Monday, December 1, 2025

Another funny solvent is better than formic acid for proteomics?

First off -- 

CHECK WITH YOUR HPLC MANUAL OR MANUFACTURER!!



Is the resolution of GIFs getting worse all the time? If so, it's the only change I've personally seen from this whole "AI revolution", except people saying "I asked ChatGPT" when they would have said "I did a Google search" back before Google reorganized and put their search algorithm teams under the control of their marketing teams. True story, that's why Google really doesn't work well anymore and AskJeeves is back, but now it needs more electricity than all of Spain will sue this year to look up stuff on Wikipedia for you. 

Okay, so someone at some time decided formic acid was a pretty good compromise. Pretty sure it was people in the John Yates lab. TFA gave you the best possible HPLC peaks for peptides, but it lowered your ionization efficiency. Acetic acid gave you the best ionization efficiency but if you were doing MuDPiT (which was a 2D chromatography system for proteomics best left forgotten today but it provided unprecedented proteomic coverage with the awful HPLCs we had at the time), acetic acid messed up your peaks too bad. So...formic acid it is.

Worth noting, formic acid has some drawbacks like poor stability in light, particularly when diluted. So when a lab dropped a paper showing acetic acid should be revisited, we jumped on it. My lab doesn't use formic acid in our HPLCs at all. We do have vendor permission and we have several thousand runs to demonstrate it hasn't been a bad idea at all

So when I was contacted by a researcher who was like - "yo, we have something better!"  we borrowed someone else's HPLC and tested it out. In our hands on (nanoflow) it's only marginally better than acetic acid, and possibly so marginal that on the sub-nanogram loads it wasn't significant by student's t-test. I forget, and Cameron actually did the work while I was visiting collaborators. But when you crank up the flow rates? 


Okay, so someone at some time decided formic acid was a pretty good compromise. Pretty sure it was people in the John Yates lab. TFA gave you the best possible HPLC peaks for peptides, but it lowered your ionization efficiency. Acetic acid gave you the best ionization efficiency but if you were doing MuDPiT (which was a 2D chromatography system for proteomics best left forgotten today but it provided unprecedented proteomic coverage with the awful HPLCs we had at the time), acetic acid messed up your peaks too bad. So...formic acid it is.

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