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Mass Spectrometry Core Facility

Ophthalmology Mass Spectrometry Core Facility/Shared Instrument Facility

Located on the 7th floor of UM Miller School of Medicine McKnight Building


The purpose of the Ophthalmology Mass Spectrometry Core Facility is to provide state of the art mass spectrometry services to bona-fide researchers at the University of Miami and its surrounding educational and health care institutions. This facility provides various types of techniques such as qualitative and quantitative proteomics, lipidomics, and metabolomics. The priority of facility is to serve UM researchers followed by others. We employ a fee-based service model and book the instruments on a first come first serve basis.

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.


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, two Agilent 7890A / 5975C Gas Chromatograph / Mass Selective Detector coupled units, four Agilent 7890A Gas Chromatograph units, an ASAP IRD II Infrared Detector, and an Agilent 6890N Gas Chromatograph unit. 

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 (Ciara Myer). Core facility manager Ms. Ciara Myer can also be approached for these questions.

Sanjoy Bhattacharya

Facility Manager - Ciara Myer
Ms. Myer 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.

Ciara Myer

Research Associate/Additional Manager– Bryan Alfonso
Bryan Alfonso assists Ms. Myer with all aspects and also performs routine calibration and runs mass spectrometers as needed. He switches the electrospray heads. He performs routine calibration and maintenance. He provides protocols and gives initial sample preparation advice based on instruction from Facility Director/Manager. He also maintains user and service logs of the instruments during the absence of Ms. Myer.

Bryan Alfonso

Financial Liaison/Oversight – Charles (“Chuck”) Yaros
As overall operator’s 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


On June 21 and 22, 2018 the Ophthalmology Department’s Mass Spectrometry Core presented a workshop for the University community on the use of mass spectrometry for proteomic analysis. The workshop was well attended. Twelve junior faculty members, post-doctoral fellows, and graduate students from the Coral Gables and Medical School campuses participated in the workshop. The attendees were charged a modest fee of $100.00 which covered course materials and lunch for both days of the workshop. The attendees were given didactic lectures, hands-on experience in the preparation of protein samples for mass spec analysis, and analysis of the sample data. At the end of the workshop, Dr. Vittorio Porciatti, Vice Chair of Research, and Dr. Carl Schulman, Executive Dean of Research and Training interacted with the attendees seeking feedback for further improvement. See photo below.


Telephone: 305-482-4987

Upcoming workshop (June 2019)  Workshop on sample preparation and bioinformatics analyses for quantitative analyses. Space is available for 12 individuals in this workshop. The fee is $100. Two didactic lectures will be followed by one half day of hands on sample preparation and data analyses. A demonstration of mass spectrometry will be performed by an operator.

Next workshop: June 20-21, 2019.

Miami Integrative Metabolomics Research Center (MIMRC): Housed in McKnight Vision Research Building and directed by Prof. Bhattacharya. The Miami Integrative Metabolomics Research Center aims to identify therapeutic intervention strategies by revealing metabolic and lipidomic differences between control and disease states. The Center has state of the art instruments that are used in consonance with Ophthalmology Mass Spectrometry Core (OMC) facility. The fees for these services are charged via OMC.

The Center also aims to serve the needs of integrative metabolic discoveries in medical sciences.  It is aiming to procure a number of instruments including an imaging mass spectrometer to enhance its capability and offer a full range investigation capability, with the goal of helping investigators perform quality high impact generating research and to attract extramural funding for support. Please inquire about how to be a member of the MIMRC.

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.