Protein Quality Control

Purified, recombinant proteins are essential tools in different fields of research, ranging from high-throughput screening to structural biology. Quality control (QC) experiments early in the protein production process ensure high-quality protein constructs and thus increase experimental reproducibility in downstream applications. Working in close collaboration with our protein sciences group, we perform mass spectrometry (MS) based protein quality controls as an integrated step of the protein production process, starting from small-scale test expression to the final purified protein batch.

  • To confirm protein identity, we carry out in-gel proteolytic cleavage followed by LC–MS/MS-based peptide mass fingerprinting using the Q-Exactive™ Plus platform. In addition, the identification of unknown bands on an SDS page allows our protein production group to apply tailored protein purification solutions. A further level of confidence is provided by intact mass analysis of our proteins, not only to confirm the protein identity, but also to probe for PTMs, such as phosphorylation, palmitoylation, and biotinylation, or confirming point mutations in a protein construct. We have experience working with a broad range of distinct protein classes, including membrane and soluble proteins, antibodies, and antibody–drug conjugates (ADC).
  • With the growing interest in RNA as potential drug targets, we employ diverse methods to explore RNA as well.
  • SAM riboswitch RNA: A) raw spectrum, B) deconvoluted

  • Additionally, we employ native MS in our quality control process to confirm, for instance, the binding of metal ions or nucleotides to a protein, which might be relevant to their catalytic activity.


Göth, M., et al., Critical Evaluation of Native Electrospray Ionization Mass Spectrometry for Fragment-Based Screening. ChemMedChem (2017)

Fernández-Montalván, AE., et al., Isoform-Selective ATAD2 Chemical Probe with Novel Chemical Structure and Unusual Mode of Action. ACS Chem Biol (2017)