MPDB Presentation
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This document describes the design and implementation of an integrated system called MPDB for the storage and analysis of metabolomics data. MPDB was created as a free open-source laboratory information system tailored for the metabolomics workflow. It includes tools for raw data cleanup, compound identification, peak alignment across samples, data normalization, and statistical analysis. The system pipeline allows users to efficiently store large amounts of analytical results and associated biological metadata, perform multi-sample analysis and data mining, and gain new biological insights from metabolomics experiments. As an example application, the document outlines a study analyzing the effects of nitrogen stress on the leaf metabolism of Populus trees using MPDB.
MPDB Presentation
- 1. MPDB - Integrated system for storage and analysis of metabolomic data Design and implementation of the data acquisition and analysis pipeline Alexander Raskind, SFRES MTU
- 2. Omics data availability http://www.ncbi.nlm.nih.gov/Genbank/genbankstats.html Transcriptomics data: ArrayExpress 3670 experiments, 109666 hybridizations http://www.ebi.ac.uk/microarray-as/aer/ Proteomics data: PRIDE 3,537 Experiments 645,869 Identified Proteins http://www.ebi.ac.uk/microarray-as/aer/ Metabolomics data: MMCD 20.306 compounds http://mmcd.nmrfam.wisc.edu/ Human Metabolome Database 2500 compounds http://www.hmdb.ca/
- 3. Shifting research paradigm genome.uiowa.edu http://www.shimadzu.com Targeted analysis High-throughput analysis
- 4. Populus as model system Wide ecological range Small genome relative to other trees Relatively easy transformation and cloning Belongs to Salicaceae Willow family, produces large amount of phenolic compounds that may influence carbon sequestration
- 5. Project rationale Affordable equipment generates limited amount of metabolomic data with modest quality Proper information storage and maximal extraction of useful information are essential Free open source laboratory information system tailored to metabolomics workflow would benefit to a large scientific community
- 6. System requirements Easy access to large arrays of analytical results and biological metadata Tools for data analysis Addition of analysis modules Accommodation of other types of analytical data USER FRIENDLY
- 8. Major analytical problems Chemical complexity of the sample o human metabolome - 2500 metabolites, plants much more Wide dynamic range of response o difference between most and least abundant components may be more than 10,000 Biological variation Matrix effects o Interactions between sample componets leading to shifts in retention time and sensitivity of detection comparative to pure compounds Instrument effects o Shifting retention time (column wearing out and maintenance) o Changes in sensitivity
- 9. Data analysis pipeline Raw data cleanup, peak detection, deconvolution and quantification Compound identification (library search) Export of analysis results and biological metadata to the database Peak alignment and normalization Final data analysis
- 10. System Outline Analyzer-Pro Result (XML format) MP-align GC/MS or LC/MS raw data MPDB Offline Online Data analysis Biological information
- 11. Compound identification NIST 2002 database for GCMS (MS only, ~140,000 entries) In-house database of essential metabolites (MS and retention time, ~200 entries)
- 12. Why we need alignment Single batch Multiple batches
- 15. Signal normalization Raw data Normalized to TIC
- 16. User interface - tasks Data entry New analysis Review analysis Quality control Help
- 18. Sample groups review and annotation
- 20. Data export
- 21. Data sorting and filtering
- 22. Data assessment and analysis Data for individual compound groups Data for individual samples and compounds Principal component analysis Clustering of samples and compounds Graphical maps of compound ratios
- 23. Individual compound group data
- 24. Mass spectral data for the group
- 25. Individual sample and peak details
- 26. PCA
- 27. Clustering
- 28. Compound ratios
- 29. Quality control
- 30. Sample analysis effects of nitrogen stress on the Populus leaf metabolism Plants grown hydroponically N-stress for 8 weeks Samples taken from leaves at different developmental stages (lamina and mid-vien) Metabolites fractionated by SPE Hydrophylic fractions additionally analyzed at 1:20 dilution Fractions were also subjected to glucosidase hydrolysis and LPE 3-5 biological and 1-2 technical replicas
- 31. Leaf hydrophilic fraction Up-regulated by N-stress: o Galacturonic acid (X7), D-Arabinonate, o Turanose, Syringin o Ribose(?), methyl-Galactoside, 3-Hydroxy-3- methylglutaric acid (HMGA), D-(-)-3- Phosphoglyceric acid
- 32. Leaf hydrophilic fraction Down-regulated by N-stress: o Most of free aminoacids and polyamines below detection level or strongly reduced. Also some sugars and polyols, but not clearly identified) o Small organic acids (fumaric, succinic, threonic, citric, malic, oxaloacetic) o Sugar phosphates (glucose, fructose) o Xylose, melibiose, cellobiose
- 33. Acknowledgements Prof. Scott Harding Prof. Chung-Jui Tsai Dr. Changyu Hu Prof. Meir Edelman (WIS)