Proteomics Core FacilitiesFacility
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
Equipment and Facility Use
- This process identifies proteins from simple and complex mixtures from different samples’ matrices using discovery proteomics through bottom-up approach, 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.
- 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
1D and 2D nanoAcquity Ultra Performance Liquid Chromatography
Ultimate RSLC3000 Ultra-High Performance Liquid Chromatography
Synapt G1 HDMS
Typhoon 9410 Variable Mode Imager
ProteomeWork Spot Cutter
MassPrep Workstation Multiprobe II
Solid Phase Extraction
Zoom IEF Fractionator
SPD1010 Integrated SpeedVac
Expedeon GELFREE 8100 Fractionation System
Departments & Facilities
The Center for Brain and Behavior Research (CBBRe) promotes outstanding training of research students and fellows, feeding the pipeline of creative independent scientists in the fields of neuroscience and behavioral science.
The University of South Dakota’s human anatomy lab offers a cadaver-based experience to undergraduate, graduate, medical and health sciences students. Our lab enables future health care professionals to assist their patients through the mastery of human anatomy.