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Mass Spectrometry

The Boyce Thompson Institute Mass Spectrometry Center (BMSC) provides mass spectrometry services to BTI and Cornell University. The instrumentation in the facility is optimized for the analysis of small molecules, facilitating identification of known and unknown metabolites as well as comprehensive metabolic profiling. The facility aims to enable biologists of all levels of expertise to perform mass spectrometric small molecule analyses.


BTI MS Facility


The Thermo Q-Exactive Orbitrap coupled to Dionex ultra-high-pressure chromatography systems is capable of ionization using heated electrospray (HESI), atmospheric pressure chemical ionization (APCI), and nano-flow electrospray (Nano-ESI). The Orbitrap Mass Analyzer combined with advanced quadrupole, S-lens, and a high-performance HCD collision cell for MS/MS plus features such as 12 hz scan rate, data-independent analysis (DIA), selected-ion monitoring (SIM), and spectral multiplexing up to ten precursors/scan make this system a state-of-the-art instrument for chemical and biochemical molecules analysis with 140,000 resolution, < 1 ppm mass accuracy, and femtogram sensitivity.

The Dionex ultra-high-pressure liquid chromatography systems coupled with multiple switch valves and UV data acquisition makes it the system of choice for fully automated high-throughput approaches in the fields of metabolomics, proteomics, and food and environmental safety.


Varian 1200L triple quadrupole MS connected to a Varian CP3800 GC equipped with CombiPal autosampler, with SPME (solid phase micro-extraction) capability, and flame ionization detector.


Micromass Quattro II triple quadrupole MS connected to a Agilent 1100 series HPLC with glass vial autosampler and diode array detector.


Micromass Quattro Ultima benchtop MS/MS connected to a Agilent 1100 series HPLC with glass vial autosampler and diode array detector.

Waters 2790 HPLC

  • Waters 2475 Multi Fluorescence Detector
  • Waters 2487 Dual Absorbance Detector

Waters 2695 HPLC

  • Waters 2996 Photodiode Array Detector
  • Waters 2700 Sample Manager


Training and assistance with the use of the mass spectrometers, software, and data analysis are available to all researchers at BTI and Cornell University. Users with previous mass spectrometry and/or GC/HPLC experience are required to take at least four hours of training. Additional training blocks are available for less experienced users. Training includes method development specifically tailored for each biological application.


Currently, the mass spectrometer is in high demand. To find out about future availability, please contact Navid Movahed.

Contact Us

To schedule an appointment for training or for questions, please contact Navid Movahed.

Our mailing address:
Navid Movahed
Manager, Mass Spectrometer Facility
Office: Room 409/412
Boyce Thompson Institute for Plant Research
533 Tower Road
Ithaca, NY 14853-1801