Q&A: Elemental Composition in Progenesis QI, with Dr Jayne Kirk

Photo of Dr Jayne KirkLast month, we released version 2.0 of Progenesis QI, with a number of improvements in its compound identification workflow. One of these new features was the ability to calculate a compound’s elemental composition.

Here, we’ll interview Dr Jayne Kirk, a Senior Applications Chemist at Waters, to learn a little more about the feature and how it can help your small molecule analysis.

Mal Ross: Hi Jayne. Thanks for talking to us. Can you start by telling us a little about your job and the type of analyses that you perform, please?

Jayne Kirk: Hi Mal, I work in the Applications Laboratory in Wilmslow, UK, and have been working on metabolomic and lipidomic applications for 8 years now. Before joining Waters, I completed my PhD at York University, UK, in Chemistry.

My role in the laboratory is to perform small molecule demonstrations for clients from all over Europe, provide training and also to offer support to our MS specialists. Last year plant metabolomics (my personal favourite) was a hot topic, whereas this year lipidomics requests are flooding in!

Mal: So, we’re here to talk about how calculating elemental composition can help your compound identification. That ability is new in Progenesis QI v2.0, but how does it work? How much control do you have over the composition?

Jayne: A QToF Mass Spectrometer provides accurate mass information. Data processing within Progenesis QI generates a list of markers with m/z, retention time (and collisional cross section) information. After acquisition and processing, identification of markers is the next step. The elemental composition calculator allows assignment of a molecular formula to those markers.

The tool within Progenesis QI gives full control over the elements and the number of elements included in the search. It’s also possible to set and save several ‘typical’ search parameters for different classes of compounds, making the process very efficient.

The Elemental Composition parameters dialog in Progenesis QI v2.0

Mal: OK, so when should I use this feature? Don’t I already get this information in the IDs returned by my compound database searches?

Jayne: There can be times when your markers may not match anything in your compound database; in these cases, it’s necessary to go to the elemental composition calculator.

Mal: So, how do you typically use the calculation of elemental composition in your own small molecule analysis?

Jayne: Elemental composition is a building block or another piece of the puzzle and without that piece of information, it’s impossible to complete the jigsaw. Getting the elemental composition, whether it’s from the calculator or database searching, is essential.

It might not be necessary (depending on the experiment) to assign an elemental composition to all of the markers, however; instead, you can use the statistical tools to determine the important markers in the metabolomic or lipidomic study. Identification of these key markers is really the critical part of the process and if no database hit is returned, a molecular formula can still be obtained, giving you a starting point for further investigation.

Integration with ChemSpider, for instance, is another new feature within Progenesis QI v2.0 and another great building block. Here, the workflow would be to perform a ChemSpider search on the markers by mass and then filter that list of hits based on the elemental composition. Depending on the application area, certain elements are going to be of more interest in the search than others, so this is a way of filtering that information appropriately.

It’s great that you’re incorporating so many tools like this, helping scientists like myself to investigate, characterise and identify the markers in what are increasingly complex experiments.

Mal: We try our best!

So, rounding off, is this something you’d recommend to most people using Progenesis QI?

Jayne: Most definitely, yes. It’s another tool in the box which can be used in combination with the isotopic match, databases and pathway options within Progenesis QI.

Mal: Thanks, Jayne. It was great talking to you.

If you want to take advantage of the support for calculating elemental composition, as well as ChemSpider, LipidBlast and pathways integration, why not download Progenesis QI today and try it out?