Biomolecular Mass Spectrometry Facility

The CUNY ASRC Biomolecular Mass Spectrometry Facility provides analytical services and expertise in mass spectrometry to CUNY researchers, industrial partners, and academic laboratories outside the University. The facility supports projects across structural biology with particular expertise in hydrogen–deuterium exchange mass spectrometry (HDX-MS) and untargeted metabolomics. Representative applications include characterization of protein conformational dynamics and interactions, intact proteins, biopharmaceuticals, complex peptide mixtures, metabolites, PEGylated biopolymers, self-assembling biomaterials, and spatial molecular analysis of tissues by mass spectrometry imaging.

The facility maintains an high-resolution Bruker maXis-II ETD ESI-qTOF mass spectrometer equipped with Dionex Ultimate 3000 U(H)PLC and RS nano-LC systems, a Bruker NeofleX MALDI TOF-TOF, and a Bruker timsTOF fleX MALDI-2 instrument. The Bruker timsTOF fleX MALDI-2 serves as the primary platform for HDX-MS, enabling studies of protein higher-order structure and conformational dynamics.

The facility provides untargeted metabolomics workflows using high-resolution LC-MS and ion mobility separations for broad molecular profiling and identification of metabolites in complex biological samples. The integration of accurate mass measurements, tandem MS, ion mobility, and advanced data analysis tools enables comprehensive metabolite characterization and improved molecular annotation.

The facility offers training on HDX-MS workflows, untargeted metabolomics, NeofleX MALDI TOF-TOF, and timsTOF fleX MALDI-2 instrumentation for researchers planning extensive independent use of the equipment.

This Core Facility uses iLab. Please click on the button below for instructions to request access and use our services.

Become a User

Facility Details

Instruments and Tools

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.
Bruker timsTOF-flex MALDI-2 with microGRID ›
The Bruker timsTOF fleX equipped with MALDI-2 and microGRID technology provides advanced capabilities for high-resolution MALDI imaging of biological tissues. MALDI-2 post-ionization significantly enhances ion yields, particularly for low-abundance and poorly ionizing molecules such as lipids and metabolites, thereby improving sensitivity and molecular coverage. The microGRID feature enables precise, reproducible laser positioning and finely controlled sampling patterns, supporting high spatial resolution and uniform pixel-to-pixel data quality across large tissue areas. Together, these capabilities allow for detailed mapping of molecular distributions with improved dynamic range and reproducibility. As a result, the system is well suited for spatial metabolomics and lipidomics studies requiring both high sensitivity and spatial fidelity.

Usage Rates

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

⁴User-Run

	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

Sample Submissions

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:

Rinat Abzalimov, Ph.D. Director, Mass Spectrometry Facility
Co-Director, MALDI-TOF MS Imaging Facility
Research Associate Professor, Structural Biology Initiative
Email: [email protected]
Phone: 212.413.3236