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CUNY Mass Spectrometry Facility @ Hunter College

*Small Molecules to Intact Proteins*

“Your Ions Are Important To Us”

The CUNY Mass Spectrometry Facility at Hunter College provides a wide variety of mass spectrometry services
to research laboratories at Hunter College, other CUNY campuses, and many outside organizations.

Hunter College Chemistry Department
Room 1315B North Building
695 Park Avenue, New York, NY 10065
Phone: (212) 650-3590 | Fax: (212) 772-5332



Agilent 6520 Q-TOF

AgilentG6520.gifHigh resolution mass spectrometer system complete with Agilent 1200 capillary HPLC system and all ionization sources listed below. The instrument has a mass range of 50-20000amu with a mass accuracy of 2ppm using an internal mass reference. Data can be collected in either positive or negative mode. Molecular formula confirmation is provided for small molecules. Analysis of intact proteins up to 250kD is accomplished by electrospray ionization, which gives multiple charging, followed by deconvolution of the data using Agilent's Bioconfirmation software. Peptide mass fingerprinting and/or MS/MS data analysis of protein digests is performed using Agilent's Spectrum Mill Software. Other software packages such as Agilent’s Mass Profiler, used for expression profiling analysis, Metlin  Metabolite Database and MassHunter Metabolite ID software, for metabolite identification.

Funding for this instrument system was provided by NIH Shared Instrumentation Grant 1S10RR022649-01 and the CUNY Instrumentation Fund. We would also like to express our appreciation to the National Center for Research Resources.

Agilent 6340 Ion Trap with Electron Transfer Dissociation

AgilentG6340.gifIon Trap mass spectrometer system complete with capillary HPLC system, electron transfer dissociation, and all ionization sources listed below. This instrument has a mass range of 50-4000amu and can perform 5 stages of automated MS/MS or 11 stages of manual MS/MS. The instrument is equipped with polarity switching allowing the collection of both positive and negative ion spectra during the analysis. Protein database searching software is available to process data.

Funding for this instrument system was provided by National Science Foundation Major Research Instrumentation Grant # 0521085

Ionization Sources

  • Electrospray Ionization
  • Atmospheric Pressure Chemical Ionization
  • Atmospheric Pressure Photoionization
  • Multimode Ionization (simultaneous electrospray and atmospheric pressure chemical ionization)
  • Matrix Assisted Laser Desorption Ionization
  • Chip Cube (nanospray interface)

Spectrum Mill Protein Database Software


Directions To The Facility:

The CUNY Mass Spectrometry Facility @ Hunter College is located in room 1315B of the North Building of Hunter College. The entrance to the building is on 69th street between Lexington and Park Avenues on the south side of the block. Upon entering the building, go to the elevator bank on your right side (they go to the higher floors). Take the elevator to the 13th floor and exit to your left. Go all the way to the end of the hallway. Make a right turn and go about 5 ft and make a left turn. Go straight down the short hallway (grey floor) for about 15ft and you will be at the door to the facility.