Mass Spectrometry and Proteomics Center (MaSPeC)

329 & 331 Snygg Hall      Phone: 315-312-2226 (315-312-2696 for Kestas Bendinksas directly)

Director: Kestutis Bendinskas

Funding Provided by:

*College of Arts and Sciences


*National Science Foundation, Major Research Instrumentation Program: "Acquisition of Proteomics Equipment and a MALDI-TOF Mass Spectrometer for Establishment of a Proteomics/Mass Spectrometry Facility"  $249,850.00

P.I.: Anthony J.A. Ouellette
Co-P.I.s: Kestutis Bendinskas, Martha Bruch, Webe Kadima, Casey C. Raymond   
Senior Personnel: J. Alden Lackey 
Instrument Specialist: Frederick G. Scoles

The Mass Spectrometry and Proteomics Center at SUNY-Oswego is a resource for students and faculty to analyze a wide variety of samples using 2 dimensional electrophoresis and Matrix Assisted Laser Desorption Ionization - Time of Flight Mass Spectrometry (MALDI-TOF MS).


Courses that make use of the MaSPeC:

  • Proteomics (Fall 2005): Bio 401/501; Che 401/501
  • College Biology II Lab: Bio 213L
  • Biochemistry II Lab: Che 462L
  • Problems in Toxic Algal Blooms (Fall 2006): Bio492

                                                     mass spectrum               

The Center has everything you need to analyze your sample, from pipettes and reagents, to matrices and a mass spectrometer.  Below are pieces of equipment in the Center that are used for separation and analysis:


Bio-Rad Protean Iso Electric Focusing Cell to separate proteins based on iso electric point:


Proteins either in solution or in the iso electric focusing strip (above) can be separated based on approximate mass using Sodium Dodecyl Sulfate Poly Acrylamide Gel Electrophoresis (SDS PAGE) with either the small format Mini Protean 3 electrophoresis system:


Or, the large format Protean II xi:

protean II xi

Amersham ImageScanner II to obtain images of gels:

image scanner

Amersham ImageMaster 2D Platinum software to analyze two dimensional gels:

2d sofware


Bruker AutoFlex Matrix Assisted Laser Desorption Ionization Time-of-Flight (MALDI-TOF) Mass Spectrometer:

autoflex                                                   autoflex andy and cody

Mass spectra and sequence data are analyzed by the following software:

BioTools and RapiDeNovo (available in-house)



BLASTP (short sequence tags) at NCBI

mMass - Open Source Mass Spectrometry Tool to analyze Bruker spectra off-site


Other Useful Mass Spectrometry and Proteomics Websites: ExPASy    ProteinProspector   Matrix Science Mascot info  IonSource    Molecular and Cellular Proteomics publication guidelines


Journals available to SUNY Oswego community (follow the links to Penfield Library):                                       

Proteomics Journals    Mass Spectrometry Journals    Proteome Science

 Books in the Center:

  • The Expanding Role of Mass Spectrometry in Biotechnology by Gary Siuzdak 2003
  • Mass Spectrometry Basics by Christopher G. Herbert, R. A. W. Johnstone 2002
  • Mass Spectrometry Desk Reference by O. David Sparkman     2000
  • Mass Spectrometry: Principles and Applications by Edmond De Hoffmann, Vincent Stroobant 2001
  • Proteomics Today: Protein Assessment and Biomarkers Using Mass Spectrometry, 2D Electrophoresis,and Microarray Technology (Wiley - Interscience Series on Mass Spectrometry) by Mahmoud H. Hamdan, Pier G. Righetti 2005
  • Time-Of-Flight Mass Spectrometry: Instrumentation and Applications in Biological Research (Acs Professional Reference Book) by Robert J. Cotter 1997

 Outside Users and User Fees:

The Bruker Autoflex is available to users from outside of SUNY-Oswego.  However, due to our limited budget (we are primarily a teaching institution) and the costs of operation and maintenance, we have instituted a fee structure for non-SUNY-Oswego users.  All users must have initial training on this instrument (typically trained by Kestas Bendinskas).  To set up initial training and schedule instrument use, call Dr. Bendinskas at 315-312-2696 or email

●Initial training (60-90 minutes, depending on skill level of user): $60

●Hourly usage fee: $20 per hour (including data analysis time)

●There is no charge for time spent preparing or spotting samples

 Visiting Campus?  click here for information on guest parking, and here for a campus parking map.


Interesting Links:  

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Molecular Biology and Biochemistry Center @ Oswego