The Proteomics Core facility is a collaborative research enterprise that provides state-of-the-art proteomics services to researchers from South Dakota and the surrounding region. Supported by the National Institute of General Medical Sciences grant and a partnership between the Sanford School of Medicine and the South Dakota Biomedical Research Infrastructure Network (SD BRIN), the core facility provides researchers with the capability to rapidly analyze and identify protein expression patterns in their experimental systems.
Along with providing proteomic analysis, the core:
This process identifies proteins from simple and complexes mixtures from different samples’ matrices using discovery proteomics through bottom-up approach, or peptide mass fingerprinting-MS or peptide fragment fingerprinting-MS/MS analysis.
The samples come in gel or in solution digestion of simple and complex mixtures (shotgun proteomics). 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 ultra performance liquid chromatography.
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 Quadrupole-Time of Flight mass spectrometer in MS and MS/MS mode. The peptide masses are used to query various databases using several search engines, including ProteinLynx global server v3.0.3 Expression analysis, Mascot server and Proteome Discoverer to identify the most probable proteins in the sample.
We also provide:
We train in peptide mass fingerprinting and peptide fragment fingerprinting 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 ultra performance liquid chromatography.
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 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 or Mascot server to identify the most probable proteins in the sample.
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.
We provide training in using the Typhoon 9410 scanner, spot cutter, image software analysis and basic excision tools for the cutter.
We offer advice related to sample preparation, technique and protocol development or proteomics applications, as well as bioinformatics tools.
A liquid chromatography system that works in nano scale and allows you to separates small quantities of samples (fentomoles) using a nanoflow (200-400 nL/min) and also resolves complexes mixtures such as whole cell lysates, secretome and subcellular fractionation (nuclei and cytoplasm).
A high-performance chromatography system with the capabilities to handle nano (50-1000 nL/min), capillary (1-10 ul/min) and micro flow settings (5-50 ul/min).
A hybrid Quadrupole-Time of Flight mass spectrometer with nano and regular spray ion sources and lockmass.
Orbitrap FTMS high resolution/mass accuracy (HR/MA) with enhanced resolution to 280,000 with a high-energy collision cell (HDC) with nano and regular spray ion source.
A scanner with capabilities to work in fluorescence mode (four lasers and different filters), chemiluminescence and Phosphor imager (32P, 33P and 35S). Applications: Gels, pvdf membranes, well plates immunohistochemistry, in situ hybridization and micro arrays.
A robot picker arm with a digital camera that allows to perform the automatic gel spots or bands cut either through visible or UV lights.
An automatic liquid handling system programmable to perform different protocols such as gel processing, protein digestion and peptides extraction.
A system with manifold and a dedicated vacuum pump to clean up and concentrate samples from different biological matrices.
Provides a method to reduce sample complexity, enrich low abundance proteins and increase the dynamic range of detection. Solution phase isoelectric focusing with the ZOOM IEF Fractionator provides reproducible separations. Fractionated samples are ready for further analysis by two dimensional gel electrophoresis, one dimensional gel electrophoresis or two dimensional liquid chromatography/mass spectrometry.
A centrifuge to dry and concentrate aqueous or non-aggressive samples with speed and cost-efficiency.
Used to analyze or purify mixtures of proteins. As in other forms of chromatography, separation is possible because the different components of a mixture have different affinities for two materials, a moving fluid (the mobile phase) and a porous solid (the stationary phase).
Labchip for quality control and quantification of RNA, DNA and proteins.