National Institute of Plant Genome Research
Digital India   Azadi Ka Amrit Mahotsav     
Metabolomics Facility, NIPGR
Mass spectrometry is a powerful analytical technique that is used to identify unknown compounds and quantify known metabolites.  The Metabolomics Facility at National Institute of Plant Genome Research (NIPGR) funded by the Department of Biotechnology (DBT), Govt. of India began in December 2019 to serve as a state-of-the-art analytical instrumentation platform for plant metabolomics.  It is a one-of-kind facility in India designed for quantification and profiling of plant phytohormones and low abundant metabolites. We provide services for mass spectrometry-based analysis and absolute quantification of various classes of metabolites for various biological studies. The facility is available for both internal and external users. Plant Metabolites that can be detected and quantified in the facility include:
  • Plant Phytohormones (Defense and Growth hormones)

  • Amino acids

  • Flavonoids

  • Primary metabolites

  • Mineral estimation

  • Other low abundant secondary metabolites

Following equipments are available in the Metabolomics facility:
  1. LC-MS/MS (Triple Quadrupole)

  2. GC-MS/MS (Triple Quadrupole)

  3. ICP-MS

  4. HPTLC

  5. U-HPLC

  6. Microwave digestion system

  7. Geno Grinder

  8. Rotatory vaccum evaporator

  9. Ultra-turrax digital homogenizer

  10. Ultra-sonicator

  11. Freezers

  12. Shaker

  13. Speed Vac

  14. Vaccum manifold with pumps

  15. Precision balances

Mass Spectrometry for state-of-art quantification of plant metabolites
1)  Gas Chromatography-Mass spectrometry - GC-MS/MS (TQ8050 NX)

Gas chromatography–mass spectrometry (GC-MS) is an analytical method that combines the features of gas chromatography and mass spectrometry, capable of performing unprecedented quantitative analyses of ultra-trace amounts in high interference matrix. Thermal Desorption System is also available with our equipment.

What can be quantified:  Most of the primary metabolites (e.g. sugars, sugar alcohols, organic acids, organic acid esters, amino acids), benzenoid and terpenoid volatile organic compounds.  Untargeted metabolite profiling on scan mode.


2) Liquid Chromatography-Mass spectrometry- LC- MS/MS (QTRAP 6500+)


The QTRAP-LC-MS/MS system is a hybrid triple quadrapole linear ion trap mass spectrometer. It is used for targeted metabolomics applications

What can be quantified:  Amino acids, Defense phytohormones (e.g. jasmonic acid, abscisic acid, and salicylic acid), Growth phytohormones (e.g. cytokinins, auxins), Secondary metabolites (e.g. phenolic acids, anthocyanins, flavonoids, conjugated phenolic compounds, alkaloids) can be measured in the facility.
3) High Performance Thin Layer Chromatography (HPTLC-CAMAG)

HPTLC is an improved form of TLC with automated devices and is used for fingerprinting of secondary metabolites. Most of the plant derived anthocyanin and flavonoids can be separated through HPTLC in high resolution.


4) Inductively coupled plasma mass spectrometry - ICP-MS (Agilent 7800)

Inductively coupled plasma mass spectrometry (ICP-MS) is a type of mass spectrometry that is used for elemental analysis and detecting trace metals and non-metal ions in a sample.

What can be quantified:  Metal and non-metal elemental ions, ionome profiling



Scientists in-charge:

Jyothilakshmi Vadassery (PI)
Senthil Kumar Muthappa (Co-PI)
Ashutosh Pandey (Co-PI)


External users are requested to contact the facility -
Sample preparation protocols and training will be provided by the facility
A) Section : Links

1) Price List

  1. Price list - GC-MS and LC-MS

  2. Price list - ICP-MS and HPTLC

2) Sample submission form- NIPGR Internal users

3) Sample submission form - External users

4) Facility Poster

5) Methods standardized

B) Section : Staff

Jagdeep Singh (STO)

Achal Prasad (TO)

Divya Goyal (TO)

Khushboo Sharma (SPA)