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:

  • Develops experimental design, protocols, data analysis and interpretation
  • Provides consulting and advice in grant proposal, as well as data preparation to be submitted to proteomics journal according to the requirements
  • Offers training in the use of common equipment such as the scanner, spot cutter, imaging software, technique and protocol issues, and sample preparation.

Services

Protein Identification

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:

  • Protein characterization, including post-translational modifications and indirect protein-protein interaction analysis
  • Protein quantification using label-free and labeled approaches

Peptide Mass Fingerprinting and Peptide Fragment Fingerprinting

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.

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.

Equipment Training

We provide training in using the Typhoon 9410 scanner, spot cutter, image software analysis and basic excision tools for the cutter.

Consultation

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

Equipment

1D and 2D nanoAcquity Ultra Performance Liquid Chromatography

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).


Ultimate RSLC3000 Ultra-High Performance Liquid Chromotography	UltimateRS3000UHPLC

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).

 

 


Synapt G1 HDMSSynapt G1 HDMS

A hybrid Quadrupole-Time of Flight mass spectrometer with nano and regular spray ion sources and lockmass.


QExactive Plus

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.


Typhoon 9410 Variable Mode Imager

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.


ProteomeWork Spot CutterSpot Cutter

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.


MassPrep Workstation Multiprobe IIMass Prep

An automatic liquid handling system programmable to perform different protocols such as gel processing, protein digestion and peptides extraction.


Solid Phase Extraction

A system with manifold and a dedicated vacuum pump to clean up and concentrate samples from different biological matrices.


Zoom IEF Fractionator

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.


SPD1010 Integrated SpeedVacSpeed Vac

A centrifuge to dry and concentrate aqueous or non-aggressive samples with speed and cost-efficiency.


Akta FPLC

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).


2100 BioanalyzerGenomics Bioanalyzer

Labchip for quality control and quantification of RNA, DNA and proteins.

 

 

Contact Us

Name Department & Office Contact
Eduardo Callegari
  • Proteomics Core Fac Manager
BASIC BIOMEDICAL SCIENCES
Lee Medicine & Science Hall 127

Proteomics Core

Campus map of Lee Med Sanford School of Medicine building
South Dakota BRIN Proteomics Core Facility
Lee Medical Sciences Building Room 127
414 East Clark Street
Vermillion SD 57069

Phone:605-658-6312

www.usd.edu/medicine/basic-biomedical-sciences/proteomics-core

Campus Map