All Facilities | All Instruments
Biomolecular Mass Spectrometry Facility
The CUNY ASRC Biomolecular 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.
This Core Facility uses iLab. Please click on the button below for instructions to request access and use our services.
Facility Details
-
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.
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
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
Phone: 212.413.3236
