Bioinformatic Treatment of Human Metabolome Profile for Diagnostics. Dr. Petr Lokhov & Dr. Alexander Archakov. Institute of Biomedical Chemistry, RAMS. Human metabolome profile for diagnostics. ?. Set of small molecules (<1500Da) in biosample.
Bioinformatic Treatment of Human Metabolome Profile for Diagnostics
Dr. Petr Lokhov & Dr. Alexander Archakov
Institute of Biomedical Chemistry, RAMS
Set of small molecules (<1500Da)
Visual or/and numerical profile of set of small molecules
Biosample from human
LC (liquid chromatography)
CE (capillary electrophoresis)
MS (Mass spectrometry)
Protocols of sample preparation
1. Add methanol
3. Take supernatant
Soft method for protein precipitation (with methanol)
Direct-infusion of plasma metabolites in ion source
High accuracy MS
Reproducible, rapid and cheap method for metabolome profiling
~ 2000 metabolite
ions are detected
~ 2000 main metabolites
in human organism
Beecher C.W.W., in: Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis, Springer, 2003 pp. 311–335.
IonLevel in blood plasma sample Remark
H+ pH ~2.8sample + formic acid
Na+ 136–145 mM physiological conditions
K+ 3.5–60 mM plasma level (3-5 mM)
plus K+ leaked from
erythrocytes (80–120 mM)
Other ions - levels too low for influencing
potassium leaks from cells when plasma is not immediately separated from collected blood, or when blood has been temporarily stored, or plasma is handled roughly
K2Cl+ peaks in mass spectrum
Distribution of K+ in samples
Metabolite profile is multivariable characteristic of an organism.
To avoid overfitting,
the rule of 10–15 samples per variable should be followed.
The dimensionality of the mass spectrometry data should be reduced.
Only PCs useful for diagnostics should be used
Support Vector Machine (SVM) may classify multidimensional data by
formation of a hyperplane in a multidimensional space.
accurate mass tag
Biochemical context for
CA CANCER J CLIN 2010;60:277–300
Lokhov, Archakov et al.
Metabolic Fingerprinting of Blood Plasma from Patients with Prostate Cancer.Biochemistry (Moscow), 2010.
Metabolite profiling of blood plasma of patients with prostate cancer. Metabolomics. 2010
Cancer stage Sensitivity (%) Selectivity (%) Accuracy (%)
I 100.0 93.9
II 91.4 92.3
III 92.3 92.4
IV 93.2 92.5
I-IV 91.1 93.3
Lokhov, Archakov et al.Diagnosis of lung cancer based on direct-infusion electrospray mass spectrometry of blood
plasma metabolites. International Journal of Mass Spectrometry. 2011
Exposure to tobacco
Metabolites reflecting exposure organism to tobacco smoke contribute in diagnostics
Cigarettes smoked per day
Individual differences in
how cigarettes are smoked
Ranges of nicotine intake per
exposure to tobacco smoke
Averaged and inexactly
to tobacco smoke
OR (odd ration) - Risk of disease development
Metabolome profile for diagnostics can be obtained by direct-infusion mass spectrometry of blood plasma sample.
The profile quality can be checked using data from profile itself.
Dimensionality reduction allows following to rule 10-15 samples per variable and select groups of metabolites useful for diagnostics.
Metabolome profile can be used for early diagnostics of lung and prostate cancers as well for calculation of risk of lung cancer development.
One metabolome profile is needed for diagnostics and prognosis of lung cancer.
Program “Proteomics for Medicine and Biotechnology” of Russian Academy of Medical Sciences.
Russian Foundation for Basic Research
Russian N.N. Blokhin Cancer Research Center