Hyper Reaction Monitoring

HRM-MS™ is the next generation high-content proteomics technology invented at Biognosys that enables reproducible and precise quantification of 1000s of proteins in a single instrument run with data independent acquisition (DIA). HRM-MS™ is the best proteomics method for discovery applications and highly multiplexed protein quantification.

Hyper Reaction Monitoring is based on three essential parts:

  • Data independent acquisition (DIA) using state of the art high-resolution mass spectrometry enables comprehensive recording of peptide ion signatures. In contrast to traditional methods, where single ions are isolated for further analysis, the novel approach programs the mass spectrometer to cycle through broad precursor windows fragmenting multiple peptide ions together. The information about single peptides in this comprehensive data is complete but highly convoluted. By using accurate template peptide spectra from a spectral libraries the data can be de-convoluted.
  • Spectral libraries contain multiple peptide ion fingerprints (assays) that serve as template for matching the recorded ion signals. An assay describes the characteristic features of peptide spectra such as fragment ion intensities and iRT, which are empirically determined in independent experiments. Through deep proteome mapping with LC-MS/MS Biognosys is able to generate high-quality spectral libraries for any sample type. The library building function is also included in the Spectronaut software.
  • Spectronaut™ software builds and uses spectral libraries to de-convolute and match the ion signals recorded by the instrument, and extracts the information about protein quantities in the sample. Spectronaut™ provides fully automated, statistically valid and lightning-fast analysis of HRM-MS™ data. It is based on the mProphet algorithms that were published in Nature Methods. The scoring has been advanced to fully exploit the advantages of high resolution MS/MS data. Spectronaut™ is available for academic researchers and industry.

Digital Biobanking – the future of proteomics

One of the features of HRM-MS™ is that it allows retrospective analysis of target proteins, including proteins or protein isoforms that were not known or not considered relevant at the time of sample measurement. At any point in time improved or enlarged spectral libraries can be developed off-line and used for re-analysis of the HRM measurement.

The digital representation of protein signals from a sample instead of the sample itself is stored in such a Digital Biobank®. One physical measurement of a sample is therefore sufficient for any future analysis of proteins that were present in the sample. 

In 2012 Biognosys has been awarded a federal grant of CHF 1.5m to further develop this technology together with the group of Ruedi Aebersold at the ETH Zurich.


Bruderer R, Bernhardt OM, Gandhi T, Miladinovic SM, Cheng LY, Messner S, et al. Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen treated 3D liver microtissues. Mol Cell Proteomics. 2015 May;14(5):1400-10. 

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Multiplexed protein

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