Wednesday, October 5, 2016

Want to do capillary/microflow proteomics? -- here's a great reference!

I hate nanoLC. I've hated it from the first time I heard of it, and I still hate it today. But its one of those necessary evils, like the IRS and alarm clocks -- and it currently still appears to be necessary for  doing proteomics.

The usage of nanoLC boosted the sensitivity of our LC-MS systems right through the ceiling. Some of the math out there suggests something like hundreds to thousands of times more signal versus analytical flow LC -- and that makes sense. But the mass specs are now hundreds -- maybe thousands of times - more sensitive than the stuff I learned to use, right?

Posts like this have appeared on this blog before, where I've worked with someone and we'd use analytical flow and get X hundreds or X thousands of peptides/proteins. What we haven't spent a lot of time on is microflow.

This great new poster that Alexander Boychenko et al., showed at HUPO 2016 shows what you can do with microflow LC (they call it capillary) versus nanoflow!

All LTQ and Orbitrap systems can use microflow -- here we're talking about 10s of uL per minute. Is it as sensitive as nano? Nope. But what kind of depth do you need in your samples? If you need comprehensive proteomics coverage -- you probably already have a nanoflow system. You could also do upstream fractionation to get the greater depth.

Do you need a lot more sample for microLC? You sure do! But...are you that sample limited? A plate of adherent cells in culture is going to give you something between 1 and 5 mg of protein depending on the cells and how you harvest them.

I'm not saying we can ditch the nanoLCs yet. Maybe we never will -- but if I was in a lab where I didn't have one this is a great app note for allowing you to do some light proteomics in between your normal small molecule workflows!

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