Metabolomics Resources

Our laboratory has the experience in performing microarray in 4 different platforms that can be using on various samples.
  • Affymetrix: This is the first microarray platform that we had performed.The chips we used were Arabidopsis ATH1 Genome Array Genechip (for Arabidopsis Thaliana) and P. aeruginosa Genome Array Genechip (for Pseudomonas aeruginosa).
  • Arabidopsis: Oligonucleotide Microarrays (Spotted array on glass-slide): We had used this for our Arabidopsis and Brassica microarray. There are ~29,000 elements on each glass-slide that represent whole of the Arabidopsis genome.
  • Illumina:We are trained to run samples in Illumina’s human chips.
  • Combimatrix: We performed our Pseudomonas microarray using this platform (CustomArray 12K and 4 x 2K). We used this to establish hypothesis and we are currently working on some of the interesting features that were revealed by the microarray analysis
  • Nimbelgen: We have worked on Nimblegen microarray platform for Arabidopsis. We have expertise in our lab to perform and analyze the data for this platform.
Currently, we are doing microarray analysis for the following two species with the help of Agilent Technologies and NimbleGen.
Metabolomics:
Our laboratory has the capability to perform metabolomics research in three different types of organisms:- Microbes, Arabidopsis and Rat.
Sample preparation is routinely performed using solid-phase extraction methods. Vacuum manifolds are used along with single cartridges (for large volumes) and 96-well plates (for smaller volumes).
We have a rapid resolution liquid chromatography system (Agilent) for high resolution analytical chromatography. We use electrospray ionization triple quadrupole mass spectrometer (Applied Biosystems) at the Protein and Proteomics Centre (PPC) in the Department of Biological Sciences, for metabolic profiling, fragmentation studies and quantitative analysis of metabolites.
ZIC®-HILIC (Hydrophilic Interaction Liquid Chromatography):
HILIC is a technique suitable for separation of polar and hydrophilic compounds. The elution order in HILIC is generally the opposite of reversed-phase liquid chromatography (RPLC). Thus, HILIC bears similarities with traditional normal-phase liquid chromatography, but with the important distinction that HILIC employs semi-aqueous eluents. Typical eluents for HILIC consist of 40-95% acetonitrile in water or a volatile buffer. HILIC is thus a very MS friendly technique, and by changing from RPLC to HILIC a 10-100 fold increase in sensitivity is often observed for hydrophilic analytes.
Separation of polar compounds :
For application notes on HILIC Separation of Oseltamavir and Oseltamavir Carboxylate please Click here
Metabolomics Data Analysis Tool :
Data analysis is done using an in house developed tool; Metabolomics Data Analysis Tool (METDAT) which enables us to perform data clean up, multivariate statistical analysis as well as data visualization. In addition, we have collaborations with laboratories that have expertise in data management and analysis.