The biomarker discovery/validation and biomolecule analysis facility characterises and quantifies specific compounds through a broad range of analytical services.
Equipment:
Electrophoresis
Ettan IPGphor I/II IEF (GE Amersham)
Rotofor Cell (Bio-Rad)
Dalt II Separation Unit (GE Amersham)
Protean Plus DodecaCell (Bio-Rad)
Ettan SE600 Ruby gel electrophoresis system with auto gel stainer
Ettan DALTtwelve, running 12 large format gels in parallel
Imaging
PharosFX (Bio-Rad)
EXQuest automated spotcutter (Bio-Rad)
PDQuest (Bio-Rad)
Image Master 2D scanner and software
HPLC
1100 nanoHPLC (Agilent Technologies)
Mass spectrometry
MAPII AutoPrep MALDI Robot system (Bruker Daltonics)
Bruker autoflex® Daltonics MALDI-TOF mass spectrometer with post-source decay
QStar Elite (ESI/MALDI) (Applied Biosystems)
Qtrap (ESI) (Applied Biosystems)
Protein-interaction
Biocore 3000 (GE Amersham)
Services:
Proteomics services are available to internal and external customers. The following services are available:
Biomarker & Drug-target discovery and validation
Gel-based proteomics
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- Fractionation: 1D / 2D PAGE;
- Protein visualisation / isolation: gel staining (Coommassie, Silver, SYPRO-Ruby, Cy dye, and Flamingo)
- Gel imaging (fluorescence, colorimetric and radioisotopic) (Biorad PharosFX)
- High-throughput spot picking (Biorad ExQuest); and
- 1D / 2D PAGE band/spot identification/confirmation (Dionex Ultimate 3000 and AB Sciex QStar Elite).
Solution-based (gel-free) proteomics
- Off-line and on-line fractionation:
- In-solution peptide/protein IEF (Biorad MicroRotofor)
- 2D HPLC (Dionex Ultimate 3000 nanoRSLC
- MRM-based During ‘validation’, putative targets are confirmed by a targeted approach where fewer analytes are monitored in a larger sample size. The main aim of this stage is to assess marker sensitivity (likelihood that an affected/diseased sample will test positive). In ‘verification’ the analysis is further extended with 100s of samples analysed in order to examine variations due to environmental, genetic and/or biological factors. Thus, candidate biomarker sensitivity is affirmed while specificity (likelihood that an unaffected/healthy sample will test negative) is gauged.”
- Mass spectrometry (iTRAQTM, peptide identification, peptide sequence identification, glycan analysis, posttranslational modification analysis)
- Protein characterisation (protein-protein / ligand interaction)
Microarrays (cDNA oligo)
- Sample preparation and hybridisation
- Conventional and high-resolution scanning*
- Expression analysis
- Quantitative Real-Time PCR
Contact information
Dr Stoyan Stoychev
Molecular Technologies
Tel: +27 12 841 2270/3001
Fax: +27 12 841 2388
Email:
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