Instruments and Software


The Proteomics Core at WCM-Q has been operational since 2011. Ever since, the laboratory has constantly been facilitating researchers in various protein identification technologies. The lab has recently acquired the latest generation of the Q Exactive series instruments, HFX (Thermo Scientific). We will also very soon allow access to one of our mass spectrometers under a subscription model. We aim to educate the scientific community through knowledge sharing and by building collaborations.

The current mass spectrometers in the lab include:

  • Q Exactive
  • Q Exactive Plus
  • Q Exactive HF
  • Q Exactive HFX

We also have the easy nano LC 1000 and LC 1200 to achieve high resolution gradients for proteomic analysis in the MS using solvent mixing.

In addition to the mass spectrometers, we also have other equipment used for protein isolation techniques such as:

  • Offgel Fractionation (3100 Offgel Fractionator, Agilent Technologies) uses the principle of separating peptides/proteins based on the isoelectric points with high resolution and easy downstream detection on LC/MS.
  • HPLC (Agilent) is an analytical chemistry technique used to separate, identify and quantify components from a liquid mixture using suitable solvents.
  • Covaris (Tissue Lyser).

Multi-Plex Proteomics

For the multiplex immune affinity assay (Olink™) we have the Biomark™ HD and IFC Controller HX from Fluidigm.


For analysis of raw data generated from mass spectrometry, the tools used are:

  • Genedata Enterprise software, which is a collective platform for analysis of mass spectrometry data and multiplex assay data.
  • Mascot for protein identification.
  • MaxQuant for protein quantification (label-free).
  • QuiC software to check the MS spectra, ion injections, scan time etc.
  • R-scripting for data analysis and interpretation.