TRACES: A Lightweight Browser for Liquid Chromatography–Multiple Reaction Monitoring–Mass Spectrometry Chromatograms
Abstract
:1. Introduction
2. Results and Discussion
2.1. Software Design Concept and Workflow
2.2. Retention Time Alignment
2.3. Compound Library
2.4. Integration Target
2.5. Isotopic Correction of Chromatograms
2.6. Application to Mouse Phospholipid Analysis
3. Materials and Methods
3.1. Chemicals
3.2. LC-MRM-MS
3.3. Software Implementation
3.4. Theories for MS2-Level Isotopic Distribution and Deisotoping
3.5. Lipid Nomenclature and Notation
3.6. Data Processing and Statistics
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Field | Type | Description |
---|---|---|
Name | string | Compound name |
Q1 | numeric | Q1 m/z value |
Q3 | numeric | Q3 m/z value |
CE ** | numeric | Collision energy |
Polarity | string | ‘Positive’ or ‘Negative’ |
Formula * | string | Formula for precursor ion |
MS2Formula * | string | Formula for product ion or neutral loss fragment |
MS2FormulaTyp e * | string | ‘ConstantProduct’ or ‘ConstantNeutralLoss’ |
Tags ** | string | Any strings for search/filter |
Compound | Isotopologue | Q1 m/z | MS1 Abundance | Q3 m/z | MS2 Abundance | Affected Compound |
---|---|---|---|---|---|---|
PC 34:2 * | M0 | 758.6+ | α | 184+ ** | β | (self) |
M1 | 759.6+ | 4.7 × 10−1 α | 184+ | 4.1 × 10−1 β | SM 38:1;O2 | |
185+ | 6.1 × 10−2 β | - | ||||
M2 | 760.6+ | 1.2 × 10−1 α | 184+ | 9.0 × 10−2 β | PC 34:1 | |
185+ | 2.5 × 10−2 β | - | ||||
186+ | 9.8 × 10−3 β | - | ||||
M3 | 761.6+ | 2.4 × 10−2 α | 184+ | 1.4 × 10−2 β | SM 38:0;O2 | |
185+ | 5.4 × 10−3 β | - | ||||
186+ | 4.0 × 10−3 β | - | ||||
187+ | 5.2 × 10−4 β | - | ||||
M4 | 762.6+ | 3.7 × 10−3 α | 184+ | 1.7 × 10−3 β | PC 34:0 | |
185+ | 8.5 × 10−4 β | - | ||||
186+ | 8.8 × 10−4 β | - | ||||
187+ | 2.1 × 10−4 β | - | ||||
188+ | 3.8 × 10−5 β | - |
Compound | Isotopologue | Q1 m/z | MS1 Abundance | Q3 m/z | MS2 Abundance | Affected Compound |
---|---|---|---|---|---|---|
PS 34:2 * | M0 | 758.5− | α | 673.5− ** | β | (self) |
M1 | 759.5− | 4.5 × 10−1 α | 673.5− | 3.7 × 10−2 β | - | |
674.5− | 4.1 × 10−1 β | - | ||||
M2 | 760.5− | 1.2 × 10−1 α | 673.5− | 4.6 × 10−3 β | - | |
674.5− | 1.5 × 10−2 β | - | ||||
675.5− | 9.9 × 10−2 β | PS 34:1 | ||||
M3 | 761.5− | 2.3 × 10−2 α | 673.5− | 1.6 × 10−4 β | - | |
674.5− | 1.9 × 10−3 β | - | ||||
675.5− | 3.7 × 10−3 β | - | ||||
676.5− | 1.7 × 10−2 β | - | ||||
M4 | 762.5− | 3.7 × 10−3 α | 673.5− | 6.3 × 10−6 β | - | |
674.5− | 6.3 × 10−5 β | - | ||||
675.5− | 4.5 × 10−4 β | - | ||||
676.5− | 6.5 × 10−4 β | - | ||||
677.5− | 2.5 × 10−3 β | PS 34:0 |
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Kita, Y.; Tokuoka, S.M.; Oda, Y.; Shimizu, T. TRACES: A Lightweight Browser for Liquid Chromatography–Multiple Reaction Monitoring–Mass Spectrometry Chromatograms. Metabolites 2022, 12, 354. https://doi.org/10.3390/metabo12040354
Kita Y, Tokuoka SM, Oda Y, Shimizu T. TRACES: A Lightweight Browser for Liquid Chromatography–Multiple Reaction Monitoring–Mass Spectrometry Chromatograms. Metabolites. 2022; 12(4):354. https://doi.org/10.3390/metabo12040354
Chicago/Turabian StyleKita, Yoshihiro, Suzumi M. Tokuoka, Yoshiya Oda, and Takao Shimizu. 2022. "TRACES: A Lightweight Browser for Liquid Chromatography–Multiple Reaction Monitoring–Mass Spectrometry Chromatograms" Metabolites 12, no. 4: 354. https://doi.org/10.3390/metabo12040354