Proteomic / Metabolomics Service

MCB offers a suite of high-throughput analytical services based upon our Mass Spectrometry platform. These services are available to researchers from UCT, other academic institutions and industry.
In addition, users are offered the opportunity to receive appropriate training in aspects of proteomic and metabolomic analysis from experimental design through sample preparation, chromatography, mass spectrometry and data analysis.

Core Services

• Analysis of single proteins isolated from 2D-gels
• Fractionation and characterization of complex protein mixtures
• Quantitative proteomics using iTRAQ isobaric labeling
• Specialist investigations (for example glycoprotein or phosphoprotein studies)

• Optimization of metabolite extraction protocols for various organisms and metabolite subsets of interest
• Targeted and untargeted studies of primary and secondary metabolomes
• Specialist metabolome subsets (for example lipidomes)
• Statistical analysis of MS data
• Assistance with identification of unknown peaks.

Ad-hoc Projects
A variety of other projects are undertaken in the unit. If you believe that one of our instruments could be helpful to your project, please get in touch with us to discuss your project idea.


Engagements with the unit on research projects may include a training component by arrangement. In this case, a research student or other user will receive one-on-one or small group instruction as dictated by project needs and budgets, including hands-on training on the MS instruments.
Other education and training activities include:
• Participation by unit staff in departmental education programmes (for example, the techniques course offered to Honours students)
• Hosting periodic workshops on topics of interest (for example Plant Metabolomics)
• Cooperation and support in training provided by other institutions


The unit is equipped with the following core instruments:

Agilent 3100 OFFGEL Fractionator
The Offgel fractionator allows the liquid-phase fractionation of complex protein mixtures by isoelectric focusing. Fractionation of complex proteomes improves the number and reliability of protein identifications in proteomic experiments.

Agilent 1200 Series Nanoflow Chromatography System
The Nanoflow HPLC platform is based on the Agilent HPLC-Chip microfluidic chromatography system. This permits high-resolution chromatography and sensitive detection of very small quantities of protein or peptide samples. In addition to general-purpose reverse-phase chromatography HPLC-Chips, a number of specialist chips are available for applications such as phosphoproteomics and glycoproteomics.

Agilent 1290 Infinity Chromatography System
This extremely versatile HPLC platform permits complex gradient separations at very high pressures on any traditional HPLC column, and provides the chromatographic capability for a wide variety of LC/MS studies, particularly on small biomolecules.

Agilent 6530 Accurate-Mass Q-TOF LC/MS
The backbone of the unit, this tandem LC/MS provides high accuracy and sensitivity for MS and MS2 studies. It is used for all protein, and many small-molecule studies in the unit.

Agilent 7000A Triple Quadrupole GC/MS
The QQQ GC-MS provides a cost-effective platform for many small-molecule analyses. It provides highly accurate, reproducible MS datasets for primary metabolomes and many other analytes that are either volatile, or can be rendered volatile by chemical derivatization.
The tandem-MS capability of the triple quadrupole analyzer also allows complex experiments and sensitive, accurate quantitation of compounds that are otherwise difficult to distinguish.

For enquiries, please contact Dr Suhail Rafudeen (