmentBIdentifier = "FA %d:%d(+[2]H9) (+O)" % "((FragmentB.chemsc)[C], (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_SM_MS_MSNL74.mfql >>

# Internal Standard SM Splash in negative mode
# written 2021/08/03 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 = Sphingomyelin;

DEFINE Precursor = 'C[35..51] H[35..200] O[8..9] N[2] P[1]' WITH DBR = (1.5,4.5), CHG = -1;
DEFINE FragmentA = 'C[32..48] H[35..200] O[6..7] N[2] P[1]' WITH DBR = (1.5,5.5), CHG = -1;

IDENTIFY
Precursor IN MS1- AND
FragmentA IN MS2-

SUCHTHAT
FragmentA.chemsc + 'C3 H6 O2' == Precursor.chemsc

REPORT
LipidSpecies = "SM %d:%d;%d" % "((Precursor.chemsc)[C] - 7, (Precursor.chemsc)[db] - 1.5, (Precursor.chemsc)[O] - 8)";
LipidClass = "SM";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+CH3COO-";
LipidCategory = "Sphingolipid";
ScanPolarity = "negative";
Intensity = FragmentA.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "FragmentA";

PrecursorIdentifier = "SM %d:%d;%d(+CH3COO)]-" % "((Precursor.chemsc)[C] - 7, (Precursor.chemsc)[db] - 1.5, (Precursor.chemsc)[O] - 8)";
FragmentAIdentifier = "-SM(74)";
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: 201215_LPE_MSMS.mfql >>

# Screening for LPE - MS/MS
# modified by Daniel Krause 01.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = LysoPhosphatidylethanolamineMSMS;

DEFINE Precursor = 'C[17..29] H[33..57] O[7] N[1] P[1]' WITH DBR = (1.5,7.5), CHG = -1;
DEFINE FragmentA = 'C[14..22] H[20..49] O[2]' WITH DBR = (1.5,7.5), CHG = -1;

IDENTIFY

Precursor IN MS1- AND
FragmentA IN MS2-

SUCHTHAT
FragmentA.chemsc + 'C5 H12 O5 N1 P1' == Precursor.chemsc AND
(FragmentA.chemsc[C]/FragmentA.chemsc[db] >= 2.9)

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

PrecursorIdentifier = "[LPE %d:%d -H]-" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
FragmentAIdentifier = "FA %d:%d (+O)" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
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_PS_MSMS.mfql >>

# Screening for PS - MS/MS
# written 2017 - 02 - 13 by Lars F. Eggers
# modified 180608 Dominik Schwudke
# modified by Daniel Krause 01.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = PhosphatidylserineMSMS;

DEFINE Precursor = 'C[30..54] H[20..200] O[10] N[1] P[1]' WITH DBR = (3.5,13.5), CHG = -1;
DEFINE FragmentA = 'C[14..22] H[20..49] O[2]' WITH DBR = (1.5,7.5), CHG = -1;
DEFINE FragmentB = 'C[14..22] H[20..49] O[2]' WITH DBR = (1.5,7.5), CHG = -1;
DEFINE FragmentC = 'C3 H5 O2 N1' WITH CHG = 0;

IDENTIFY
Precursor IN MS1- AND
FragmentA IN MS2- AND
FragmentB IN MS2- AND
FragmentC IN MS2-

SUCHTHAT
FragmentA.chemsc + FragmentB.chemsc + FragmentC.chemsc + 'C3 H6 P1 O4' == Precursor.chemsc AND
(FragmentA.chemsc[C]/FragmentA.chemsc[db] >= 2.9) AND
(FragmentB.chemsc[C]/FragmentB.chemsc[db] >= 2.9) AND
FragmentA.chemsc[C] <= FragmentB.chemsc[C]

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

PrecursorIdentifier = "[PS %d:%d_%d:%d -H]-" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5, (FragmentB.chemsc)[C], (FragmentB.chemsc)[db] - 1.5)";
FragmentAIdentifier = "FA %d:%d (+O)" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
FragmentBIdentifier = "FA %d:%d (+O)" % "((FragmentB.chemsc)[C], (FragmentB.chemsc)[db] - 1.5)";
FragmentCIdentifier = "-PS(87)";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = FragmentB.intensity;
FragmentCIntensity = FragmentC.intensity;
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "%2.2f" % "(FragmentB.errppm)";
FragmentCERRppm = "%2.2f" % "(FragmentC.errppm)";
;
################ end script ##################

>> filename: 201215_LPA_MSMS.mfql >>

# Screening for LysoPA - MS/MS
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause 01.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = LysoPhosphaticAcidMSMS;

DEFINE Precursor = 'C[15..27] H[20..80] O[7] P[1]' WITH DBR = (1.5,7.5), CHG = -1;
DEFINE FragmentA = 'C[14..22] H[20..49] O[2]' WITH DBR = (1.5,7.5), CHG = -1;

IDENTIFY
Precursor IN MS1- AND
FragmentA IN MS2-

SUCHTHAT
FragmentA.chemsc + 'C3 H7 P1 O5' == Precursor.chemsc AND
(FragmentA.chemsc[C]/FragmentA.chemsc[db] >= 2.9)

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

PrecursorIdentifier = "[LPA %d:%d -H]-" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
FragmentAIdentifier = "FA %d:%d (+O)" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
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: 210806_neg_TAG_Ac_MS.mfql >>

# Screening for in negative mode TAG IS - MS1 as acetate adduct
# written 2018 - 03 -27 by Lars F. Eggers, Dominik Schwudke
# modified by Daniel Krause
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = TAGs;

DEFINE Precursor = 'C[41..77] H[50..250] O[8]' WITH DBR = (2.5,10.5), CHG = -1;


IDENTIFY
Precursor IN MS1-

REPORT
LipidSpecies = "TAG %d:%d" % "((Precursor.chemsc[C]-5), (Precursor.chemsc[db]-3.5))";
LipidClass = "TAG";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+CH3COO-";
LipidCategory = "Glycerolipid";
ScanPolarity = "negative";
Intensity = Precursor.intensity;
IdentificationLevel = "MS1";
QuantificationIon = "Precursor";

PrecursorIdentifier = "[TAG %d:%d(+[2]H7) +CH3COO]-" % "((Precursor.chemsc[C]-5), (Precursor.chemsc[db]-3.5))";
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: 210609_CL_D5.mfql >>

# Screening for Cardiolipin Standard
# 18:2 Cardiolipin-d5
# https://avantilipids.com/product/791108
# Chemical Formula: C81H135D5O17P22-
# Molecular Weight: 1452.9731
# Adduct: -2H+
# m/z: 725.9945
# m/z: with 1 C13 726.4962 (87.6%)
# written by Daniel Krause 09.06.21
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = CardiolipinStandard;

DEFINE Precursor = 'C[80] Ci[1] H[135] D[5] O[17] P[2]' WITH DBR = (-1.5,24), CHG = -2;
DEFINE FragmentA = 'C[18] H[31] O[2]' WITH DBR = (-1.5,7.5), CHG = -1;

IDENTIFY
Precursor IN MS1- AND
FragmentA IN MS2-

REPORT
LipidSpecies = "IS Cardiolipin(+[2]H5) (18:2/18:2)(18:2/18:2)";
LipidClass = "CL";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "-2H+";
LipidCategory = "Internal standard";
ScanPolarity = "negative";
Intensity = FragmentA.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "FragmentA";

PrecursorIdentifier = "[CL(+[2]H5) 72:8 -2H]-";
FragmentAIdentifier = "FA %d:%d (+O)" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
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_PG_FA_D7.mfql >>

# Screening for PG
# modified by Daniel Krause 01.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = PGSplash;

DEFINE Precursor = 'C[39] H[67] D[7] O[10] P[1]' WITH DBR = (2.5,9.5), CHG = -1;
DEFINE FragmentA = 'C[15] H[20..50] O[2]' WITH DBR = (1.5,7.5), CHG = -1;
DEFINE FragmentB = 'C[18] H[20..49] D[7] O[2]' WITH DBR = (1.5,7.5), CHG = -1;

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

SUCHTHAT
FragmentA.chemsc + FragmentB.chemsc + 'C6 H12 P1 O6' == Precursor.chemsc

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

PrecursorIdentifier = "[PG %d:%d_%d:%d(+[2]H7) -H]-" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5, (FragmentB.chemsc)[C], (FragmentB.chemsc)[db] - 1.5)";
FragmentAIdentifier = "FA %d:%d (+O)" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
FragmentBIdentifier = "FA %d:%d(+[2]H7) (+O)" % "((FragmentB.chemsc)[C], (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: 210204_LPE_FA_D7.mfql >>

# Screening for LPE
# modified by Daniel Krause 01.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = LPESplash;

DEFINE Precursor = 'C[23] H[38] D[7] O[7] N[1] P[1]' WITH DBR = (1.5,7.5), CHG = -1;
DEFINE FragmentA = 'C[18] H[20..49] D[7] O[2]' WITH DBR = (1.5,7.5), CHG = -1;

IDENTIFY
Precursor IN MS1- AND
FragmentA in MS2-

SUCHTHAT
FragmentA.chemsc + 'C5 H12 O5 N1 P1' == Precursor.chemsc

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

PrecursorIdentifier = "[PE %d:%d(+[2]H7) -H]-" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
FragmentAIdentifier = "FA %d:%d(+[2]H7) (+O)" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
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_PI_MSMS.mfql >>

# Screening for PI - MS/MS
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause 01.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = PhosphatidylinositolMSMS;

DEFINE Precursor = 'C[33..57] H[30..140] O[13] P[1]' WITH DBR = (3.5,13.5), CHG = -1;
DEFINE FragmentA = 'C[14..22] H[20..49] O[2]' WITH DBR = (1.5,7.5), CHG = -1;
DEFINE FragmentB = 'C[14..22] H[20..49] O[2]' WITH DBR = (1.5,7.5), CHG = -1;
DEFINE FragmentC = 'C6 H10 O8 P1' WITH CHG = -1;

IDENTIFY
Precursor IN MS1- AND
FragmentA IN MS2- AND
FragmentB IN MS2- AND
FragmentC IN MS2-

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

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

PrecursorIdentifier = "[PI %d:%d_%d:%d -H]-" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5, (FragmentB.chemsc)[C], (FragmentB.chemsc)[db] - 1.5)";
FragmentAIdentifier = "FA %d:%d (+O)" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
FragmentBIdentifier = "FA %d:%d (+O)" % "((FragmentB.chemsc)[C], (FragmentB.chemsc)[db] - 1.5)";
FragmentCIdentifier = "PI(241)";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = FragmentB.intensity;
FragmentCIntensity = FragmentC.intensity;
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "%2.2f" % "(FragmentB.errppm)";
FragmentCERRppm = "%2.2f" % "(FragmentC.errppm)";
;

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

>> filename: 210802_PC_O-p_D9.mfql >>

# Screening for PC O-p
# written by Daniel Krause 10.06.21
# C18(plasm)-18:1(d9) PC
# Fatty acid 18:1 R-O-C(=O)-C-C-C-C-C-C-C-C=C-C-C-C-C-C(D2)-C(D2)-C(D2)-C(D3)
# Vinyl ether, plasmenyl, fatty acid R-O-C=C-C-C-C-C-C-C-C-C-C-C-C-C-C-C-C-C
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = PCOpStandard;

DEFINE Precursor = 'C[46] H[80] D[9] O[9] N[1] P[1]' WITH DBR = (2.5,12.5), CHG = -1;
DEFINE FragmentA = 'C[25] H[51] N[1] O[6] P[1]' WITH DBR = (1.5,7.5), CHG = -1;
DEFINE FragmentB = 'C[18] H[24] D[9] O[2]' WITH DBR = (1.5,7.5), CHG = -1;
DEFINE FragmentC = 'C[3] H[6] O[2]' WITH CHG = 0;

IDENTIFY
Precursor IN MS1- AND
FragmentA IN MS2- AND
FragmentB IN MS2- AND
FragmentC IN MS2-

SUCHTHAT
FragmentA.chemsc + FragmentB.chemsc + 'C3 H6 O2' == Precursor.chemsc + 'O1 H1'

REPORT
LipidSpecies = "IS PC O-18:0p-18:1(+[2]H7)";
LipidClass = "PC O-p";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+CH3COO-";
LipidCategory = "Internal standard";
ScanPolarity = "negative";
Intensity = FragmentB.intensity; #deuterated fragment used for quantification
IdentificationLevel = "MS2";
QuantificationIon = "FragmentB";

PrecursorIdentifier = "[PC O-18:0p_18:1(+[2]H7) +CH3COO]-";
FragmentAIdentifier = "FA O-18:0p (+O)";
FragmentBIdentifier = "FA %d:%d(+[2]H7) (+O)" % "((FragmentB.chemsc)[C], (FragmentB.chemsc)[db] - 1.5)";
FragmentCIdentifier = "-PC(74)";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = FragmentB.intensity;
FragmentCIntensity = FragmentC.intensity;
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "%2.2f" % "(FragmentB.errppm)";
FragmentCERRppm = "%2.2f" % "(FragmentC.errppm)";
;

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

>> filename: 210803_SM_D9_MS_MS_NL74.mfql >>

# Internal Standard SM Splash in negative mode
# written 2021/08/03 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 = SMSplash;

DEFINE Precursor = 'C[43] H[75] D[9] O[8] N[2] P[1]' WITH DBR = (2.5,12.5), CHG = -1;
DEFINE FragmentA = 'C[40] H[69] D[9] O[6] N[2] P[1]' WITH DBR = (1.5,7.5), CHG = -1;

IDENTIFY
Precursor IN MS1- AND
FragmentA IN MS2-

SUCHTHAT
FragmentA.chemsc + 'C3 H6 O2' == Precursor.chemsc

REPORT
LipidSpecies = "IS SM 18:1(+[2]H9)";
LipidClass = "SM";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+CH3COO-";
LipidCategory = "Internal standard";
ScanPolarity = "negative";
Intensity = FragmentA.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "FragmentA";

PrecursorIdentifier = "SM %d:%d(+[2]H9) +CH3COO]-" % "((Precursor.chemsc)[C] - 7, (Precursor.chemsc)[db] - 2.5)";
FragmentAIdentifier = "-SM(74)";
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: 201215_CL.mfql >>

# Screening for Cardiolipin
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause 01.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = CardiolipinIsotope;

DEFINE Precursor = 'Ci[1] C[56..104] H[90..250] O[17] P[2]' WITH DBR = (5,24), CHG = -2; # Ci is 13C

IDENTIFY
Precursor IN MS1-

SUCHTHAT
isEven(Precursor.chemsc[H])

REPORT
LipidSpecies = "CL %d:%d" % "((Precursor.chemsc)[C] - 8, (Precursor.chemsc)[db] - 5)";
LipidClass = "CL";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "-H+";
LipidCategory = "Glycerophospholipid";
ScanPolarity = "negative";
Intensity = Precursor.intensity;
IdentificationLevel = "MS1";
QuantificationIon = "Precursor";

PrecursorIdentifier = "[CL %d:%d -H]-" % "((Precursor.chemsc)[C] - 8, (Precursor.chemsc)[db] - 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: 201215_LPG_MSMS.mfql >>

# Screening for LysoPG - MS/MS
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause 01.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = LysoPhosphatidylglycerol;

DEFINE Precursor = 'C[18..30] H[20..80] O[9] P[1]' WITH DBR = (1.5,7.5), CHG = -1;
DEFINE FragmentA = 'C[14..22] H[20..49] O[2]' WITH DBR = (1.5,7.5), CHG = -1;

IDENTIFY

Precursor IN MS1- AND
FragmentA IN MS2-

SUCHTHAT
FragmentA.chemsc + 'C6 H13 P1 O7' == Precursor.chemsc AND
(FragmentA.chemsc[C]/FragmentA.chemsc[db] >= 2.9)

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

PrecursorIdentifier = "[LPG %d:%d -H]-" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
FragmentAIdentifier = "FA %d:%d (+O)" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
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_PA_MSMS.mfql >>

# Screening for PA - MS/MS
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause 01.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = PhosphaticAcidMSMS;

DEFINE Precursor= 'C[27..51] H[30..130] O[8] P[1]' WITH DBR = (2.5,14.5), CHG = -1;
DEFINE FragmentA = 'C[14..22] H[20..49] O[2]' WITH DBR = (1.5,7.5), CHG = -1;
DEFINE FragmentB = 'C[14..22] H[20..49] O[2]' WITH DBR = (1.5,7.5), CHG = -1;

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

SUCHTHAT
FragmentA.chemsc + FragmentB.chemsc + 'C3 H6 P1 O4' == Precursor.chemsc AND
(FragmentA.chemsc[C]/FragmentA.chemsc[db] >= 2.9) AND
(FragmentB.chemsc[C]/FragmentB.chemsc[db] >= 2.9) AND
FragmentA.chemsc[C] <= FragmentB.chemsc[C]

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

PrecursorIdentifier = "[PA %d:%d_%d:%d -H]-" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5, (FragmentB.chemsc)[C], (FragmentB.chemsc)[db] - 1.5)";
FragmentAIdentifier = "FA %d:%d (+O)" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
FragmentBIdentifier = "FA %d:%d (+O)" % "((FragmentB.chemsc)[C], (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: 210204_PA_FA_D7.mfql >>

# Screening for PA
# modified by Daniel Krause 01.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = PASplash;

DEFINE Precursor = 'C[36] H[61] D[7] O[8] P[1]' WITH DBR = (2.5,9.5), CHG = -1;
DEFINE FragmentA = 'C[15] H[20..50] O[2]' WITH DBR = (1.5,7.5), CHG = -1;
DEFINE FragmentB = 'C[18] H[20..49] D[7] O[2]' WITH DBR = (1.5,7.5), CHG = -1;

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

SUCHTHAT
FragmentA.chemsc + FragmentB.chemsc + 'C3 H6 P1 O4' == Precursor.chemsc

REPORT
LipidSpecies = "IS PA 15:0-18:1(+[2]H7)";
LipidClass = "PA";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "-H+";
LipidCategory = "Internal standard";
ScanPolarity = "negative";
Intensity = FragmentB.intensity; #deuterated fragment used for quantification
IdentificationLevel = "MS2";
QuantificationIon = "FragmentB";

PrecursorIdentifier = "[PA %d:%d_%d:%d(+[2]H7) -H]-" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5, (FragmentB.chemsc)[C], (FragmentB.chemsc)[db] - 1.5)";
FragmentAIdentifier = "FA %d:%d (+O)" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
FragmentBIdentifier = "FA %d:%d(+[2]H7) (+O)" % "((FragmentB.chemsc)[C], (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: 210804_neg_Cer_D7_MS.mfql >>

# Screening for CerD7 - acetate adduct in negative ione mode
# written 2018 - 03 - 28 by Lars F. Eggers, Dominik Schwudke, Franziska Waldow
# 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
#
# deuterated Ceramide standard
# Cer(d18:1-d7/15:0), C33 H58 D7 NO3, 530.5404 exact mass
# 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]+

QUERYNAME = CeramideStandard;

DEFINE Precursor = 'C[35] H[61] D[7] N[1] O[5]' WITH DBR = (-1.5,6.5), CHG = -1;


IDENTIFY
Precursor IN MS1-
REPORT
LipidSpecies = "IS Cer d18:1(+[2]H7)/15:0";
LipidClass = "Cer";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+CH3COO-";
LipidCategory = "Internal standard";
ScanPolarity = "negative";
Intensity = Precursor.intensity;
IdentificationLevel = "MS1";
QuantificationIon = "Precursor";

PrecursorIdentifier = "[Cer %d:%d;%d(+CH3COO)-]" % "((Precursor.chemsc)[C] - 2, (Precursor.chemsc)[db] - 1.5, (Precursor.chemsc)[O] - 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_PS_FA_D7.mfql >>

# Screening for PS Standard
# modified by Daniel Krause 01.10.19
# Precursor -H+
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = PSSplash;

DEFINE Precursor = 'C[39] H[66] D[7] O[10] N[1] P[1]' WITH DBR = (3.5,3.5), CHG = -1;
DEFINE FragmentA = 'C[15] H[29] O[2]' WITH DBR = (1.5,3.5), CHG = -1; #241.217304
DEFINE FragmentB = 'C[18] H[26] D[7] O[2]' WITH DBR = (1.5,3.5), CHG = -1; #288.292541
DEFINE FragmentC = 'C[3] H[5] O[2] N[1]' WITH CHG = 0;

IDENTIFY
Precursor IN MS1- AND
FragmentA IN MS2- AND
FragmentB IN MS2- AND
FragmentC IN MS2-

SUCHTHAT
FragmentA.chemsc + FragmentB.chemsc + FragmentC.chemsc + 'C3 H6 P1 O4' == Precursor.chemsc

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

PrecursorIdentifier = "[PS %d:%d_%d:%d(+[2]H7) -H]-" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5, (FragmentB.chemsc)[C], (FragmentB.chemsc)[db] - 1.5)";
FragmentAIdentifier = "FA %d:%d (+O)" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
FragmentBIdentifier = "FA %d:%d(+[2]H7) (+O)" % "((FragmentB.chemsc)[C], (FragmentB.chemsc)[db] - 1.5)";
FragmentCIdentifier = "-PS(87)";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = FragmentB.intensity;
FragmentCIntensity = FragmentC.intensity;
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "%2.2f" % "(FragmentB.errppm)";
FragmentCERRppm = "%2.2f" % "(FragmentC.errppm)";
;

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

>> filename: 210204_PCO_Ac_MSMS.mfql >>

# Screening for PC O- - MSMS
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause 01.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = PhosphatidylcholineEther;

DEFINE Precursor = 'C[34..58] H[69..117] O[9] N[1] P[1]' WITH DBR = (1.5,11.5), CHG = -1;
DEFINE FragmentA = 'C[21..29] H[20..50] N[1] O[6] P[1]' WITH DBR = (0.5,6.5), CHG = -1;
DEFINE FragmentB = 'C[14..22] H[20..49] O[2]' WITH DBR = (1.5,7.5), CHG = -1;

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

SUCHTHAT
FragmentB.chemsc + FragmentA.chemsc + 'C3 H6 O2' == Precursor.chemsc + 'O1 H1' AND
((FragmentA.chemsc[C] + 7)/FragmentA.chemsc[db] + 1 >= 2.9) AND
(FragmentB.chemsc[C]/FragmentB.chemsc[db] >= 2.9)

REPORT
LipidSpecies = "PC O-%d:%d/%d:%d" % "((FragmentA.chemsc)[C] - 7, (FragmentA.chemsc)[db] - 0.5, (FragmentB.chemsc)[C], (FragmentB.chemsc)[db] - 1.5)";
LipidClass = "PC O-";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+CH3COO-";
LipidCategory = "Glycerophospholipid ";
ScanPolarity = "negative";
Intensity = FragmentB.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "FragmentB";

PrecursorIdentifier = "[PC O-%d:%d/%d:%d +CH3COO]-" % "((FragmentA.chemsc)[C] - 7, (FragmentA.chemsc)[db] - 0.5, (FragmentB.chemsc)[C], (FragmentB.chemsc)[db] - 1.5)";
FragmentAIdentifier = "FA %d:%d (+O)" % "((FragmentA.chemsc)[C] - 7, (FragmentA.chemsc)[db] - 0.5)";
FragmentBIdentifier = "FA %d:%d (+O)" % "((FragmentB.chemsc)[C], (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: 210204_PG_MSMS.mfql >>

# Screening for PG - MS/MS
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause 01.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = PhosphatidylglycerolMSMS;

DEFINE Precursor = 'C[30..54] H[30..120] O[10] P[1]' WITH DBR = (2.5,9.5), CHG = -1;
DEFINE FragmentA = 'C[14..22] H[20..49] O[2]' WITH DBR = (1.5,7.5), CHG = -1;
DEFINE FragmentB = 'C[14..22] H[20..49] O[2]' WITH DBR = (1.5,7.5), CHG = -1;

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

SUCHTHAT
FragmentA.chemsc + FragmentB.chemsc + 'C6 H12 P1 O6' == Precursor.chemsc

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

PrecursorIdentifier = "[PG %d:%d_%d:%d -H]-" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5, (FragmentB.chemsc)[C], (FragmentB.chemsc)[db] - 1.5)";
FragmentAIdentifier = "FA %d:%d (+O)" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
FragmentBIdentifier = "FA %d:%d (+O)" % "((FragmentB.chemsc)[C], (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: 210204_LPC_Ac_MSMS.mfql >>

# Screening for LPC - MSMS
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause 01.10.19
# 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[22..34] H[46..70] O[9] N[1] P[1]' WITH DBR = (1.5,7.5), CHG = -1;
DEFINE FragmentA = 'C[14..22] H[20..49] O[2]' WITH DBR = (1.5,7.5), CHG = -1;
DEFINE FragmentB = 'C[3] H[6] O[2]' WITH CHG = 0;

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

SUCHTHAT
FragmentA.chemsc + FragmentB.nlsc + 'C7 H16 P1 O5 N1' == Precursor.chemsc AND
(FragmentA.chemsc[C]/FragmentA.chemsc[db] >= 2.9)

REPORT

LipidSpecies = "LPC %d:%d" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
LipidClass = "LPC";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+CH3COO-";
LipidCategory = "Glycerophospholipid";
ScanPolarity = "negative";
Intensity = FragmentA.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "FragmentA";

PrecursorIdentifier = "[LPC %d:%d +CH3COO]-" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
FragmentAIdentifier = "FA %d:%d (+O)" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
FragmentBIdentifier = "-PC(74)";
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: 210303_PEO.mfql >>

# Screening for PE O- - MS/MS
# modified by Daniel Krause 01.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = PhosphatidylethanolamineEther;

DEFINE Precursor = 'C[29..53] H[57..105] O[7] N[1] P[1]' WITH DBR = (1.5,11.5), CHG = -1;
DEFINE FragmentA = 'C[19..27] H[35..60] O[6] N[1] P[1]' WITH DBR = (0.5,6.5), CHG = -1;
DEFINE FragmentB = 'C[14..22] H[20..49] O[2]' WITH DBR = (1.5,7.5), CHG = -1;

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

SUCHTHAT
FragmentB.chemsc + FragmentA.chemsc - 'O1 H1' == Precursor.chemsc AND
((FragmentA.chemsc[C] + 5)/FragmentA.chemsc[db] + 1 >= 2.9) AND
(FragmentB.chemsc[C]/FragmentB.chemsc[db] >= 2.9)

REPORT
LipidSpecies = "PE O-%d:%d/%d:%d" % "((FragmentA.chemsc)[C] - 5, (FragmentA.chemsc)[db] - 0.5, (FragmentB.chemsc)[C], (FragmentB.chemsc)[db] - 1.5)";
LipidClass = "PE O-";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "-H+";
LipidCategory = "Glycerophospholipid";
ScanPolarity = "negative";
Intensity = FragmentB.intensity;
IdentificationLevel = "MS2";
QuantificationIon = "FragmentB";

PrecursorIdentifier = "[PE O-%d:%d/%d:%d -H]-" % "((FragmentA.chemsc)[C] - 5, (FragmentA.chemsc)[db] - 0.5, (FragmentB.chemsc)[C], (FragmentB.chemsc)[db] - 1.5)";
FragmentAIdentifier = "-FA %d:%d (+HO)" % "((FragmentB.chemsc)[C], (FragmentB.chemsc)[db] - 1.5)";
FragmentBIdentifier = "FA %d:%d (+O)" % "((FragmentB.chemsc)[C], (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: 210204_PC_FA_D7.mfql >>

# Screening for PC
# written 2017 - 02 - 13 Lars F. Eggers
# modified by Daniel Krause 01.10.19
# 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[43] H[76] D[7] O[10] N[1] P[1]' WITH DBR = (2.5,12.5), CHG = -1;
DEFINE FragmentA = 'C[15] H[20..50] O[2]' WITH DBR = (1.5,7.5), CHG = -1;
DEFINE FragmentB = 'C[18] H[20..49] D[7] O[2]' WITH DBR = (1.5,7.5), CHG = -1;
DEFINE FragmentC = 'C[3] H[6] O[2]' WITH CHG = 0;

IDENTIFY
Precursor IN MS1- AND
FragmentA IN MS2- AND
FragmentB IN MS2- AND
FragmentC IN MS2-

SUCHTHAT
FragmentA.chemsc + FragmentB.chemsc + FragmentC.nlsc + 'C7 H15 P1 O4 N1' == Precursor.chemsc

REPORT
LipidSpecies = "IS PC 15:0-18:1(+[2]H7)";
LipidClass = "PC";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+CH3COO-";
LipidCategory = "Internal standard";
ScanPolarity = "negative";
Intensity = FragmentB.intensity; #deuterated fragment used for quantification
IdentificationLevel = "MS2";
QuantificationIon = "FragmentB";

PrecursorIdentifier = "[PC %d:%d_%d:%d(+[2]H7) +CH3COO]-" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5, (FragmentB.chemsc)[C], (FragmentB.chemsc)[db] - 1.5)";
FragmentAIdentifier = "FA %d:%d (+O)" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
FragmentBIdentifier = "FA %d:%d(+[2]H7) (+O)" % "((FragmentB.chemsc)[C], (FragmentB.chemsc)[db] - 1.5)";
FragmentCIdentifier = "-PC(74)";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = FragmentB.intensity;
FragmentCIntensity = FragmentC.intensity;
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "%2.2f" % "(FragmentB.errppm)";
FragmentCERRppm = "%2.2f" % "(FragmentC.errppm)";
;

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

>> filename: 210204_PG_CL_MSMS.mfql >>

# Screening for CL
# modified by Daniel Krause 01.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = CLSplash;

DEFINE Precursor = 'C[39] H[67] D[7] O[10] P[1]' WITH DBR = (2.5,9.5), CHG = -1;
DEFINE FragmentA = 'C[15] H[13..50] O[2]' WITH DBR = (1.5,7.5), CHG = -1;
DEFINE FragmentB = 'C[18] H[13..49] D[7] O[2]' WITH DBR = (1.5,7.5), CHG = -1;

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

SUCHTHAT
FragmentA.chemsc + FragmentB.chemsc + 'C6 H12 P1 O6' == Precursor.chemsc

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

PrecursorIdentifier = "[CL %d:%d_%d:%d(+[2]H7) -H]-" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5, (FragmentB.chemsc)[C], (FragmentB.chemsc)[db] - 1.5)";
FragmentAIdentifier = "FA %d:%d (+O)" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
FragmentBIdentifier = "FA %d:%d(+[2]H7) (+O)" % "((FragmentB.chemsc)[C], (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: 220720_neg_PC_Acetate_MS_MS.mfql >>

# Screening for PC - MSMS
# written 2017 - 02 - 13 by Lars F. Eggers
# modified by Daniel Krause 01.10.19
# according to "Proposal for a common nomenclature for fragment ions in mass spectra of lipids" JK Pauling et al Nov 2017

QUERYNAME = Phosphatidylcholine;

DEFINE Precursor = 'C[34..58] H[69..117] O[10] N[1] P[1]' WITH DBR = (2.5,12.5), CHG = -1;
DEFINE FragmentA = 'C[14..22] H[20..49] O[2]' WITH DBR = (1.5,7.5), CHG = -1;
DEFINE FragmentB = 'C[14..22] H[20..49] O[2]' WITH DBR = (1.5,7.5), CHG = -1;
# DEFINE FragmentC = 'C[3] H[6] O[2]' WITH CHG = 0;

IDENTIFY

Precursor IN MS1- AND
FragmentA IN MS2- AND
FragmentB IN MS2-
# AND FragmentC IN MS2-

SUCHTHAT
FragmentA.chemsc + FragmentB.chemsc + 'C3 H6 O2' + 'C7 H15 P1 O4 N1' == Precursor.chemsc AND
(FragmentA.chemsc[C]/FragmentA.chemsc[db] >= 2.9) AND
(FragmentB.chemsc[C]/FragmentB.chemsc[db] >= 2.9) AND
FragmentA.chemsc[C] <= FragmentB.chemsc[C]

REPORT
LipidSpecies = "PC %d:%d_%d:%d" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5, (FragmentB.chemsc)[C], (FragmentB.chemsc)[db] - 1.5)";
LipidClass = "PC";
Mass = Precursor.mass;
IsobaricClass = Precursor.isobaric;
ChemicalFormula = Precursor.chemsc;
DerivatizedForm = "None";
AdductIon = "+CH3COO-";
LipidCategory = "Glycerophospholipid";
ScanPolarity = "negative";
Intensity = sumIntensity(FragmentA.intensity, FragmentB.intensity)/2;
IdentificationLevel = "MS2";
QuantificationIon = "FragmentA and FragmentB";

PrecursorIdentifier = "[PC %d:%d_%d:%d +CH3COO]-" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5, (FragmentB.chemsc)[C], (FragmentB.chemsc)[db] - 1.5)";
FragmentAIdentifier = "FA %d:%d (+O)" % "((FragmentA.chemsc)[C], (FragmentA.chemsc)[db] - 1.5)";
FragmentBIdentifier = "FA %d:%d (+O)" % "((FragmentB.chemsc)[C], (FragmentB.chemsc)[db] - 1.5)";
FragmentCIdentifier = "None"; # "-PC(74)";
PrecursorIntensity = Precursor.intensity;
FragmentAIntensity = FragmentA.intensity;
FragmentBIntensity = FragmentB.intensity;
FragmentCIntensity = "None"; # FragmentC.intensity;
PrecursorERRppm = "%2.2f" % "(Precursor.errppm)";
FragmentAERRppm = "%2.2f" % "(FragmentA.errppm)";
FragmentBERRppm = "%2.2f" % "(FragmentB.errppm)";
FragmentCERRppm = "None"; # "%2.2f" % "(FragmentC.errppm)";
;

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