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CSHL Cancer Center - Mass Spectrometry

The Mass Spectrometry Shared Resource provides services to elucidate the primary structure of novel proteins and to analyze protein/protein interactions, post-translational modifications and protein levels. The Resource also offers the ability to detect lipids, metabolites, and other small molecules. The equipment in the facility has been upgraded to provide state-of-the-art analysis using microcapillary LC-MS/MS on linear ion traps and Orbitraps, hybrid quadrupole-TOF mass spectrometers and MALDI-TOF.

Shared Resource Staff
Resource Head Research Associate Staff
Darryl Pappin, Ph.D.  
 
Keith Rivera  
516.367.8452
Charles Shaw  
 

Facility staff is available to discuss project design and progress. Contact Keith Rivera to schedule an appointment. Services include:

  • Quantitative global proteomic profiling using iTRAQ and SILAC, including data analysis, merging of separate datasets and statistical treatment of results.
  • Quantitative cysteine profiling for global redox proteomics.
  • GSH/GSSG measurement (MRM) for redox assessment.
  • Multiple reaction monitoring (MRM) assays for:
    • Phosphatidylinositols (PIs) including head group, chain length, degree of saturation and phosphorylation state for 20 different PI lipid species.
    • Small molecule/drug measurement & clearance in serum & tissues (e.g. Clozapine and Clozapine N-Oxide, Vitamin C, Vitamin K).
  • Lipid Analysis, including sample preparation and extractions, MRM assay development, LC-MS/MS and data analysis. 
  • Quantitative iTRAQ for protein complex IP.
  • Quantitative metabolite profiling of ~250 core metabolites.
  • Intact protein mass measurement for drug binding and to support crystallographic studies.
  • Training in LCMS and MS/MS, both for instrument operation and data analysis.
  • Consultation in experimental planning and customized experimental design.

The Shared Resource currently has four mass spectrometers in operation:

  • Thermo Scientific Linear ion trap-orbitrap (Velos Pro): iTRAQ screens, protein identification, protein complexes (iTRAQ), post-translational modification analysis (PTM, including phospho, acetyl, ubiquitination, glycosylation and oxidation).
  • Thermo Scientific Linear ion trap-orbitrap (XL): protein ID, PTM analysis and intact mass measurement.
  • Thermo Scientific Vantage Triple Quadrupole mass spectrometer (TSQ): peptide MRM, lipids, carbohydrates, small molecules & metabolites
  • Thermo Finnigan Linear ion trap (LTQ).

Sample preparation for the instruments is supported by a number of capillary liquid chromatography systems from Agilent and Proxeon.

Proteomics data is analyzed with the following data analysis packages:

  • Mascot and Mascot Integra
  • InSpecT
  • PVIEW
  • Scaffold
NCIlogo Cold Spring Harbor Laboratory is an NCI-designated Cancer Center. As a basic research institution, CSHL does not treat patients. Information about individual cancers is available at the NCI CancerNet. Questions about CSHL's cancer research program should be directed to our Public Affairs Department.