obtained with the use of XCMS and Mzmine packages. Full scan data have been used to generate results. PLS score plots for GC-MS urine analysis showing ...
Proceedings of the 54th ASMS Conference on Mass Spectrometry and Allied Topics
Profiling of Urinary Metabolites. Vladimir V. Tolstikov# , Tobias Kind #, Kindra D. Brooks#, Robert H. Weiss* UC Davis Genome Center, Davis, CA GC-TOF-MS profiling
Introduction - Measurement of the small molecules in urine samples has been a part of clinical practice and clinical chemistry for more than 100 years. Since patients with metastatic kidney cancer (RCC) frequently have few if any presenting signs or symptoms, a non-invasive urinary assay for this disease, when applied to high-risk patients, has the potential to markedly reduce disease mortality. In this pilot study, we utilized urine samples from 6 patients with clear cell RCC (various stages and grades) and 6 control patients. We approached urinary metabolic profiling as a method of investigation with the techniques developed and validated in our laboratory.
http://metabolomics-core.ucdavis.edu/
LC-MS profiling
The Pegasus III TOF mass spectrometer (LECO) offers acquisition of up to 500 spectra per second within mass range ~20 - 600 Da and automated peak deconvolution software for unbiased and high quality peak detection and chromatogram comparisons. We have equipped this instrument with robotic derivatization (GERSTEL) and exchange liner (ALEX) in order to diminish externally induced deviations by reaction times, matrix carryovers and analyte cross contaminations.
The ACQUITY UPLC System designed to match the performance needs of WATERS column chemistries with robust hardware and easy-to-use software. With UPLC we have the ability to work more efficiently with higher speed, sensitivity and resolution at a much wider range of linear velocities, flow rates and backpressures to obtain superior results. High speed acquisition offered by FINNIGAN LTQ allows to perform online fragmentation experiments in both positive and negative modes providing detected components with the valuable structural information.
We have tested a number of software packages for sufficient deconvolution, peak picking, and alignment. Here we present the data obtained with the use of XCMS and Mzmine packages. Full scan data have been used to generate results. PLS score plots for GC-MS urine analysis showing clear separation of sick and healthy individuals by 50 important features. Left panels illustrate data aligned by XCMS, right ones aligned by Mzmine 80
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Overview
*- Division of Nephrology, UC Davis, Davis, CA
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PLS score plots for RP-LC-MS (reversed phase) urine analysis showing clear separation of sick and healthy Individuals by 50 important features. 10
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- Samples have been analyzed by GC-TOF-MS, RP-LC-ESIMS and HILIC-LC-ESI-MS. - Multivariate statistics has been applied for data mining.
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PLS score plots for HILIC-LC-MS (hydrophilic interaction) urine analysis showing separation of sick and healthy individuals by 50 important features. 60
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GC-TOF- MS profiles of the identical human urine samples
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Categorized Box & Whisker Plot for HILIC-LC-MS (hydrophilic interaction) components C3061 and C1776. The left plot shows a component which is suppressed in sick individuals. The right plot shows a component which is highly elevated in sick individuals. The plots show the variable mean ± 1.96 times the variable standard deviation (95% confidence interval). 120
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Urinary Metabolites Analysis
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- Results obtained from ANOVA and PLS experiments demonstrated the presence of the important components or metabolites which can be used to discriminate between urine samples from cancer patients and control samples from healthy volunteers based on their urine metabolic profiles.
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Conclusions • GC-MS and LC-MS are two complementary methods providing sufficient information for metabolomics studies. • Three complementary profiling techniques capable of analysis of the polar and non-polar urinary metabolites concluded with the same promising results of possible diagnostics. • Biomarkers finding procedure can be based and supported with the presented results.
