Orbitrap ID-X Tribrid mass spectrometerTransforming small molecule identification and characterization
A leap ahead for small molecule analysesAcquisition and interpretation of mass spectra to characterize and identify small-molecule unknowns is a formidable task. Sample complexities, background interferences, compound structural diversity, and the lack of robust data processing tools can make it difficult to set up analytical methods and interpret data. Overcoming these bottlenecks requires advances in both data acquisition and computational tools.
Equipped with the novel, automated AcquireX intelligent data acquisition workflow including various characterization capabilities using intelligent MSn and a multitude of mass spectral data processing tools, the Thermo Scientific™ Orbitrap ID-X™ Tribrid™ mass spectrometer can help you extract meaningful data faster and with the highest confidence.
Acquisition and interpretation of mass spectra to characterize and identify small-molecule unknowns is a formidable task. Sample complexities, background interferences, compound structural diversity, and the lack of robust data processing tools can make it difficult to set up analytical methods and interpret data. Overcoming these bottlenecks requires advances in both data acquisition and computational tools.
Equipped with the novel, automated AcquireX intelligent data acquisition workflow including various characterization capabilities using intelligent MSn and a multitude of mass spectral data processing tools, the Thermo Scientific™ Orbitrap ID-X™ Tribrid™ mass spectrometer can help you extract meaningful data faster and with the highest confidence.
2
Focus on science, not instrument setup The unique combination of Thermo Scientific™ Tribrid™ mass spectrometer architecture, built-in method editor templates, and ready-to-use experimental parameters enable you to analyze complex samples without extensive expertise or effort. The easy-to-use method templates support a variety of small molecule applications to define data acquisition using combinations of high-resolution accurate-mass (HRAM) and ion trap mass analyzers, and MSn fragmentation using either collision-induced dissociation (CID) or high-energy collision dissociation (HCD) techniques.
Collect more meaningful data, not just more dataMS and MSn data acquisition methods for compound identification have been limited by the relative abundances of compounds of interest relative to the background and/or sample matrices. Duty cycle is often wasted triggering on background. Manually excluding background and creating inclusion lists for relevant features is too laborious. A breakthrough in intelligent automation, AcquireX, increases profiling efficiency by automating inclusion/exclusion list creation for MSn data acquisition so you find more compounds with distinguishable fragmentation patterns.
Meet data analysis requirements for speed, simplicity, and flexibility High-quality MSn data generated by the Orbitrap ID-X Tribrid mass spectrometer reduces compound identification bottlenecks. Confidently identify knowns and unknowns, and elucidate structures of unknowns using spectral library searching, MSn mass spectral tree annotation, in silico fragmentation, and precursor ion fingerprinting. High-certainty identification and characterization of small molecules is now remarkably fast.
Demystifying unknown annotation using high-quality MSn data Confidently identify known unknowns and elucidate structures of unknown unknowns with novel spectral prediction tools and processing routines. New data processing methods leverage custom library searching, in silico fragmentation modeling, and precursor ion fingerprinting to associate high-quality MSn data from unknown precursors with compound structures.
Break your bottlenecks with intelligence and technology— from acquisition to analysisGo beyond today’s small molecule analyses and capture more low-abundance analytes in complex samples using intelligent automation and streamlined mass spectral processing, elucidation, and identification software.
3
Building on proven Tribrid architectureThe Orbitrap ID-X Tribrid mass spectrometer is based on the proven and trusted tribrid architecture that combines the best of quadrupole ion trap and HRAM Thermo Scientific™ Orbitrap™ mass analyzer technology for acquisition of the richest MSn data for every sample run. Dual fragmentation techniques—CID and HCD—are available at any stage of MSn, with subsequent mass analysis in either the ion trap or ultra-high-resolution Orbitrap mass analyzer.
t
4
Active Beam GuidePrevents neutrals and high-velocity clusters from entering the mass resolving quadropole
Optional EASY-IC Ion SourceGenerates internal calibrant ions for real-time mass calibration
t
S-LensOptimizes ion transmission into the mass spectrometer, while minimizing in-source fragmentation
Quadrupole Mass FilterSelects precursor ion with resolution up to 0.4 amu; Yields high ion transmission from 50 to 2000 m/z
Dual-Pressure Linear Ion TrapProvides MSn rates up to 40 Hz and sensitive mass analysis of CID and HCD fragment ions
Ultra-High-Field Orbitrap Mass AnalyzerOffers resolution up to 500,000 FWHM and MSn scan rates up to 30 Hz
Ion-Routing MultipoleEnables parallel analysis; Allows HCD at any MSn stage
5
6
Focus on your science, not on instrument setupThe intuitive method editor features a user-friendly interface with predesigned optimized method templates for a wide range of applications.
Effortlessly run advanced experiments
for a variety of applications using validated method
templates Ready-to-use templates with predefined instrument parameters enable generation of high-quality data regardless of analyte chemical structure.
0.86 0.87 0.88 0.89 0.90 0.91 0.92 0.93
Time (min)
0
50
100
Rel
ativ
e A
bund
ance
132.0766-1.5ppm
0.92132.0767-0.75ppm
0.87
132.0767-0.75ppm
0.88
132.0767-0.75ppm
0.88
132.0767-0.75ppm
0.89
132.0767-0.75ppm
0.89
132.0767-0.75ppm
0.90
132.0767-0.75ppm
0.90
132.0767-0.75ppm
0.90
132.0767-0.75ppm
0.91
132.0767-0.75ppm
0.91
Background ExclusionIncrease the MSn sampling efficiency of unknown compounds within one replicate individual, or batch analysis.
Exclusion and Component Inclusion Increase the breadth and depth of compound identification and structural elucidation using various ion tree experiments.
Deep Scan with inclusion and exclusion Attain exhaustive characterization using fully-automated, complex data acquisition enabling comprehensive sample interrogation.
Excellent scan-to-scan mass measurement accuracy Unprecedented run-to-run mass measurement accuracy
Cumulative mass measurement accuracy for replicate LC-MS analyses of 24 small molecule standards conducted over 72 hours.
Orbitrap ID-X Tribrid mass spectrometer analysis of creatine (theorectial m/z of 132.0768) LC-MS analysis.
–3
–2
–1
1
3
5
0 200 400
Molecular weight (DA)
600 800 1000
Match experimental design to your challenging samplesThree modes of AcquireX intelligent data acquisition enable rapid profiling of multiple samples or exhaustive interrogation of replicate sample injections. Each mode increases the number of compounds sampled with distinguishable fragmentation spectra to use for sample and study characterization.
MS internal calibration adds confidenceThe Orbitrap ID-X Tribrid mass spectrometer instrument calibration routine ensures high mass measurement accuracy over the mass range used for small molecule analysis, regardless of the MSn level. The result is high confidence in structural analysis and elucidation for low m/z ions within a sample and over extended periods of time.
7
Collect more meaningful data, not just more dataIntelligent AcquireX efficiently acquires data with significantly less manual experimental setup and interpretation expertise required.
8
The three modes of AcquireX data acquisition permit rapid profiling across multiple samples or exhaustive sample interrogation through replicate injections. Initial analysis of a blank and representative sample enables automated creation of an inclusion/exclusion list used to direct DDA sample analysis. Each replicate injection increases the number of compounds sampled with distinguishable fragmentation spectra for sample and study characterization.
INCLUSION LISTINCLUSION LIST
400.253 400.253
468.271EXCLUSION LIST
322.561
418.253
579.457
EXCLUSION LIST
322.561
418.253
468.271
579.457
EXCLUSION LIST
322.561
400.253
418.253
468.271
579.457
EXCLUSION LIST
Blank Full MSSample Full MS
Sample Iterative DDA
Sample Iterative DDA
Sample Iterative DDA
INCLUSION LIST
MS Method
INCLUSION LIST
MS Method
MS Method
9
Detect up to 140% more unique unknown compounds that are truly experimentally related, even at low abundance as shown in this example of three replicate injections of the NIST SRM 1950 plasma extract sample.
The AcquireX Intelligent data acquisition approach samples more compounds with distinguishable product ion spectra. With each iteration and subsequent injection, the same compounds chosen to be fragmented are eliminated, minimizing redundancy.
Injection1
Injection2
Injection3
1 2Total number of DDA injections
3
73% increase
125% increase139% increase
Traditional DDA DDA with AcquireX
915
1578
1013
2282
1061
2534
Obtain more distinguishable fragmentationFragment more unique unknown compounds
The Orbitrap ID-X Tribrid mass spectrometer improves precursor sampling by automatically updating the inclusion/exclusion lists following each replicate. The data-informed AcquireX approach utilizes sequential injections to interrogate more unique sample components through MSn acquisition. AcquireX more than doubled the number of unique compounds with fragmentation spectra in human plasma (NIST SRM1950) in comparison to traditional DDA, resulting in a greater metabolome coverage.
HIG HE R E FFIC IE NCY
10
Go beyond traditional untargeted metabolomics Increase metabolome coverage and confidence in unknown identification.
Insufficient metabolome annotation has limited the biological interpretation of untargeted metabolomics studies. The Orbitrap ID-X mass spectrometer provides a streamlined approach to routinely achieve comprehensive metabolome coverage with confident compound annotation against spectral libraries to provide compound annotations or perform de novo structural elucidation of unknown metabolites. The power of HRAM Orbitrap mass analyzer technology with AcquireX intelligent acquisition of MSn spectra reinvents the way metabolomics is done today.
Number of compounds with fragmentation spectra
Injection 1
Injection 2
Injection 3
No MS/MS
Traditional DDA DDA with AcquireX
192.0656
94.0651
136.0757
174.0551209.0923
m/z
146.0596
146.0596
128.0493
118.0645
77.038675.0229
m/z
HCD MS/MS
CID MS3
The Orbitrap ID-X Tribrid mass spectrometer offers MSn fragmentation and the flexibility of complementary HCD and CID techniques to increase the probability of generating information-rich product-ion spectra across more compound classes. In this example, fragmentation of the metabolite kynurenine illustrates the complementarity of HCD and CID.
Annotation of more high-quality spectra leads to improved metabolome coverage, comprehensive pathway annotation, and functional interpretation of results. Confident annotations of metabolites in the tryptophan degradation pathway enabled detection of changes in the levels of anthranilic acid in a comparison among healthy donors and donors with Crohn’s disease.
HIG HE R QUA LIT Y
11
“ Confident metabolite identification remains a challenging step in the untargeted metabolomics workflow where the data acquired are applied to derive the structure of all metabolites detected. Progress has been made to putatively annotate metabolites using MS or MS/MS data using established UHPLC/MS assays through the use of metabolomics database and mass spectral library searching workflows. The Orbitrap ID-X Tribrid MS delivers complementary information with multiple dissociation techniques and robust MSn data required to deduce structural information and increase confidence in metabolite annotation. With built-in intelligent data acquisition, AcquireX, we now collect more informative data, and not just more data, we can maximize metabolome coverage and increase confidence in the identification on unknowns applying intelligent-DDA approaches.”
— Warwick Dunn, PhD, Professor in Analytical and Clinical Metabolomics, Phenome Centre Birmingham, School of Biosciences and Institute of Metabolism and Systems Research, University of Birmingham, UK
Complimentary MSn fragmentation of kynurenine metabolite Metabolite intermediate kynurenine identified in a Crohn’s disease study
1.13.11.111.13.11.52
Tryptophan
N-formylkynurenine Kynurenine
Alanine
OH
O
NH2
NH
OH
O
NH
H2N
O
Anthranilic acid
1.60 -0.952.55
O
HN2
HO
OH
O
O
H2N
NH
O
O
OHH2N
O
3.5.1.9
3.7.1.3
In pharmaceutical research and development, small molecule characterization plays a critical role in active pharmaceutical ingredient (API) impurity and metabolite identification, degradation profiling, and analysis of extractables and leachables. High-resolution mass spectrometry (HRMS) is a pivotal tool for these applications. The Orbitrap ID-X Tribid mass spectrometer elevates HRMS to a new level. With AcquireX intelligent data acquisition, complex matrix interferences are removed by automatic background exclusion, ensuring the capture of low-abundance analytes and significantly improving identification. Information-rich MSn fragments provide in-depth structural knowledge of compounds, and facilitate high-confidence identification of unknown or unexpected compounds.
Coupled with the powerful spectral library and data processing software, the Orbitrap ID-X Tribrid mass spectrometer provides the ultimate solution for small molecule structural analysis, significantly increasing accuracy, efficiency, and overall productivity in drug impurity and metabolite identification, extractable and leachable analysis, and other related applications.
Abundantly certain in no time Identify and characterize structures of small molecule pharmaceuticals.
12
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17
Time (min)
0
20
40
60
80
100
Rel
ativ
e A
bun
dan
ce
0
20
40
60
80
100
Rel
ativ
e A
bun
dan
ce
13.3913.5213.29 15.2412.576.336.04 6.52 13.566.755.826.855.365.22 13.61
7.09 12.424.87 12.387.14 14.914.72 14.61 15.4112.347.264.51
7.38 12.2415.774.10 16.0312.093.893.44 10.747.57 10.66 16.617.743.071.211.15 2.43 10.008.88 9.40 17.130.36
14.06
14.22
12.8711.68 13.8910.38
714 716 718 720 722 724 726 728 7300
20
40
60
80
100
Rel
ativ
e A
bun
dan
ce
718.4763
718.9782
725.4829
728.5124726.4994722.2712720.1359 729.5181714.1635724.4760715.7983
723.2744717.9698714.4966
700 705 710 715 720 725 730 7350
20
40
60
80
100
Rel
ativ
e A
bun
dan
ce
702.4810724.9962722.2719
701.4735
700.4627 728.5131
703.4876
732.8096715.1379 731.1905
0.22 ppm
0.22 ppm
Impurity analysis performed using AcquireX data acquisition
Analysis of the excipient sample, along with an analysis to determine background precursors was performed. Background precursors were automatically incorporated into an exclusion list and imported into the refined method. The exclusion list significantly decreased the number of compounds of interest targeted during the DDA method, resulting in more efficient MS/MS and MS3 data acquisition. The highlighted retention times show the measured elution times for two isomeric impurities.
TIC
MS
XIC m/z 722.2715
13
MS3 spectral analysis enables differentiation of impurity structures Overlaying ion tree spectra with in silico dissociation mechanisms to propose impurity structures
Plausible precursor and product ion structures were evaluated using the Fragments and Mechanisms tool in Thermo Scientific™ Mass Frontier™ 8.0 software. The fragmentation pathways of two plausible structures were evaluated for fragmentation pathways to predict formation of the m/z 583.1873 product ion. Structure A has a direct fragmentation pathway justifying the fragmentation of m/z 704 to form the m/z 583 product ion. Structure B predicts that m/z 583.1873 fragment would originate from the m/z 601 MS/MS product ion instead of the m/z 704 product ion.
HRAM MS/MS and MS3 spectra acquired at the retention times 11.68 and 14.06 minutes. The comparative MS/MS spectra show complex, but conserved fragmentation, reducing the confidence in proposing precursor structures that lead to different elution profiles. Specifically, the MS/MS product ions at m/z 704 and 583 are detected for both m/z 722 precursors, however when the m/z 704 MS/MS product ion is isolated and fragmented, only the structure eluting at 11.1 minutes has an MS3 product ion at m/z 583, indicating different precursor structures.
RT 11.68 min Structure “A”
RT 14.06 minStructure “B”
50 100 150 200 250 300 350 400 450 500 550 600 650 700m/z
0
20
40
60
80
100
Rel
ativ
e A
bund
ance
0
20
40
60
80
100
Rel
ativ
e A
bund
ance
722.2714704.2610133.0883
122.0811
201.1276104.0705
89.0596
343.0728188.0555362.1970
279.1106159.1169504.1413 557.209281.0698
583.1879 686.2501
50 100 150 200 250 300 350 400 450 500 550 600 650 700
704.2604
722.2707
201.1274
133.0883
91.0541122.0811
343.0727188.0554 362.1966279.1107
504.140781.0697 686.2489575.2177583.1868
200 250 300 350 400 450 500 550 600 650 700
686.2532
504.1432
362.1962530.1206201.9671
583.1810334.2036
280.3376207.7233
200 250 300 350 400 450 500 550 600 650 700
504.1428
686.2523
362.1957530.1220343.0721
415.9328
OH
H+
HN
HN+H
HN
HOOH
HO
NH
OH
OH
OH
OO
m/z 722.2717
m/z 722.2717
OO
N
FF
F
O
O
O
S
S
FF
F
N
OH
HN
NH
OH
OH
OO
m/z 704.2612
OO
S
FF
F
NNH
OO
m/z 583.1873
OO
+
S
FF
F
N
OO
HN
HN
HOOH2
HO
m/z 722.2717
N
FF
F
O
O
O
S
OO
HN
HN
HO
HO
m/z 704.2612
N
FF
F
O
O
O
S
OO
Lib Lib
-H2O
+
+
H+
RT 11.68 min Structure “A”
RT 14.06 minStructure “B”
50 100 150 200 250 300 350 400 450 500 550 600 650 700m/z
0
20
40
60
80
100
Rel
ativ
e A
bund
ance
0
20
40
60
80
100
Rel
ativ
e A
bund
ance
722.2714704.2610133.0883
122.0811
201.1276104.0705
89.0596
343.0728188.0555362.1970
279.1106159.1169504.1413 557.209281.0698
583.1879 686.2501
50 100 150 200 250 300 350 400 450 500 550 600 650 700
704.2604
722.2707
201.1274
133.0883
91.0541122.0811
343.0727188.0554 362.1966279.1107
504.140781.0697 686.2489575.2177583.1868
200 250 300 350 400 450 500 550 600 650 700
686.2532
504.1432
362.1962530.1206201.9671
583.1810334.2036
280.3376207.7233
200 250 300 350 400 450 500 550 600 650 700
504.1428
686.2523
362.1957530.1220343.0721
415.9328
OH
H+
HN
HN+H
HN
HOOH
HO
NH
OH
OH
OH
OO
m/z 722.2717
m/z 722.2717
OO
N
FF
F
O
O
O
S
S
FF
F
N
OH
HN
NH
OH
OH
OO
m/z 704.2612
OO
S
FF
F
NNH
OO
m/z 583.1873
OO
+
S
FF
F
N
OO
HN
HN
HOOH2
HO
m/z 722.2717
N
FF
F
O
O
O
S
OO
HN
HN
HO
HO
m/z 704.2612
N
FF
F
O
O
O
S
OO
Lib Lib
-H2O
+
+
H+
RT 11.68 min Structure “A”
RT 14.06 minStructure “B”
50 100 150 200 250 300 350 400 450 500 550 600 650 700m/z
0
20
40
60
80
100
Rel
ativ
e A
bund
ance
0
20
40
60
80
100
Rel
ativ
e A
bund
ance
722.2714704.2610133.0883
122.0811
201.1276104.0705
89.0596
343.0728188.0555362.1970
279.1106159.1169504.1413 557.209281.0698
583.1879 686.2501
50 100 150 200 250 300 350 400 450 500 550 600 650 700
704.2604
722.2707
201.1274
133.0883
91.0541122.0811
343.0727188.0554 362.1966279.1107
504.140781.0697 686.2489575.2177583.1868
200 250 300 350 400 450 500 550 600 650 700
686.2532
504.1432
362.1962530.1206201.9671
583.1810334.2036
280.3376207.7233
200 250 300 350 400 450 500 550 600 650 700
504.1428
686.2523
362.1957530.1220343.0721
415.9328
OH
H+
HN
HN+H
HN
HOOH
HO
NH
OH
OH
OH
OO
m/z 722.2717
m/z 722.2717
OO
N
FF
F
O
O
O
S
S
FF
F
N
OH
HN
NH
OH
OH
OO
m/z 704.2612
OO
S
FF
F
NNH
OO
m/z 583.1873
OO
+
S
FF
F
N
OO
HN
HN
HOOH2
HO
m/z 722.2717
N
FF
F
O
O
O
S
OO
HN
HN
HO
HO
m/z 704.2612
N
FF
F
O
O
O
S
OO
Lib Lib
-H2O
+
+
H+
RT 11.68 min Structure “A”
RT 14.06 minStructure “B”
50 100 150 200 250 300 350 400 450 500 550 600 650 700m/z
0
20
40
60
80
100
Rel
ativ
e A
bund
ance
0
20
40
60
80
100
Rel
ativ
e A
bund
ance
722.2714704.2610133.0883
122.0811
201.1276104.0705
89.0596
343.0728188.0555362.1970
279.1106159.1169504.1413 557.209281.0698
583.1879 686.2501
50 100 150 200 250 300 350 400 450 500 550 600 650 700
704.2604
722.2707
201.1274
133.0883
91.0541122.0811
343.0727188.0554 362.1966279.1107
504.140781.0697 686.2489575.2177583.1868
200 250 300 350 400 450 500 550 600 650 700
686.2532
504.1432
362.1962530.1206201.9671
583.1810334.2036
280.3376207.7233
200 250 300 350 400 450 500 550 600 650 700
504.1428
686.2523
362.1957530.1220343.0721
415.9328
OH
H+
HN
HN+H
HN
HOOH
HO
NH
OH
OH
OH
OO
m/z 722.2717
m/z 722.2717
OO
N
FF
F
O
O
O
S
S
FF
F
N
OH
HN
NH
OH
OH
OO
m/z 704.2612
OO
S
FF
F
NNH
OO
m/z 583.1873
OO
+
S
FF
F
N
OO
HN
HN
HOOH2
HO
m/z 722.2717
N
FF
F
O
O
O
S
OO
HN
HN
HO
HO
m/z 704.2612
N
FF
F
O
O
O
S
OO
Lib Lib
-H2O
+
+
H+
RT 11.68 min Structure “A”
RT 14.06 minStructure “B”
50 100 150 200 250 300 350 400 450 500 550 600 650 700m/z
0
20
40
60
80
100
Rel
ativ
e A
bund
ance
0
20
40
60
80
100
Rel
ativ
e A
bund
ance
722.2714704.2610133.0883
122.0811
201.1276104.0705
89.0596
343.0728188.0555362.1970
279.1106159.1169504.1413 557.209281.0698
583.1879 686.2501
50 100 150 200 250 300 350 400 450 500 550 600 650 700
704.2604
722.2707
201.1274
133.0883
91.0541122.0811
343.0727188.0554 362.1966279.1107
504.140781.0697 686.2489575.2177583.1868
200 250 300 350 400 450 500 550 600 650 700
686.2532
504.1432
362.1962530.1206201.9671
583.1810334.2036
280.3376207.7233
200 250 300 350 400 450 500 550 600 650 700
504.1428
686.2523
362.1957530.1220343.0721
415.9328
OH
H+
HN
HN+H
HN
HOOH
HO
NH
OH
OH
OH
OO
m/z 722.2717
m/z 722.2717
OO
N
FF
F
O
O
O
S
S
FF
F
N
OH
HN
NH
OH
OH
OO
m/z 704.2612
OO
S
FF
F
NNH
OO
m/z 583.1873
OO
+
S
FF
F
N
OO
HN
HN
HOOH2
HO
m/z 722.2717
N
FF
F
O
O
O
S
OO
HN
HN
HO
HO
m/z 704.2612
N
FF
F
O
O
O
S
OO
Lib Lib
-H2O
+
+
H+
RT 11.68 min Structure “A”
RT 14.06 minStructure “B”
50 100 150 200 250 300 350 400 450 500 550 600 650 700m/z
0
20
40
60
80
100
Rel
ativ
e A
bund
ance
0
20
40
60
80
100
Rel
ativ
e A
bund
ance
722.2714704.2610133.0883
122.0811
201.1276104.0705
89.0596
343.0728188.0555362.1970
279.1106159.1169504.1413 557.209281.0698
583.1879 686.2501
50 100 150 200 250 300 350 400 450 500 550 600 650 700
704.2604
722.2707
201.1274
133.0883
91.0541122.0811
343.0727188.0554 362.1966279.1107
504.140781.0697 686.2489575.2177583.1868
200 250 300 350 400 450 500 550 600 650 700
686.2532
504.1432
362.1962530.1206201.9671
583.1810334.2036
280.3376207.7233
200 250 300 350 400 450 500 550 600 650 700
504.1428
686.2523
362.1957530.1220343.0721
415.9328
OH
H+
HN
HN+H
HN
HOOH
HO
NH
OH
OH
OH
OO
m/z 722.2717
m/z 722.2717
OO
N
FF
F
O
O
O
S
S
FF
F
N
OH
HN
NH
OH
OH
OO
m/z 704.2612
OO
S
FF
F
NNH
OO
m/z 583.1873
OO
+
S
FF
F
N
OO
HN
HN
HOOH2
HO
m/z 722.2717
N
FF
F
O
O
O
S
OO
HN
HN
HO
HO
m/z 704.2612
N
FF
F
O
O
O
S
OO
Lib Lib
-H2O
+
+
H+
MS3MS/MS
MS3MS/MS
Demystifying unknowns using high-quality MSn data annotationTake advantage of superior MSn data coupled with selective mass-spectral prediction tools and conquer unknown identification challenges.
High-quality MSn data generated by the Orbitrap ID-X Tribrid mass spectrometer combines precursor ion fingerprinting with substructure analysis to facilitate unknown identification. MSn provides more relevant ion fragment information, helps identify isomeric species, and aides unknown compound structure annotation. By performing an MSn tree/subtree search in Mass Frontier 8.0 software against the mzCloud mass spectral library, the substructures present in an unknown compound can be identified by matching the partial MSn spectral tree data. The partial matches can be rank ordered using mzLogic and/or the FISh score to propose the best candidates.
14
Comparative MS/MS spectra for two flavonoid structural isomers where the only structural difference is associated with an aglycone substructure. The addition of the two sugar rings to the base aglycone substructure results in similar MS/MS spectra, prohibiting correct structural identification despite low mass errors for precursor and MS/MS product ions. Incorporation of neutral-loss triggered MS3 acquisition and subsequent analysis results in clearly defining two isomeric compounds.
287.0546
449.1072
433.1124
449.1074
287.0546
433.1125
241.0492165.0180
213.0543
153.0180
258.0519121.0282
231.0648
269.0441133.0282
197.0594
287.0546
111.0075
153.0180
241.0493161.0231135.0439 287.0547259.0598269.0442
219.0648231.0650116.8602
3.7.1.3
1.13.11.111.13.11.52
3.5.1.9
+
L-Tryptophan
Oxygen
N-Formylkynurenine L-Kynurenine
Formate
0.17 0.120.05
0.29 -0.160.35 -0.16 0.14-0.30
L-Alanine-0.20 -0.270.07
Anthranilate1.60 -0.952.55
H
H H
OH
OH
OH
OH
OH
O
OO
O
O
H2N
H2N
NH2NHHN2
+H
HO+
+
+
H
H2N
O
NH2
NH
+
+
OH
OH
OH
O
O
OH
O O
HO
HO
HO
HO
OHO
O
OH
OH
OH
OH
OH
OO
O
O O
OHO
HO
HO
HO
H
H
H
H
HH
H
H
H
H
OH
OH
O
O
O
O
OO
O O
OO
HO
OH
OH
OHHO
HO
HO
HO
HO
H HO
3.7.1.3
1.13.11.111.13.11.52
3.5.1.9
+
L-Tryptophan
Oxygen
N-Formylkynurenine L-Kynurenine
Formate
0.17 0.120.05
0.29 -0.160.35 -0.16 0.14-0.30
L-Alanine-0.20 -0.270.07
Anthranilate1.60 -0.952.55
H
H H
OH
OH
OH
OH
OH
O
OO
O
O
H2N
H2N
NH2NHHN2
+H
HO+
+
+
H
H2N
O
NH2
NH
+
+
OH
OH
OH
O
O
OH
O O
HO
HO
HO
HO
OHO
O
OH
OH
OH
OH
OH
OO
O
O O
OHO
HO
HO
HO
H
H
H
H
HH
H
H
H
H
OH
OH
O
O
O
O
OO
O O
OO
HO
OH
OH
OHHO
HO
HO
HO
HO
H HO
3.7.1.3
1.13.11.111.13.11.52
3.5.1.9
+
L-Tryptophan
Oxygen
N-Formylkynurenine L-Kynurenine
Formate
0.17 0.120.05
0.29 -0.160.35 -0.16 0.14-0.30
L-Alanine-0.20 -0.270.07
Anthranilate1.60 -0.952.55
H
H H
OH
OH
OH
OH
OH
O
OO
O
O
H2N
H2N
NH2NHHN2
+H
HO+
+
+
H
H2N
O
NH2
NH
+
+
OH
OH
OH
O
O
OH
O O
HO
HO
HO
HO
OHO
O
OH
OH
OH
OH
OH
OO
O
O O
OHO
HO
HO
HO
H
H
H
H
HH
H
H
H
H
OH
OH
O
O
O
O
OO
O O
OO
HO
OH
OH
OHHO
HO
HO
HO
HO
H HO
3.7.1.3
1.13.11.111.13.11.52
3.5.1.9
+
L-Tryptophan
Oxygen
N-Formylkynurenine L-Kynurenine
Formate
0.17 0.120.05
0.29 -0.160.35 -0.16 0.14-0.30
L-Alanine-0.20 -0.270.07
Anthranilate1.60 -0.952.55
H
H H
OH
OH
OH
OH
OH
O
OO
O
O
H2N
H2N
NH2NHHN2
+H
HO+
+
+
H
H2N
O
NH2
NH
+
+
OH
OH
OH
O
O
OH
O O
HO
HO
HO
HO
OHO
O
OH
OH
OH
OH
OH
OO
O
O O
OHO
HO
HO
HO
H
H
H
H
HH
H
H
H
H
OH
OH
O
O
O
O
OO
O O
OO
HO
OH
OH
OHHO
HO
HO
HO
HO
H HO
MS/MS results are indistinguishable without spectra from standards
MS3 results easily distinguish the isomers
Luteolin 7-rutinoside
Kaempferol 3-O-β-rutinoside
3.7.1.3
1.13.11.111.13.11.52
3.5.1.9
+
L-Tryptophan
Oxygen
N-Formylkynurenine L-Kynurenine
Formate
0.17 0.120.05
0.29 -0.160.35 -0.16 0.14-0.30
L-Alanine-0.20 -0.270.07
Anthranilate1.60 -0.952.55
H
H H
OH
OH
OH
OH
OH
O
OO
O
O
H2N
H2N
NH2NHHN2
+H
HO+
+
+
H
H2N
O
NH2
NH
+
+
OH
OH
OH
O
O
OH
O O
HO
HO
HO
HO
OHO
O
OH
OH
OH
OH
OH
OO
O
O O
OHO
HO
HO
HO
H
H
H
H
HH
H
H
H
H
OH
OH
O
O
O
O
OO
O O
OO
HO
OH
OH
OHHO
HO
HO
HO
HO
H HO
3.7.1.3
1.13.11.111.13.11.52
3.5.1.9
+
L-Tryptophan
Oxygen
N-Formylkynurenine L-Kynurenine
Formate
0.17 0.120.05
0.29 -0.160.35 -0.16 0.14-0.30
L-Alanine-0.20 -0.270.07
Anthranilate1.60 -0.952.55
H
H H
OH
OH
OH
OH
OH
O
OO
O
O
H2N
H2N
NH2NHHN2
+H
HO+
+
+
H
H2N
O
NH2
NH
+
+
OH
OH
OH
O
O
OH
O O
HO
HO
HO
HO
OHO
O
OH
OH
OH
OH
OH
OO
O
O O
OHO
HO
HO
HO
H
H
H
H
HH
H
H
H
H
OH
OH
O
O
O
O
OO
O O
OO
HO
OH
OH
OHHO
HO
HO
HO
HO
H HO
Meet your data analysis requirements with speed, simplicity, and flexibility Overcome challenges in small molecule full-scan data analysis and interpretation with Compound Discoverer software.
Thermo Scientific™ Compound Discoverer™ software efficiently extracts high-confidence insights from information-rich, small-molecule HRAM data. It serves as a hub to seamlessly connect you to the tools needed to analyze large amounts of HRAM data productively and confidently.
15
mzCloud™ mass spectral libraryRank search more effectively with the industry-leading online spectra fragmentation library
mzLogic algorithmFast, automated logical analysis eliminates thousands of candidates and hours of work
Mass Frontier spectral interpretation softwareSupports MSn spectral ion tree searching and custom libraries
Leverage MSn data to find best candidate structures
Monitor your system, access your data and system remotely and securely from anywhere in the world. Leverage real-time monitoring of your instrument with automatic email notifications anytime, anywhere. Store data in secure accounts and share with colleagues and collaborators around the world.
Technical support: peak performance for your instruments
Helping you keep your instruments running at peak performance is our goal. Whether you’re looking for an instrument manual or spare parts or want to submit a repair request or check on the status of your warranty or service contract, we have every support option you’re looking for.
Protecting your investments: unparalleled laboratory services
Unity™ Lab Services provides a single source for integrated lab service, support, and supply management. Our customized service offerings and world-class service experts have the flexibility and experience to effectively address your laboratory’s business needs. We provide a complete portfolio of services and support solutions designed to help you improve productivity, reduce total cost of ownership, and ensure performance throughout your laboratory—from instrument and equipment acquisition to disposition.
Thermo Fisher Cloud
Find out more at thermofisher.com/orbitrapID-X
For Research Use Only. Not for use in diagnostic procedures. © 2018 Thermo Fisher Scientific Inc. All rights reserved. mzCloud is a registered trademark of HighChem LLC. All other trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. BR65171-EN 0818M