Purpose | Target | Untargeted |
---|---|---|
Target | Known | Unknown compounds |
MS mode | SIM/MRM | Full Scan |
Quantification | Absolut | Relative quantification |
Qualitation | Standards | Semi qualitative |
Study | Validation | Discovery |
Information | Subset analysis | Global analysis |
Demo of GC/LC-MS data
Demo of Obiwarp
Prince, J. T., & Marcotte, E. M. (2006). Chromatographic Alignment of ESI-LC-MS Proteomics Data Sets by Ordered Bijective Interpolated Warping. Analytical Chemistry, 78(17), 6140–6152. doi:10.1021/ac0605344
Loess alignment use local region to align the peaks. However, obiwarp alignment with bijective interpolated dynamic time warping. Raw data from two LC−MS runs, whether successive fractions or across different biological conditions, (1) is interpolated into a (2) uniform matrix (or rectilinear matrix). (3) An all vs all similarity matrix of the spectra is constructed. (4) The similarity matrix distribution is mean centered and normalized by the standard deviation. (5) Dynamic programming is performed by adding similarity scores along a recursively generated optimal path while off-diagonal transitions are penalized by either a local or global gap penalty to give (6) an additive score matrix. (7) Pointers are kept in a traceback matrix used to deliver (8) the optimal alignment path. (9) High scoring points in the optimal path are selected to create a bijective (one-to-one) mapping, which is used as anchors for PCHIP interpolation to generate a smooth warp function. (II) Verification and optimization. (11) MS/MS spectra from the raw MS runs are searched via SEQUEST and Peptide/Protein Prophet to determine peak identities. (12) High-confidence identifications are selected and (13) the overlapping set of peptide identifications (after filtering outliers) is used as the alignment standard. (14) The warp function produced through the comparison of MS data is applied to the standards. (15) The ideal alignment would shift all standards to the diagonal. The accuracy of an alignment is calculated as the sum of the square residuals from the diagonal.
Demo of many GC/LC-MS data
Annotation is similar to find real cat in this picture
Predefined rules between peaks/features and compounds
Generate pseudo-spectrum
Search database or in silico prediction to identify compounds
Build the links between compounds by pathway/network analysis
Features -> Compounds -> Relationship among compounds
Problems
Features -> Compounds -> Relationship among compounds
From Wikipedia Commons:A Sunday on La Grande Jatte, Georges Seurat
Features ->
Compounds-> Relationship among compounds
Unit: Gene(5) < Protein(20+2) < Metabolite(100K) < Compound(100M)
Combination: Gene(20,000-25,000) < Protein(20,000-25,000) < Compound(???)
Small molecular combination is chemical reaction or paired mass distance
Δm=ZmH+Nmn−M
The missing mass was converted into energy ( E=mc2 ) and emitted when the atom made
Atoms -> Compounds -> Mass distances between compounds
Paired Mass Distances(PMD) is unique
High resolution mass spectrometry WINs
Isotopologues
in source reaction
Homologous series
Xenobiotic metabolism
PMD | Freq | Example |
---|---|---|
1.008 | 2037 | NAD(+) + succinate <=> fumarate + H(+) + NADH |
2.016 | 1748 | NAD(+) + propanoyl-CoA <=> acryloyl-CoA + H(+) + NADH |
15.995 | 1170 | ATP + GDP <=> ADP + GTP |
13.979 | 1122 | deoxynogalonate + O2 <=> H(+) + H2O + nogalonate |
17.003 | 929 | H2O + hypotaurine + NAD(+) <=> H(+) + NADH + taurine |
79.966 | 750 | ATP + H2O <=> ADP + H(+) + phosphate |
14.016 | 611 | acetyl-CoA + propanoate <=> acetate + propanoyl-CoA |
0 | 533 | L-glutamate <=> D-glutamate |
162.053 | 365 | H2O + lactose <=> D-galactose + D-glucose |
18.011 | 361 | L-serine <=> 2-aminoprop-2-enoate + H2O |
C | H | O | |
---|---|---|---|
14.016 | 1 | 2 | 0 |
2.016 | 0 | 2 | 0 |
28.031 | 2 | 4 | 0 |
26.016 | 2 | 2 | 0 |
15.995 | 0 | 0 | 1 |
12 | 1 | 0 | 0 |
56.063 | 4 | 8 | 0 |
42.047 | 3 | 6 | 0 |
30.011 | 1 | 2 | 1 |
24 | 2 | 0 | 0 |
PMD | frequency | accuracy | PMD | frequency | accuracy | |
---|---|---|---|---|---|---|
+C2H | 14.016 | 4934 | 0.9755 | 14.02 | 8003 | 0.6014 |
+2H | 2.016 | 4909 | 0.9703 | 2.02 | 7959 | 0.5984 |
+2C4H | 28.031 | 4878 | 0.9783 | 28.03 | 7799 | 0.6119 |
+2C2H | 26.016 | 4229 | 0.9775 | 26.02 | 7343 | 0.5630 |
+O | 15.995 | 4214 | 0.9808 | 15.99 | 7731 | 0.5346 |
+C | 12.000 | 3861 | 0.9826 | 12.00 | 7145 | 0.5310 |
+4C8H | 56.063 | 3861 | 0.9653 | 56.06 | 6699 | 0.5564 |
+3C6H | 42.047 | 3771 | 0.9737 | 42.05 | 6558 | 0.5599 |
+C2HO | 30.011 | 3698 | 0.9440 | 30.01 | 6761 | 0.5163 |
+2C | 24.000 | 3689 | 0.9810 | 24.00 | 6963 | 0.5197 |
PMD | frequency | accuracy | PMD | frequency | accuracy | |
---|---|---|---|---|---|---|
+C2H | 14.0 | 50419 | 0.0955 | 14 | 156245 | 0.0354 |
+2H | 2.0 | 50467 | 0.0944 | 2 | 156260 | 0.0352 |
+2C4H | 28.0 | 50797 | 0.0939 | 28 | 155410 | 0.0356 |
+2C2H | 26.0 | 48517 | 0.0852 | 26 | 154346 | 0.0309 |
+O | 16.0 | 51278 | 0.0806 | 16 | 155811 | 0.0307 |
+C | 12.0 | 49335 | 0.0769 | 12 | 155339 | 0.0283 |
+4C8H | 56.1 | 36417 | 0.1026 | 56 | 151894 | 0.0286 |
+3C6H | 42.0 | 49808 | 0.0737 | 42 | 153764 | 0.0275 |
+C2HO | 30.0 | 51241 | 0.0681 | 30 | 154369 | 0.0260 |
+2C | 24.0 | 48099 | 0.0752 | 24 | 154278 | 0.0273 |
A | B | Ins ratio | C | D | Ins ratio | E | F | Ins ratio |
---|---|---|---|---|---|---|---|---|
100 | 50 | 2:1 | 100 | 50 | 2:1 | 30 | 40 | 3:4 |
1000 | 500 | 2:1 | 10 | 95 | 2:19 | 120 | 160 | 3:4 |
Target analysis could capture peaks with low intensity
Untargeted analysis would loss sensitivity to capture all peaks
Send unknown while independent peaks for MS/MS
Mahieu, N. G., & Patti, G. J. (2017). Systems-Level Annotation of a Metabolomics Data Set Reduces 25 000 Features to Fewer than 1000 Unique Metabolites. Analytical Chemistry, 89(19), 10397–10406. doi:10.1021/acs.analchem.7b02380
Yu, M., Olkowicz, M., & Pawliszyn, J. (2019). Structure/reaction directed analysis for LC-MS based untargeted analysis. Analytica Chimica Acta, 1050, 16–24. doi:10.1016/j.aca.2018.10.062
Independent peaks | Target compounds found | |
---|---|---|
pmd | 985 | 18 |
CAMERA | 1297 | 15 |
RAMclust | 461 | 12 |
profinder | 6628 | 7 |
Only use GlobalStd peaks for MS/MS analysis
MS/MS spectral library annotation on GNPS
Compare with Data Dependent Acquisition (DDA) (173 compounds)
Use pmd and rank of pmd for annotation
Intensity filter(10%) and robust for noise
957/1098 PMDR/HMDB QqQ data
some compounds share the same pmd 87%
Phase I
Phase II
Mass defect analysis to screen Brominated Compounds
Confirmation by synthesized standards
Hou, X., Yu, M., Liu, A., Wang, X., Li, Y., Liu, J., … Jiang, G. (2019). Glycosylation of Tetrabromobisphenol A in Pumpkin. Environmental Science & Technology. doi:10.1021/acs.est.9b02122
Hou, X., Yu, M., Liu, A., Wang, X., Li, Y., Liu, J., … Jiang, G. (2019). Glycosylation of Tetrabromobisphenol A in Pumpkin. Environmental Science & Technology. doi:10.1021/acs.est.9b02122
T3DB Endogenous (255) vs Exogenous (705)
Use top 20 high frequency PMDs
MTBLS28 1005 human urine samples
PMD 2.02 Da show differences among control and diseases
Paper method v.s. Practical method in Metabolomics
Purpose | Target | Untargeted |
---|---|---|
Target | Known | Unknown compounds |
MS mode | SIM/MRM | Full Scan |
Quantification | Absolut | Relative quantification |
Qualitation | Standards | Semi qualitative |
Study | Validation | Discovery |
Information | Subset analysis | Global analysis |
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