fragment prediction and assignment for experimental … · fragment prediction and assignment for...
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Advanced Chemistry Development, Inc. (ACD/Labs)
www.acdlabs.comwww.acdlabs.com
Fragment Prediction and Assignment for Experimental Mass
Spectra – v11 updates
Dr Graham A. McGibbonNew Jersey Users Meeting
25 September 2007Hyatt Regency New Brunswick, NJ
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When is a negative a positive?
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Answer:
O
OH
CH3
CH3
CH3
?
When we add negative ion fragmentation to MS Fragmenter and MS
Manager AutoAssign!
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MS Fragmenter negative ion
C- O
OH
CH3
CH3
CH3
m/z 205C13H17O2
M + H - H2
-CO2CH-
CH3
CH3
CH3
m/z 161C12H17
M + H - CH2O2
-CH4 CH-
CH3
CH2
m/z 145C11H13
M + H - C2H6O2
-C3H4 CH-
CH3
m/z 105C8H9
M + H - C5H10O2
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Negative ions rules
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Objectives
Part II: Fragment Assignment of tandem MS data
Part III (optional): Automated Fragment Screening using IntelliXtract
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Example Fragmentation Work FlowIntroduction
Extract fragmentation data – (not covered in this presentation)
Add potential StructureApply Auto-Assignment RulesVerify fragmentation assignmentUpdate fragmentation if requiredStore fragment assignmentsStore fragment schemasReport elucidations
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Adding a structure to a spectrum
Route 1 :- Access to a dictionary of public domain structures using ACD/Dictionary (V9 > 125,000 Entries)
Route 2 :- Cut & Paste from Corporate Structure Editor
Route 3 :- Manually Draw Structure
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Example - SulfadimethoxineRoute 1
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Add Structure
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Attach structure to extracted spectrum
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Fragment generation using Auto-Assignment rule set
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Algorithmic based fragmentation analysisMS2 -Propanolol
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Advanced Spectral Annotation
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Assignment Quality Index (AQI)
Useful for fragmentation spectra containing isotopic fragmentsAQI =
Calculates theoretical isotope contribution using fragment empirical formulaThe experimental contribution of ion intensities are analyzed as a function of the calculated isotope pattern and their m/z0.000 = no match1.000 = exact match
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Impact of AQI in fragment assignment
Assignment of complete spectrum = 85.4 %
Isotopes are excluded in the fragmentation
analysis
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Impact of AQI in fragment assignment
Assignment of complete spectrum = 98.8 %
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Impact of AQI in spectral assignment
Isotopes are included in the fragmentation
analysis
Theoretical m/z & Intensity – supporting accurate mass data
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Rule set improvements in N-Oxide fragmentation
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Visualization of Golden PairsEase of analysis
Linked Golden Pair
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Manual addition of Fragment Ionscomplimentary with algorithmic assignment
Lasso potential fragment region on structure
Adjust for proton addition/loss
Adjust for charge addition/loss
If fragment mass is present in the spectrum <equals +/-mass accuracy> mass of selected fragment then fragment structure can be added to the fragment table
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Neutral Loss Spectrum ModeUseful for spotting classical losses
-2[H2O] -[H2O]
-[C3H6]
Parent Mass Referenced
at 0 Da mass shift
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Partial Structure Representations in support of Elucidation
NH
O
CH3
O
OHOH
OH
OH
O
OH
NH
O
CH3
O
OHOH
OH
OH
O
+[17]
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Linking Partial Structures and Fragmentation spectra
Manual Fragmentation Analysis Method
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ACD/MS Fragmenter example outputStructure based fragmentation schema creation
43N
5 N2
S1
N12
O8
NH19 20
O15
109 18
13 17OH11
1614
CH321
CH3 22
CH323
O6 O
7m/z 348
C13H24N4O5SM
43N
5 N2
S1
N12
O8
NH2+
19 20
O15
109 18
13 17OH11
1614
CH321
CH3 22
CH323
O6 O
7m/z 349
C13H25N4O5SM + H
43N
5 N2
S1
N12
O8
NH3+
19
O15
109 18
13 17OH11
1614
O6 O
7m/z 293
C9H17N4O5SM + H - C4H8
-C4H8
43N
5 N2
S1
N12
O8
NH19 20
O15
109 18
13 17OH11
1614
CH321
CH3 22
CH323
O6 O
7m/z 348
C13H24N4O5SM
43N
5 NH+
2S1
N12
O8
NH19 20
O15
109 18
13 17OH11
1614
CH321
CH3 22
CH323
O6 O
7m/z 349
C13H25N4O5SM + H
43N
5 NH2+
2S1
N12
O8
O15
13 17
1614
O6 O
7m/z 220
C6H10N3O4SM + H - C7H15NO
-C7H15NO
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Databasing fragmentation schemasACD/ChemFolder
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Templated Report
350300250200150100m/z
20
40
60
80
100
Rel
ativ
e In
tens
ity (%
)
332.1
293.2
275.1235.0
220.1
200.0174.1
130.2
43
N5
N2S
1
N12
O8
NH19 20
O15
109 18
13 17OH11
1614
21
2223
O6 O
7
Fragmentation Analysis Report
Operator pdp Parent Ion 349 Plot Type StickSample ID tim p1 ms2 Scan 358Spectrum Assigned 98.8 % [99-355/0-100/0] Spectrum Title TIMP1MS2.D
43N
5 N2
S1
N12
O8
NH19 20
O15
109 18
13 17OH11
1614
CH321
CH3 22
CH323
O6 O
7m/z 348
C13H24N4O5SM
43N
5 N2
S1
N12
O8
NH2+
19 20
O15
109 18
13 17OH11
1614
CH321
CH3 22
CH323
O6 O
7m/z 349
C13H25N4O5SM + H
43N
5 N2
S1
N12
O8
NH3+
19
O15
109 18
13 17OH11
1614
O6 O
7m/z 293
C9H17N4O5SM + H - C4H8
-C4H8
43N
5 N2
S1
N12
O8
NH19 20
O15
109 18
13 17OH11
1614
CH321
CH3 22
CH323
O6 O
7m/z 348
C13H24N4O5SM
43N
5 NH+
2S1
N12
O8
NH19 20
O15
109 18
13 17OH11
1614
CH321
CH3 22
CH323
O6 O
7m/z 349
C13H25N4O5SM + H
43N
5 NH2+
2S1
N12
O8
O15
13 17
1614
O6 O
7m/z 220
C6H10N3O4SM + H - C7H15NO
-C7H15NO
Parent Structure
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Fragment-vendor integration
Able to AutoAssign spectra from:ABI & MDS Sciex LightSight™Waters MassLynx™Thermo Electron Corp. Xcalibur (Qual Browser)™Agilent Technologies ChemStation™(Ion Trap)
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Import additions
Agilent 6000 series LC-MS (*.d\*.bin)
Shimadzu GCMS (*.qgd)
Varian (*xms)
What will you promote next?What will you promote next?
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Recognizing Structure and Spectrum Similarities
Most drug metabolites have some chemical structural similarities to the parent drug
Their mass spectra may thus have similarities
A modification to the parent compound will shift the mass of the metabolite by a set mass (e.g., a hydroxylated metabolite will differ from the mass of the parent by +16 Da).
Modified structural regions may yield fragment ions that are shifted by the same set mass. The metabolite and parent compound may have common substructures, and this may yield common fragment ions.
It is logical to use mass spectral similarities to identify potential metabolites and easy to understand how the similarities can be exploited to extract and elucidate metabolites…but in practice this is can be difficult.
Use the structure-spectrum relationship to identify the sites of modification on the parent drug and display this information, since it is difficult for the user to keep track of when it is difficult to visualize.
P+F+
P+Δ+F+
P+Δ+F+Δ+
Transformation(e.g. Δ = O)
N
N+Δ
N
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ExperimentalMetabolite Incubation
A metabolism study was performed using the drug verapamil. The drug was incubated with human microsomes under the following conditions:
Incubation:Human microsomes/S937°C shaking water bath50 mM Tris buffer @ pH 7.4NADPH regenerating system (NRS) in 2%NaHCO3 (Sigma S-5761) Solution containing:0.5 mg/ml b-NADP (Sigma N-0505)2.0 mg/ml Glucose-6-phosphate (Sigma G7879)1.5 units/ml Glucose-6-phosphate dehydrogenase (Sigma G7877)Equal volume MeCN quenchDrug concentration 100 μl 0.1 mg/ml (final quench volume 2 ml)
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ExperimentalInstrumental
Waters Acquity SDS UPLC™ & Waters Micromass LCT Premier oa-Tof mass spectrometer.
ESI +ve Cone voltage of 40 V to induce Source CIDAccurate Mass CentroidedInternal Calibrant Reference = Leucine enkephalin
A Waters Acquity UPLC BEH C18 column (100 x 2.1 mm, 1.7 μm particle size) was used for the separation, with the following gradient:
Time(min)
AH2O:0.1% HCOOH
BCH3CN:0.1%
HCOOH
0 95 5
15 5 95
18 5 95
18 95 5
21 95 5
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IntelliXtract™ ActiveVerapamil Fragment Analysis
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IntelliXtract Active Fragment Summary
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Demethylation Variant #1
260.2165.2
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Demethylation Variant #2
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Possible Data Input
13C NMR (standard, APT, DEPT)1H NMR1H/13C HS/MQC, HETCOR1H/13C HMBC, long-range HETCOR or variants MW or MF 1H/1H COSY, DQF-COSY, TOCSYNOESY, ROESY, XCORFE, INADEQUATEMultinuclear NMR: 15N, 17O, 31P, 29Si, 19F, 33SIR, MS, elemental compositionPartially assigned NMR data
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Initial Data
MF acquired from an HR/MSStarting material1H, 13C, HMQC, HMBC NMR
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MCD (Molecular Connectivity Diagram)
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Final Result
MF (13C)3.171 ppm1.579 ppm
#1 #2
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Summary
ACD/MS Manager & ACD/MS Fragmenter offer extensive capabilities for manual and assisted spectral interpretationFragmentation analysis for spectra including isotopic peaks can significantly improve fragment assignment quality
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Summary
Combination reporting can enable complex reports to be created to meet a demanding range of applicationsFragmentation schemas can be databased for future reference
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Acknowledgements
Patrick Perkins - Agilent Technologies Inc. for access to example data