Two-dimensional gas chromatography with time of flight mass spectrometer facility

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Two-dimensional Gas Chromatography with time of flight mass spectrometer (GC-GC-TOF-MS) system with gerstel auto sampler can facilitate high end separation of volatile organic compounds in highly complex mixtures and environmental samples. The two-dimensional output helps in resolving the peak of target analytes even when matrix interferences are present. The enhanced spectral collection rate of the TOF-MS detector together with the software capabilities can help in de-convolution of co-eluting compounds.

Make and Model

Leco, Pegasus 4D with Agilent 7890B GC

Available mode for use

  • Following injection modes are possible:

    • Liquid/gas injection
    • Cooled injection system and thermal desorption unit (CIS-TDU)
    • Headspace injection
    • Stir bar sorptive extraction (twister) and solid phase micro-extraction (SPME)
    • Pyrolysis


  • High resolution gas chromatographic separation can be achieved for complex samples, when operated in 2-D mode

  • Independent temperature programming for each of the columns possible

  • MS can collect > 20 full range spectra across a 50ms GC peak

  • High dynamic range can be achieved


  • The system is particularly suitable for applications from following fields:

    • Environmental
    • Geochemistry
    • Biological
    • Chemical/Chemistry


Facility in-charge

Contact Email

gcgctofms[at] iitb[dot] ac[dot] in


Room No. 114, Ground floor,

Centre for Research in Nanotechnology and Science

Registration Link:

Submit New Request

Information-External users

GCxGC ToF_Usage_Charges_18_4_2022.pdf12.35 KB

Registration form-External users

Sample_Proforma_GC_GC_TOF_MS_ext_2018-02-09.pdf90.28 KB
Technical Specifications

Injection Mode
The GC-GC-TOF-MS coupled with Gerstel Sampler can be operated routinely in the following injection modes:

  • Liquid injection mode-Back injector: Only liquid injection is possible
  • Cooled injection system and thermal desorption unit (CIS-TDU)-Front injector: liquid injection; headspace injection, stir bar sorptive extraction (twister) and solid phase micro-extraction (SPME)
  • Pyrolysis mode
  • As of now only liquid injection and headspace injection will be possible. Operation in other modes will be possible at a later date when manpower with specialized training is available.

The columns currently equipped are:
Primary Column: Rxi 5-MS (30 m)
Secondary Column: Rxi 17Sil MS (2 m)

Although column change is possible, column change will not be done frequently. Analysis may be delayed if column change is required.


  • When operated in 2-D mode, higher resolution can be achieved for complex samples
  • Independent temperature programming for each of the columns can be done to enhance resolution.
  • The MS is capable of collecting 20 full range spectra or more across a 50 ms chromatographic peak
  • Higher dynamic range can be achieved due to software capabilities
  • Higher sensitivity


Facility Detailed Application

Facility details are available in the following  link on SAIF page:

The GC-GC-TOF-MS facility was installed in Centre for Research in Nanotechnology and Science (CRNTS) in January 2016 as a Central Facility as per RIFC norms. The facility is available for meeting the research needs of all IIT Bombay internal users. 

It can perform all analysis that a typical GC-TOF-MS can perform. Its particular benefit is for analysis of organic compounds from complex mixtures and environmental samples where high end separation is involved. It involves two columns (that can achieve separation based on different attributes). A thermal modulator ensures cryo focusing of effluent from the first column before its release to the second column. The two-dimensional output helps in resolving the peak of target analytes even when matrix interferences are present. The enhanced spectral collection rate of the TOF-MS detector together with the software capabilities can help in de-convolution of co-eluting compounds.

Central facility presentation
Presented Date Presentation File Presentation by (Prof.) Department
04-12-2017 View Presentation959.64 KB Prof. Suryendu Dutta Centre for Environmental Science and Engineering
28-02-2019 View Presentation925.27 KB Prof. Suryendu Dutta Earth Sciences
Publications using data from this facility

Publications (SCI-Indexed)
• Chand, P. Dutta, S. and Mukherji, S. (2022) “Characterization and Biodegradability Assessment of the Water Accommodated Fraction of Oily Sludge Using Stir Bar Sorptive Extraction and GCxGC-TOF-MS” Environmental Pollution, Accepted. March 2022.

• Umamaheswaran, R., Dutta, S., Khan, M.A., Bera, M., Bera, S., Kumar, S., 2022. Identification of Chitin in Pliocene Fungi Using Py-GC×GC-TOFMS: Potential Implications for the Study of the Evolution of the Fungal Clade in Deep Time. Analytical Chemistry 94, 1958-1964.

• Umamaheswaran, R., Dutta, S., Singh, H., Kumar, S., 2022. Pyrolysis-GC×GC-TOFMS as a tool for distinguishing the macromolecular structure of nitrogen-bearing animal biopolymers in fossil tissues. Journal of Analytical and Applied Pyrolysis 161, 105362.

• Kumar, S., Dutta, S., Bhui, U.K., 2021. Provenance of organic matter in an intracratonic rift basin: insights from biomarker distribution in Palaeogene crude oils of Cambay Basin, western India. Organic Geochemistry 162, 104329.

• Bhattacharya, S., Dutta, S., Kumar, S., 2021. Identification of lanostanes, A-ring methylated steranes and secosteranes in late Neoproterozoic crude oils by GC×GC-TOFMS: New insights into molecular taphonomy of steroids. Geobios68, 47-59.

• Dhiman, H., Dutta, S., Kumar, S., Verma, V., Prasad, G.V.R., 2021. Discovery of proteinaceous moieties in Late Cretaceous dinosaur eggshell. Palaeontology 64, 585-595.

• Mishra, S., Dutta, S., Singh, V.P., Kumar, S., Mathews, R.P., Jha, N., 2021. A new acritarch spike of Leiosphaeridiadessicata comb. nov. emend. from the Upper Permian and Lower Triassic sequence of India (Pranhita-Godavari Basin): Its origin and palaeoecological significance. Palaeogeography,
Palaeoclimatology, Palaeoecology 567, 110274.

• Menon, N.G., Tatiparti, S.S.V. and Mukherji, S. (2021) “Efficacy and reusability of mixed-phase TiO2- ZnO nanocomposites for the removal of estrogenic effects of 17β-estradiol and 17α-ethinylestradiol from water” Journal of Environmental Management, 288:112340.

• Niyolia, D., Dutta, S., Samant, B., 2021. Biomarker Signatures in Cretaceous Sediments of an Island Continent. 30th International Meeting on Organic Geochemistry, Virtual Conference. DOI:

• Mukherji S. “Opportunities and Challenges in Photocatalytic Removal of Micropollutants and Emerging Contaminants” 11th Young Environmental Scientists (YES) Meeting, Society for Environmental Toxicology and Chemistry (SETAC), 7th-9thMarch 2022. Virtual Conference. Keynote Lecture.

• Mukherji S. “Removal of Pharmaceuticals and Pesticides from Water Using Photocatalytic Nanocomposites” Invited Presentation in Half day Symposium on “Detection and Remediation of Emerging Water Contaminants” organized by Department of Instrumentation and Control Engineering, Manipal Institute of Technology (MIT), Manipal, India, 1st March, 2022.

• Ghosh, P. and Mukherji, S. “Development of Methods for Identification and Quantification of Selected PAHs, Heterocyclics, and their Degradation Products” International Conference on Environmental Science & Engineering, Organized by Environmental Science & Engineering Department, IIT Bombay, 20th-22nd January 2022. Poster Presentation.

• Mukherji, S., Jasmine, J. Chand, P. and Dutta, S. “Perspectives on Oily Tank Bottom Sludge and its Slurry Phase Treatment using Indigenous Microbes”, 4th Virtual Conference on “Waste Management Technology Trend and Developments” Organized by MattCorr, 19th and 20th August 2021.

• Mukherji, S., Chand, P. and Datta S. “Slurry phase Biodegradation of Aged Oily Sludge from a Refinery by Indigenous Bacteria and Insights Gained from GCxGC TOF MS Analysis” International Conference on Biotechnology for Sustainable Agriculture, Environment and Health (BSAEH-2021), Jaipur, India, 4th-8th April 2021. Invited Oral Presentation.

Instructions for sample preparation/submission


  • Analysis should be discussed with Dr. Vijaylakshmi/ TA/ facility in-charge before proceeding. Prior literature review for similar sample analysis is recommended for better quality results
  • Users should register online through IRCC webpage
  • Appointment will be given as per queue and user would be informed by e-mail.
  • If an appointment is given but the user cannot come an e-mail should be immediately sent to gcgctofms [at] iitb [dot] ac [dot] in to cancel his/her slot.
  • USB drives are not allowed for copying data to minimize virus related issues. Instead, data must be copied in a new blank CD.

Notes on Sample Preparation for liquid injection

  • The sample should be dissolved in volatile organic solvents, preferably hexane or isooctane.
  • Other solvents like, methanol, ethanol, ethyl acetate etc. can also be used.
  • Solvents such as DMSO, THF and water are not acceptable.
  • The sample should be free of particulates of size > 0.45 μm