Stony Brook Proteomics Center

Overview of Services


The Proteomics Center at Stony Brook (formerly the Center for the Analysis and Synthesis of Macromolecules, CASM) was established in the Health Sciences Center at the University at Stony Brook in 1985 with a Shared Instrumentation Grant from the National Institutes of Health.
The Proteomics Core Facility at Stony Brook University School of Medicine supports basic and clinical research programs by performing mass spectrometry-based analyses of proteins and peptides. 
The facility offers state-of-the-art instrumentation and software for qualitative (e.g. protein identification), quantitative proteomics analysis (e.g. relative quantification), and post-translational modification (PTM) analysis. 
The Proteomics Center also supports small molecule analysis. 
We offer services of sample preparation, LC-MS/MS analysis, statistical analysis, and data mining for large-scale proteomic projects. 
Center directors are available to provide expert consultation on experimental approaches and design.



  • Protein Identification from less complex samples
  • Analysis of full length proteins
  • Global protein expression profiling (shotgun proteomics)
  • Identification of post-translational modifications
  • De-novo sequencing of monoclonal antibodies
  • Analysis of small molecules
  • Pharmacokinetics


Thermo Fisher Scientific LTQ Orbitrap XL ETD: This is the most powerful instrument for proteomics analyses that is available to our customers. The instrument combines high resolution (up to 100,000) and high mass accuracy (<5ppm) with the high speed of an LTQ. The instrument is equipped with three different and complementary fragmentation techniques CID, HCD, and ETD (this method will be installed later in the year). It is the most comprehensive solution for complex PTM analysis, intelligent sequencing of peptides, top-down and middle-down analysis, and protein quantitation via stable isotope labelling such as iTRAQ or label-free quantitation.


Applied Biosystem Voyager DE-STR workstation: The instrument is a floor standing MALDI-TOF (matrix assisted laser desorption Ionization /time-of-flight) mass spectrometer . It features delayed extraction in linear and reflector modes of operation for low and high resolution acquisitions. It has a mass range in excess of 300 kDa, and sensitivity to less than 5 fM. It is mainly used for the mass analysis of peptides, proteins, DNA and the identification of proteins by Peptide Mass fingerprinting (PMF).

Thermo Fisher Scientific LTQ XL: This mass spectrometer is mainly used for our shot-gun proteomics approaches, where the fast MS/MS scan speed allows to identify more peptides in a given time. It also comes with multiple dissociation techniques, PQD, ETD and CID. Pulsed Q Collision Induced Dissociation (PQD) is a patented technique that eliminates the low mass cut-off concern inherent with all ion traps.

Thermo Fisher Scientific TSQ Quantum Access: This mass spectrometer is a triple quadrupole mass spectrometer used for quantitative as well as qualitative work. It is equipped with two different ion sources, ESI and APCI, which allow us to analyze different types of samples. The instrument is mainly used to analyze DNA, peptides, proteins and small molecules.

Additional instrumentation:


Biacore2000: The BIACORE 2000 is an instrument which can be used by individual investigators. The instrument is designed to perform basic kinetics, heterogeneous ligand analysis, heterogeneous analyte analysis, epitope mapping, multi-site binding, concentration analysis, and other applications.

2-D Gel Electrophoresis (Bio-Rad):

Imaging and Analysis of 2-D Gels using the Versa Doc Imaging System (Bio-Rad) and PDQuest Advanced ver.8.0 2-D Analysis Software (Bio-Rad)

Automated excision of protein spots from gels using the Proteome Works Plus Spotcutter (Bio-Rad)





Lina M. Obeid, MD
Vice Dean for Research


Location and Hours of Operation



8:00am - 5:00pm Monday thru Friday



Proteomics Center
Basic Science Tower
T-9, Rm 167
Stony Brook NY 11794-8691


Links and Resources


Links to Software Tutorials

How to Log In

Using your Home Page

Managing Lab Settings (for Lab Managers and PIs)

Making Service Requests




Name Role Phone Email Location
Thomas Fischer

(631) 444-2398

Robert Rieger

(631) 444-3789

Dwight Martin

(631) 444-1266




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