Proteomics Core

The mission of the Mayo Clinic Proteomics Core is to provide consultation, technology and services in proteomics at Mayo Clinic and other institutions that will impact the prediction, prevention and treatment of human disease.

The Proteomics Core is located on the third floor of the Medical Sciences Building in Rochester, Minnesota. The Proteomics Core is a shared resource of the Department of Biochemisty and Molecular Biology, Mayo Clinic Cancer Center, and the Center for Individualized Medicine.

Since it was organized in 2002, the Proteomics Core has focused on developing new services, methodologies and instrumentation to support a broad diversity of programs and projects in cancer, genomics and basic science research. Many of the core's services provide direct support of human disease-related investigations in differential proteomics, protein identification, determination of protein post-translational modifications, small molecule analysis and biomarker discovery research for the development of diagnostic clinical tests (for example, light chain amyloidosis).

The mass spectrometry component of the Proteomics Core is equipped with state-of-the-art instrumentation and includes the following equipment:

  • Four LTQ-Orbitrap mass spectrometers
  • A quadrupole time-of-flight (Q-TOF) mass spectrometer
  • Three TSQ quantum triple quadrupole mass spectrometers
  • An LTQ ion trap mass spectrometer
  • An Agilent LC/MSD TOF system

The center supports one full-time bioinformatician programmer for data analysis support and development of new software for proteomics and biomarker analysis of patient samples from disease-related investigations. Computing resources comprise a 16 node Dell cluster with 144 cores, 576 GB RAM and a 10 TB SAN RAID array. Database search engines available for protein identification include Mascot, Sequest and X! Tandem, which are integrated through a bioinformatics platform (SWiFT) that was developed in-house.

In addition, the Proteomics Core provides consultation and a wide range of services in protein chemistry. Protein chemistry services include the following:

  • Solid phase peptide synthesis
  • Protein purification and quantification
  • Chemical protein sequencing
  • Protein separation by 2-D polyacrylamide gel electrophoresis (PAGE)
  • Computer-aided design of synthetic polypeptides

Instrumentation includes a Perkins Elmer 2400 Series II CHN Elemental Analyzer for quantification of peptides and small molecules and a Cell Biosciences NanoPro 1000 for the characterization of cell signaling proteins in small samples, such as fine-needle aspirates).

Current services provided by the Proteomics Core to Mayo investigators and their allied health staff include:

  • Solid-phase peptide synthesis by Fmoc orthogonal protection chemistry
  • Synthesis of peptide and protein specific immunogens on KLH or BSA carrier proteins
  • Elemental nitrogen analysis for the absolute quantification of peptides and small molecules
  • Protein separation and purification by reverse phase HPLC and FPLC methods
  • Computer-aided analysis of protein sequences for the design of synthetic peptides and custom anti-peptide antibodies
  • 1-D and 2-D PAGE of complex protein mixtures including Western blot services
  • Protein identification by nano LC-MS/MS methods
  • Differential proteomics and biomarker discovery by tandem MS and targeted MS methods, for example, SRM and MRM
  • Small molecule analysis and quantification by LC-MS
  • Protein PTM analysis and site-specific mapping enhanced by electron transfer dissociation mass spectrometry
  • Nanoimmunoassay of complex protein mixtures

The core's intranet site describes services, rates, instrumentation and resources in detail. (User must be logged in to the Mayo Clinic network)