Last week, Nonlinear Dynamics attended ASMS, this year being held in the lovely city of Vancouver, in Canada. While the weather demonstrated why the city has the nickname of Rain City, Vancouver and its Convention Centre made a great venue, leaving Minneapolis with a lot to live up to next year.
Given the announcement of our collaboration with Waters this year, we needed a larger presence than usual, and I was one of the lucky ones to make the trip. It’s always a privilege for a developer to attend a conference like ASMS, as the direct exposure we get to the science is unrivalled; it’s both an excellent opportunity to learn more about the our customers’ needs and for them to learn about our latest developments.
Alignment in immunoprecipitation experiments
In among the huge number of posters was a poster by one of our customers, who routinely uses Progenesis LC-MS for their immunoprecipitation (“IP”) work. Fold changes between the precipitated sample and the original, complex sample are used to judge the effectiveness of the enrichment process. While many people find IP samples difficult to align due to the high degree of variation in peptides, there’s a tip we can share that can overcome this difficulty:
In short, use a few manual vectors to aid the alignment process.
In Progenesis, the alignment process is used to compensate for drifts in retention time (“RT”) between runs. The RT offsets are represented as vectors, where each vector is a line linking a landmark in one run with the equivalent in another run. More often than not, the automatic alignment option is good enough to compensate for drifting retention time. However, you also have the option to manually align a few features in your runs before using automatic alignment to complete the job.
See also: Alignment of LC-MS profile data (PDF, 1.3MB)
This manual option is especially helpful in runs that have very few peptide ions in common – which is exactly the situation in IP experiments. For more information on using manual vectors in your alignment, see the KnowledgeBase article linked above.
Progenesis LC-MS and targeted proteomics
The abundance of targeted proteomics using MRM and SRM was something else that I noticed at ASMS, both in posters and talking with visitors to our booth. As a developer immersed in the world of discovery proteomics, it’s easy to overlook this. In particular, it was interesting for me to see the number of mentions of Skyline, which seems to be a good complement for the discovery work you can do with Progenesis LC-MS.
Indeed, another of our Progenesis LC-MS users (Dr Ben Collins, University College Dublin) recently published a paper demonstrating “an integrated discovery to targeted proteomics approach” that employed both Progenesis and Skyline. You can download the paper free of charge here:
Development of a pharmaceutical hepatotoxicity biomarker panel using a discovery to targeted proteomics approach (Molecular & Cellular Proteomics, April 2012)
Of course, if you weren’t able to meet us at ASMS this year, simply check out our website or contact us and we’ll tell you all about the latest developments and how to get the most out your Progenesis software.