Proteomics Facility at the CSIR

Proteomics represents an important new phase in the post-genomics era, providing the opportunity to analyze the entire protein complement of a cell under different physiological conditions.

Researchers in the Proteomics section of the Systems Biology group at CSIR apply techniques that allow global analysis of the state of proteins in biological systems. This ability to probe expression, posttranslational modifications and interaction of proteins at any given time is an important component of the systems biology approach. The ultimate goal is to integrate proteomics data with genomic, transcriptomic, metabolomic, and structural bioinformatics data to get a more complete view of the biological system. This represents a vital tool in the search for new drug targets, which may provide opportunities for rational drug design, as well as providing links between methods of identifying the genetic predisposition to disease.

The ACGT proteomics facility is equipped with the following equipment:

  • 1x Dionex nanoRSLC with UV detector and fraction collector
  • 1x Dionex proflow nanoRSLC (funded by Diplomics)
  • 1x AB Sciex 6600 TripleTOF mass spectrometer
  • 1x Bruker Autoflex MALDI TOF mass spectrometer
  • 3x Thermofisher King Fisher Duo magnetic handling stations
  • 1x CentriVap Proteomics vacuum concentrator system (funded by Diplomics)
  • 1x Agilent 2D HPLC
  • 1x LEAP HDx-3 PAL hydrogen deuterium exchange preparatory system
  • 1x Applied Photophysics Chirascan circular dichroism spectrophotometer
  • 1x Shimadzu Fluorescence spectrophotometer
  • 1x BioTek PowerWave HT UV-Vis plate reader
  • 1x Pressure Biosciences PCT barocyler


  • AB Sciex Protein Pilot and Peak View database search and spectra integration software
  • AB Sciex Biopharmaview intact protein deconvolution software
  • Peaks v6 database search software
  • Biognosys QuiC quality control software for DDA and DIA data
  • Skyline and MSStats targeted proteomics data extraction software
  • MaxQuant and Perseus quantitative proteomics software
  • SearchGui and Peptide Shaker database search and visualization software


The Proteomics facility is used for a range of research programmes within the ACGT. In addition, Proteomics services are available to internal and external customers.

The types of analysis performed within the facility can be split into two major areas (i) Proteomics and (ii) Biomolecule characterization.

  1. Proteomics: the main focus in this respect is to perform bottom-up analysis for biomarker identification and drug-target discovery and verification, as well as to identify mechanisms of action in certain studies. The main technique applied for this is SWATH via fast scanning time of flight (TOF) instrumentation coupled to electrospray ionization (ESI) and nanoflow ultra-high-pressure liquid chromatography (nano UPLC). The following assays are routinely run in our lab (major associated equipment is indicated in brackets):
    • Protein and peptide lysate concentration determination using range of colorimetric and fluorescence assays (BioTek PowerWave HT UV-Vis plate reader)
    • Automated protein capture, clean-up and on-bead digestion for complex lysates using MagReSyn® microparticles and magnetic handling stations (KingFisher® Duo)
    • Automated phosphopeptide enrichment using MagReSyn® microparticles and magnetic handling stations (KingFisher® Duo)
    • FFPE sample extraction and processing of archival tissue (Pressure Biosciences PCT barocyler)
    • Spectral library building for SWATH assays using 1D and 2D chromatography (Dionex UV nanoRSLC coupled to Sciex 6600 TripleTOF)
    • Label-free SWATH based quantitative profiling of complex lysates with and without phosphopeptide enrichment (Dionex UV nanoRSLC coupled to Sciex 6600 TripleTOF)
    • In-gel and in-solution based protein identification and confirmation (Dionex nanoRSLC coupled to AB Sciex 6600 TripleTOF)

2.  Biomolecule characterization: the primary focus is on the structural characterisation of recombinantly produced proteins and antibodies (Ab):

    • UV based protein concertation determination (BioTek PowerWave® HT UV-Vis plate reader)
    • Intact mass analysis (Dionex UV nanoRSLC coupled to Sciex 6600 TripleTOF)
    • N-glycan profiling and polymer analysis (Bruker Autoflex MALDI-TOF)
    • In-solution sequence confirmation and PTM analysis (Dionex UV nanoRSLC coupled to Sciex 6600 TripleTOF)
    • Probing structural dynamics to understand the effects of mutations, buffer additives and stabilizers, ligand binding and protein-protein interactions using continuous and pulsed hydrogen-deuterium exchange (HDX) coupled mass spectrometry (LEAP HDx-3 PAL coupled to Agilent 2D HPLC coupled to AB Sciex 6600 TripleTOF)
    • Probing secondary structure conformation (Applied Photophysics Chirascan)
    • Probing tertiary and higher order structure conformation (Shimadzu Fluorescence spectrophotometer)


Contact information:
Dr Stoyan Stoychev, email:
Dr Previn Naicker, email: