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Mass Spectrometry Core Facility

The purpose of the Ophthalmology Mass Spectrometry Core Facility is to provide state-of-the-art mass spectrometry services to researchers at the University of Miami and its surrounding educational and health care institutions. This facility provides various types of techniques, including qualitative and quantitative proteomics, lipidomics, and metabolomics. We employ a fee-based service model and book the instruments on a first come first serve basis. NEI-R01 funded investigators have priority of access to the facility.

We accept work from outside institutions. Currently, the charges for outside institutions are the same as the charges for services to UM Researchers. Outside institutions are strongly encouraged to inquire about our services.  

In addition to assisting researchers with the preparation of their samples for analysis, we perform bioinformatics analysis of the results of protein and protein modifications using Proteome Discoverer and visualization using Scaffold software. We also perform various labeled quantitative proteomics, for example, 8-plex iTRAQ labeled protein quantification. Lipidomics results are analyzed with MZmine and Lipid SearchTM software. We use isotopic ratio outlier analysis (IROA) method for the determination of metabolites in conjunction with Clusterfinder software from IROA Technologies.


The Ophthalmology Mass Spectrometry Core Facility is located on the 7th floor of Bascom Palmer Eye Institute's McKnight Building


This facility is equipped with a Q Exactive Hybrid Quadrupole Orbitrap Mass Spectrometer and a TSQ Quantum Access Max Triple Quadrupole Mass Spectrometer. These instruments have interchangeable front ends such as Accela HPLC, Easy nano-LC 1000, and Triversa Nanomate for chromatography or direct infusion respectively. Agilent 7100 CE Capillary Electrophoresis can also be interchangeably used for front end fractionation prior to mass spectrometry. We have a team of interdisciplinary analysts who specialize in chemidraw, MZmine 2.17, LipidSearch, and LipiXplorer. They also specialize in analyzing lipid protein pathways and conduct full spectrum analyses of lipids and metabolites. Additionally, we have an Agilent 7100 CE Capillary Electrophoresis System, a Thermo Scientific Nicolet 380 FT-IR Spectrometer, an Agilent 7890A / 5975C Gas Chromatograph / Mass Selective Detector coupled units.


Q Exactive Q Exactive

TSQ Quantum TSQ Quantum

The OMSC Proteomics

Current Resources

  • Protein Complex Identification (specialized single protein ID and complexes)
  • Post-Translational Modification Identification (acetylation, phosphorylation, ubiquitination, etc. as well a lab generated modifications)
  • Nano-spray technology and Nano-separation of protein complexes. (EASY-nLC 1000)
  • Specified Protein Quantification (Label-free quantification, iTRAQ, SILAC, etc.)

OMSC Metabolomics and Lipidomics

Qualitative and Quantitative Analysis of multiple lipid classes

  • Lipid profiling and comparison.
  • Lipid quantification through standard normalization.
  • Accurate delivery of ionized lipid samples through chip-based direct infusion on a Nano-spray application instrument. (Advion Triversa Nanomate)
  • Isotopic ratio outlier analysis of metabolites using IROA technology metabolite standards and Clusterfinder software.
  • Duel NMR analysis of metabolites prior to IROA analysis can be arranged as a service with the University of Florida (


Service and Fees

Following is the fee structure for users (service fees are in $)

Proteomics Services

1) Sequencing from gel bands (preprocessed by the user): $150 per band

2) Sequencing from lysates (preprocessed by the user): $150

3) Labeled (8-plex iTRAQ) Quantitative Proteomics (preprocessed by the user): $1500 (reagent prices included). For outside users protocol and reagents are sent after payment.

4) Preprocessing: Processing gel bands or lysates, digestion with one enzyme (usually sequencing grade Trypsin), and extraction of peptides. Preprocessing iTRAQ samples: $750 for up to 20 samples. In general, we prefer users to preprocess their samples.

5) Lipidomics experiments: $50 per run per mode, that is, $200 per sample. Includes two positive and two negative mode runs per sample, alignment, identification, and quantification in LipidSearch software.

6) Metabolomics (IROA): $200 per sample. Includes mass spectrometry and one bioinformatics identification/quantification analysis. The user is trained on Clusterfinder as gratis when possible so that they can carry out additional analysis.

7) Lipidomics profiling on TSQ Quantum Access Max with direct infusion: $1000 per samples (includes one MZ mine analysis).

8) GC-MS and capillary electrophoresis: $30 per run.

9) GC-MS training and capillary electrophoresis training: Currently free for internal users. 

10) SILAC experiments: Fee determined after discussion of the experiment and extent of analysis needed.

11) Other services, pharmacokinetics, cross-linking peptide identification services; determined after an initial discussion and the extent of work required.

12) We write support letters and provide assistance with MetaboAnalyst or other high-end analysis as gratis or as fee based service depending upon the availability of time and quantity of work. Please inquire.

All UM Internal users are required to submit their Workday driver worktag to charge prior to analyses. One scientific consultation is free. Subsequent consultations charges can be waived on a case to case basis. Users are encouraged to prepare their own samples (preprocessing) for analyses. Protocols are available on request.

External users are encouraged to inquire (see personnel below).


Facility Director - Professor Sanjoy Bhattacharya, Ph.D. 
Contact Prof. Bhattacharya for consultation about overall study design. Simple questions about sample preparations or service fee can be directed to mass spectrometry operator (Faith Harvey). Core facility manager Ms. Faith Harvey can also be approached for these questions.

Sanjoy Bhattacharya

Facility Manager – Isabella Moceri
Ms. Moceri maintains the oversight of instrument maintenance and user logs. She coordinates the procurement of parts and supplies. She undertakes the day-to-day management in absence of facility director. She performs routine calibration and runs both mass spectrometers. She switches the electrospray heads, switches the liquid chromatography systems as needed, performs routine calibration and maintenance, provides protocols, gives initial sample preparation advice, and maintains user and service logs of the instruments.

Financial Liaison/Oversight – Charles (“Chuck”) Yaros
As module’s overall manager, Mr. Yaros oversees the financial aspects of the facility. He coordinates the user charge / billing processes and manages mass spectrometry facility related accounts with instrument operators/manager/director. He provides financial oversight of the operations.

Chuck Yaros


Brief History of the Shared Instrument Facility 
The Ophthalmology Mass Spectrometry Core Facility has become a reality from singular perseverance of Dr. Sanjoy Bhattacharya, professor at Department of Ophthalmology, Bascom Palmer Eye Institute. Dr. Bhattacharya was recruited in December 2005 from Cleveland Clinic Foundation, Cleveland, Ohio. He applied mass spectrometry for the discovery of proteins associated with glaucomatous trabecular meshwork. Dr. Bhattacharya's independent research in glaucoma and in demyelinating diseases heavily employs mass spectrometry in conjunction with in vitro approaches and mouse models. The ophthalmology mass spectrometry shared instrument facility became a reality and now serves the entire UM community.



Telephone: 305-482-4987