Summary
To improve protein identification and mapping of post-translational modifications we will further explore, develop and use electron transfer dissociation (ETD). Therefore, novel platforms developed by Thermo-Fisher, Bruker and/or Agilent given to us via β-test-site agreements, will be evaluated and tested. ETD is a novel dissociation technology that may be used to fragment peptides. It is an alternative to the current standard collision induced dissociation (CID). Analysis of PTMs, such as phosphorylation and glycosylation, is difficult with CID since these modifications are labile and can often result in little to no peptide sequence information. ETD may be helpful in these areas since it sequences peptides using very different principles, which do not affect acid labile moieties. An additional benefit of ETD is its ability to analyze larger, more basic, non-tryptic peptides, thus potentially allowing for the detection of the entire sub-peptidome that was previously inaccessible. However, ETD will require a re-evaluation of sample preparation and data-analysis techniques. Furthermore, since the peptides/proteins delivered to the ETD ion trap might have different physicochemical properties to those accessible to CID, this project will also focus on the development of alternative chromatographic methods.