Services offered

  • Gel-bands - We perform sample preparation for samples that will be run on 1D or 2D gel electrophoresis and analyzed by mass spectrometry-based methodology.
  • In solution digestion - We perform sample preparation for in solution digestion using mass spectrometry-compatible lysis buffers. Typical samples for in solution digestion include frozen cell pellets, bound proteins from affinity purification/immunoprecipitation (IP), frozen tissues, FFPE tissues, etc. We also perform subcellular fractionation and albumin depletion of serum, urine, and other biological fluids.

Mass Spectrometry

We have four mass spectrometers in our laboratory which can handle almost all your proteomics/mass spectrometry needs. Please see Instrumentation page.

Data Analysis

  • MS spectra analysis - We analyze our proteomics data with several different search engines, including Sequest/ProLucid (web-based database search platform via the Integrated Proteomics Applications or IP2), X!Tandem, Inspect, Mascot, Scaffold and ProMass.
  • Data processing after database search - DTASelect (via IP2), Scaffold (Proteome Software), and ProteoIQ (NuSep).
  • Data mining software - in house statistic analysis and algorithm, Ingenuity Pathway Analysis (Ingenuity Systems), MetaCore (GeneGo), etc.
  • Stony Brook University Biostatistics Core is available for complex statistical analysis.

Additional resources

  • 15N labeled tissues available for mouse and human protein quantification.

Gel Electrophoresis

We will run 1D or 2D gel electrophoresis with your sample. 2D gel electrophoresis can be done on either 10cm or, for added resolution, 18cm IPG strips. Gels will be stained with Sypro Ruby and analyzed with BioRad PDQuest analysis program to find differences between gels.