Thermo's new way to study proteomics

By Dr Matt Wilkinson and Mike Nagle

- Last updated on GMT

Related tags Thermo fisher scientific Amino acid Protein

A new piece of equipment could enable scientists to study changes
in protein structure, including those necessary to cancer tumour
growth, both faster and more accurately, according to its

Thermo Fisher Scientific recently released its new LTQ XL mass spectrometer (MS) featuring electron transfer dissociation (ETD), which represents the first time ETD has been available on a linear ion trap MS, according to the company. ETD is a large peptide fragmentation technique, which enables proteins to be identified more accurately and also provides specific information about the nature and site of changes in the structure of the proteins, such as phosphorylation. This reaction is just one example of a structural change that can occur after the protein has been built - called post-translational modifications. These changes to protein structure play an important role in cell signalling and the regulation of other proteins - for example those associated with tumour growth. However, the reactions are reversible, meaning the MS often struggles to pin down exactly where on the protein these changes occur. As well as ETD, the instrument also combines collisionally induced dissociation (CID) and Pulsed-Q Dissociation (PQD) on a linear ion trap mass spectrometer. This trap can store a large number of ions and its fast cycle times allows researchers to conduct rapid, alternating fragmentation experiments during liquid chromatography (LC)/MS. The combination of ETD and CID compliments each other and increases the coverage for each protein by giving a more comprehensive analysis of each sample, according to Thermo. "We believe ETD performed on a linear ion trap is a major turning point for the proteomics community, enabling researchers to pinpoint, identify and fully characterise more post-transitional modificatons such as phosphorylation and glycosylation than ever before,"​ said Greg Herrema, president of Scientific Instruments at Thermo Fisher Scientific. The ETD technique works by introducing negatively-charged fluoranthene ions into the trap along with peptides carrying multiple positive charges. Electrons are exchanged between the oppositely charged particles before the 'gentle' dissociation causes the peptide to break apart, yet preserve any post-translational modifications on the fragments. A recent study at the Max Planck Institute for Biochemistry and headed by Matthias Mann showed that 6,600 phosphorylation sites could be identified on 2,284 proteins using the technique. The results were published in 3 November 2006 edition of the journal Cell. This technique can also be used to study: how different cells and their proteins interact to pass each other signals - an important process associated with drug resistance; structural changes when proteins bind together; and the deactivation of genes or other molecules by, for example, small interfering RNA (siRNA). The approach can also be applied to any cells system that can be labelled by a process called SILAC - stable isotope labelling with amino acids in cell culture. "Within five years, everyone will be using ETD for proteomics research,"​ predicted Dr Ian Jardine, vice president of Global R&D at Thermo Fisher Scientific. The LTQ XL with ETD was unveiled last month at the 58th​ Pittsburgh Conference on Analytical Chemistry and Applied Spectroscopy, where it won silver in the Pittcon Editor's Awards​.

Related topics Preclinical Research QA/QC

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