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Mass Spectrometry Facility

The CUNY ASRC Mass Spectrometry Facility provides analytical services and expertise in mass spectrometry to CUNY researchers and their industrial partners, academic research labs outside the University. Current services support projects from across structural biology, chemistry, and bio-nanotechnology areas. Examples include characterization of new self-assembling biomaterials, intact proteins, small molecule and complex peptide mixtures, PEGylated biopolymers.

The facility maintains ultra-high resolution maXis-II / ETD ESI-q-TOF, equipped with Dionex Ultimate-3000 U(H)PLC and RS-nano-LC systems, and Autoflex-Speed MALDI TOF-TOF mass-spectrometers. Bruker’s maXis-II/ETD features latest developments in TOF technology to provide confidence for accurate mass measurements and molecular formula determination. Bruker’s Autoflex-Speed hardware options include both linear and high-resolution reflectron modes, LIFTTM technology for structural analysis of peptides. Several orders of magnitude dynamic range of both instruments ensure highly sensitive mass measurements at sufficient speed.

The facility offers training on Autoflex MALDI TOF-TOF for researchers planning to use the equipment extensively.

Complete the online application to become a user of this and other ASRC facilities.

Facility Details

  • Bruker Autoflex Speed TOF-TOF

    Bruker Autoflex Speed TOF/TOF ›

    Features a number of options, including linear mode, high-resolution reflectron mode, LIFT technology to enable the use of various MS/MS techniques and fully automated plate management for label-free high throughput screening.
  • Bruker Maxis II ETD

    Bruker maXis-II ETD ESI-qTOF ›

    Equipped with Dionex Ultimate-3000 LC system; combines latest hardware innovations in TOF technology with unique software packages that deliver sub-ppm mass accuracy and up to 80,000 mass resolution.

Standard Service by Staff

Academic Rate – CUNY Academic Rate – External Start-Up Industry
1Standard MM by ESI-MS $50/sample $60/sample $100/sample $150/sample
1Standard MM by MALDI-MS $50/sample $60/sample $80/sample $150/sample

2Advanced Data Acquisition/Analysis

Academic Rate – CUNY Academic Rate – External Start-Up Industry
HDX-MS / Omics-projects $50/hour $55/hour $80/hour $150/hour
Native-ESI-MS / SEC-MS of proteins $50/hour $55/hour $80/hour $150/hour
3 Staff-run data analysis $50/hour $55/hour $80/hour $150/hour


Academic Rate – CUNY Academic Rate – External Start-Up Industry
maXis-II-ETD ESI-QqTOF $50/hour $55/hour $80/hour $150/hour
AutoFlex-TOF-TOF $40/hour $50/hour $65/hour $100/hour

1 Standard mass measurement (MM) by ESI-MS in direct infusion (DI) or LC-MS mode may include between 1- 3 hours of method development time at $50/hour fee.

2 Advanced data acquisition/analysis (minimum 2 hours) implies usage of maXis-II-ESI-Qq-TOF mass-spectrometer in combination with HDX-LEAP robotics, Dionex-3000 and/or Nano-LC systems. This type of analysis includes e.g., HDX-MS, Native-ESI-MS, online Size-Exclusion-MS analysis of proteins, targeted phosphorylated sites analysis, various metabolomics projects. Our regular academic users will receive discounts (please contact Dr. Rinat Abzalimov for details).

3 Staff-run Data analysis implies usage of Metaboscape-2022, HDExaminer-3.3 and other software, and preparation of preliminary data analysis report

4 Our Monday-Friday user-booking policies: max 2 days / week per instrument in advance instrument booking. Minimum usage time – 0.5 hour

Please download Sample Submission Form and fill it out electronically using Adobe Acrobat. Submitter and sample information parts must be filled out completely. Print out the form and attach your labeled sample at the top-right corner of the form (within “attach your sample here” box). We ask internal/external users to deliver samples with completed submission forms to:

CUNY Advanced Science Research Center
Mass Spectrometry Core Facility, SBI 3rd floor
85 Saint Nicholas Terrace
New York, NY 10031

General Information on Sample Preparation

Water, methanol, acetonitrile, tetrahydrofuran, propanol, ethanol, toluene, dichloromethane, nitromethane are MALDI-MS and ESI-MS  compatible solvents, whereas non-volatile solvents as e.g. dimethilformamide or dimethyl sulfoxide are not (though tolerable in small amounts) – so please avoid using them. Protein samples for ESI or MALDI MS should be prepared using ultra-pure water (MilliQ 18MΩ cm, or LC-MS grade bottled water). Common buffers (Tris-HCl, HEPES, phosphate buffers, NaCl) are also not compatible with direct infusion ESI-MS analysis as they cause suppression of ESI/MALDI signal and/or extensive adduct formation.  Appropriate volatile buffers for protein intact mass analysis include formic acid (up to 1%), acetic acid (up to 5%), ammonium acetate (up to 150mM), ammonium formate (up to 10mM), ammonium bicarbonate (up to 20 mM) and ammonium hydroxide.

Measurement accuracy expected at Low-Res is about +-0.05 Da for ESI-MS methods. Mass accuracy at High-Res is better than 5ppm and needed in general for publication purposes.

For more information, please contact: