ETD is a unique new peptide and protein fragmentation technique that preserves functionally important post-translational modifications (PTMs), such as phosphorylation or glycosylation. With ETD in a high-capacity ion trap, protein scientists can sequence peptides easily, and in addition they can simultaneously identify both the type and location of various PTMs.
It is well known that phosphorylations play a very important role in cell signalling, and the emergence of phosphorylation analysis as part of proteomics research is hardly surprising. Depending on the available MS instrumentation, there are many routine ways to study phosphorylations.
However, the results have proved to be poorly reproducible. Other physiologically important modifications, such as glycosylation, are even more challenging, and there are several projects underway aimed at more sophisticated PTM analyses.
"Modern proteomics has moved beyond simple identification, and one of the primary goals of functional proteomics is now the unraveling of the many subtle modifications arising in proteins which often are very important for their biological activity," said Dr Detlev Suckau, head of proteomics applications development at Bruker Daltonics.
Proteomics can help to enhance the efficiency and control of the processes used in the biotechnology industry to produce bioactive compounds. New targets for drug development can be identified and validated, diagnostics can be improved by proteomic profiling, and novel biomarkers can be found. Applicable to the theranostics and personalised medicine of the future, the more precise biomarkers will bring diagnostic and clinical research capabilities to new levels.
Suckau said that ETD capabilities would be made available to all protein scientists for specific PTM analyses on the HCTultra ion trap. "We have previously pioneered important related developments such as commercial ECD on our FTMS, and our T3-sequencing on the Ultraflex TOF/TOF," he added.
ETD MS/MS spectra of peptides can now be collected on-the-fly during LC/MS/MS runs using the HCTultra. Due to its non-ergodic nature, ETD typically creates clean MS/MS spectra with intact PTMs. On the HCTultra, the new ETD implementation often provides complete amino acid series down to immonium ion masses, without the low-mass cut-off traditionally encountered in ion trap MS/MS.
The combination with the mass accuracy of the HCTultra enables de novo sequencing capabilities. Using the PhosphoScan mode of the HCTultra with ETD offers a system for single run auto-LC/MS/MS/MS CID/ETD experiments specifically for phosphorylation analysis.
ETD and CID data are supported by Bruker Daltonics' bioinformatics suite ProteinScape. It can handle large numbers of MS/MS spectra created by the HCTultra in proteomics studies. The HCTultra integrates into the Proteineer solution for LC/MS/MS and 2D gel-MS/MS based proteomics projects, as well as into the Metabolic Profiler solution for metabolic studies.
The discipline of proteomics - the simultaneous analysis of all the proteins in a cell at a given point in time, is undergoing strong development and growth. The market is estimated to be worth $2.9 billion (€2.4 billion) in 2005. A recent report by the Cambridge Healthtech Institute estimated the expenditure on proteomics to increase by 15 per cent to 50 per cent in 2003, compared with 2002.
Major areas of increase were sample preparation (increase in two- and multi-dimensional liquid chromatography systems) and mass spectrometric analysis. Of the estimated $2.9 billion proteomics market in 2005, two-dimensional sample separation is expected to account for approximately 30 per cent. Regarding protein analysis, 300 per cent more mass spectra were expected to be generated in 2003, compared with 2002. Interestingly, the biggest increase in market value was envisaged for protein chips.
During the past few years, proteomics has evolved as intellectual property-intensive activity. The number of proteomics-related patent applications has doubled every year since the early days of proteomics. The great majority of the applications (60 per cent) have been filed in the USA, followed by Japan and Germany. China is among the top four countries, in front of the United Kingdom and France.