Proteomics

The SD BRIN Proteomics Core Facility provides state-of-the-art proteomics services to researchers from South Dakota and the region. Since 2002, the USD PCF has been providing proteomic analyses, as well as collaborating in the training of the use of common equipment such as the scanner, spot cutter, imaging software, technique and protocol issues, and sample preparation. Our goal is to provide all South Dakota researchers with the capability to rapidly analyze and identify protein expression patterns in their experimental systems.

Services

Peptide mass fingerprinting (LC-MS analysis) or/and peptide fragment fingerprinting (LC-M/MS analysis) through in gel or in solution digestion of simple and complex mixtures. Typically, protein spots or bands excised from 1D or 2D gels or from in solution are digested with trypsin and/or Trypsin/Lys-C and the peptides resolved using a 1D or 2D NanoAcquity UPLC (Ultra Performance Liquid Chromatography). Specifically, tryptic peptides are desalted and concentrated using a reverse-phase trapping column and then resolved using a C18 reverse phase analytical column. The mass of peptides are determined using a nano-ESI Q-ToF (Quadrupole-Time of Flight) mass spectrometer in MS and MS/MS mode. The peptide masses are used to query various databases, using ProteinLynx global server v3.0 Expression analysis (Waters-Micromass) or Mascot server (www.matrixscience.com) to identify the most probable proteins in the sample.

Intact protein analysis: This type of analysis determines the molecular weight of an intact protein and can be used to identify post-translational modifications (phosphorylation, acetylation, etc.), proteolytic modifications, and to determine the number of proteins in a sample. A typical procedure involves injecting the sample into the mass spectrometer using a regular electrospray or nano-electrospray configuration. Multiple charged spectra are generated, and the spectra is deconvoluted using maximum entropy conversion software.

Training and assistance in common equipment and tools located in the facility: Typhoon 9410 scanner, spot cutter, image software analysis, and basic excision tools for the cutter.

Consultation and advice related to sample preparation, technique and protocol development or proteomics applications, as well as bioinformatics tools.

Equipment