Webinar Review: What columns should I use in proteomics?

Our trainees review webinars in their given fields and share abstracts to help colleagues outside their discipline make an informed choice about watching them. As our program bridges diverse disciplines, these abstracts are beneficial for our own group in helping one another gain key knowledge in each other’s fields. We are happy to share these here for anyone else who may find them helpful.

What columns should I use in proteomics?

Dr. Brett S. Phinney

Core Director, Proteomics Core–UC Davis Genome Center

November 3, 2022


Watch on the Bruker website >>

Shannon BernecheSummary and Analysis by Shannon Berneche:

In this webinar, Dr. Phinney describes how to use different types of columns for proteomics with LC-MS. I’d recommend this to anyone interested in either using LC-MS for proteomics or understanding a little better what considerations need to be taken into account when using this technique.

He mentions that his lab sometimes packs their own LC columns (which my ERE lab at Northwestern also does) and describes the costs and benefits of doing this. It can be more cost effective and offers more flexibility in the parameters of your columns, but is time consuming and usually less reliable than using commercially available columns.

He also lists lots of samples which they analyze using the columns described here. These are very diverse and interesting, including plants, clinical and forensic samples, etc. which this lab analyzes after being sent from their collaborators, and which have varying amounts and types of protein which can be analyzed by LC-MS using the columns described in this webinar.

I also found it helpful that he talked about how to shorten separation gradients (i.e. the amount of time taken for each sample), in order to make this technique higher throughput, which is a very helpful practical consideration when doing proteomics with LC-MS. He talks about how long of a gradient is needed for different column lengths and other parameters which are commonly used in proteomics, talking about a specific commercial column as an example.

Finally, he explains their entire proteomics workflow, mentioning the techniques which are used for sample prep, instruments used for acquiring the data, and data analysis. This is important and helpful because it shows how the columns he is recommending fit into the larger workflow. He focuses on several commercially available columns and how these can be used and their throughput can be maximized, in addition to talking about the option of packing your own columns, so this webinar gives a good overview of lots of things you need to know about choosing and putting into practice different columns used for analyzing proteins with LC-MS.