Collaboration with Uppsala University (2007)

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Uppsala University plays an active role in society, promoting growth and innovation. In the last ten years some one hundred new companies have been created to develop research breakthroughs.

Scientists from Uppsala University

The scientists who developed GS4FTMS, DeNoS, PhosTShunter and ModifiComb are:

  • Roman A. Zubarev, Professor, PhD (Uppsala University, Karolinska Institutet, Sweden)
  • Mikhail Savitski, PhD (Uppsala University, Sweden)
  • Michael Lund Nielsen, PhD (Uppsala University, Sweden)

Professor Roman Zubarev

In 2007, the Biemann Medal was awarded to Professor Roman Zubarev at the 55th ASMS Conference. Professor Roman Zubarev was awarded this medal for his discovery and development of Electron Capture Dissociation (ECD) in Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). ECD offers a new approach of sequencing biological molecules which has had a tremendous impact on proteomics since its initial discovery in 1998. Roman's landmark contribution has been recognized by the scientific community in the whole world.

Roman's contributions to the development of different algorithms such as THRASH, ModifiComb, and PhosTShunter has enabled hundreds of laboratories to capture the value of peptide fragmentation data with <5 part-per-million mass accuracy.

This data acquisition philosophy will likely expand in the coming years, given the now widespread use of Fourier transform instrumentation - in part due to innovations directly traceable to Roman Zubarev.

Article Source: "Focus in Honor of Roman Zubarev, Recipient of the 2007 Biemann Medal", ScienceDirect, Journal of the American Society for Mass Spectrometry 19(6): 751-752, June 2008

GS4FTMS, DeNoS, PhosTShunter and ModifiComb

MedicWave collaborates with a research group from Uppsala University in Sweden. Together we are developing a software program for Tandem MS (MS/MS). The software program is called PAS™ and it contains 4 unique software with algorithms: GS4FTMS, DeNoS, PhosTShunter and ModifiComb.

GS4FTMS performs golden and complementary pair extraction from collisionally activated dissociation CAD and electron capture dissociation ECD data. DeNoS performs de novo sequencing of peptides fragmented using CAD and ECD. PhosTShunter detects all phosphorylated peptides in MS/MS data. ModifiComb detects all types of peptide modification, for known and unknown peptides.

Click here to learn more about PAS™ and GS4FTMS, DeNoS, PhosTShunter, and ModifiComb.

Publications concerning GS4FTMS, DeNoS, PhosTShunter and ModifiComb

Open for collaboration

MedicWave develops state-of-the-art algorithms for data mining and machine learning in collaboration with renowned researcher from around the world. These algorithms are implemented into our bioinformatics products and used for differential proteomics studies, quantification and validation of regulated proteins, and the discovery of biomarkers.

Collaboration: Read more...