MS & Proteomics Resource


Resource Description

The Mass Spectrometry (MS) and Proteomics Resource of the W.M. Keck Foundation Biotechnology Resource Laboratory strives to provide investigators with access to the most advanced protein profiling technologies. These technologies are implemented with a broad spectrum of mass spectrometry based techniques and protein/peptide chemistries to separate, characterize and quantify analytes from complex biological samples. The resource has 11 staff including 4 with Ph.D. level appointments, with well over 100 years of mass spectrometry and protein chemistry experience. It is equipped with 9 state-of-the-art diverse tandem mass spectrometer systems including TOF-TOF, Quadrupole-TOF, Triple-Quadrupole, FT-ICR, and LTQ-Orbitrap type analyzers with either matrix assisted laser desorption ionization (MALDI) or Electrospray ionization (ESI) sources coupled to HPLC systems.


Given these diverse technology platforms, the resource supports a wide array of scientific research from both Yale and external investigators. Samples for MS analysis includes proteins, oligonucleotides, lipids, carbohydrates, synthetic peptides, and a wide range of small molecules including chemical intermediates. In FY 2008, for example, the MS and Proteomics Resource, with its dedicated staff and extensive knowledgebase, carried out 11,528 MS analyses for investigators from more than 100 institutions in 10 Countries ranging from government laboratories to academic and private research institutions.

To address the broad range of complexity inherent in many proteomics projects, the Keck Laboratory offers a comprehensive array of instrumentation and services, and if necessary can develop complementary methods to achieve successful sample analysis. The methods generally follow two mainstream workflows. One workflow uses a gel based Quantitative or Differential 2D gel electrophoresis (DIGE) combined with tandem mass spectral identification of proteins, and another, uses an automated “bottom-up” or “shot-gun” tandem mass spectral peptide identification approach. Both of these approaches can be quantitative with chemical and stable-isotope tagging of proteins or peptides (e.g., ICAT, iTRAQ, SILAC). In addition, two new cutting edge MS based technology services involving phosphoproteome profiling, and absolute quantitative (“targeted”) proteomic analysis of multiple pre-selected biomarker proteins have been recently developed and being implemented.

Finally, a web based platform called Yale Protein Expression Database (YPED) is utilized for users to integrate, analyze, and visualize their results.