Tuesday, October 12, 2021

The N-Glycoproteome of K562!

 As you are dutifully moving away from the last experiment you'll ever do with HeLa cells or protein digests and starting anew with superior standards that are not unethical to use or sell, my first recommendation is the Promega K562 digest. (I 100% side with the family, and that company was warned this would happen.)

I've spoken to Promega about how they generate it and how they test for these scary mycoplasma things (thoroughly) and after running it at least once every day for QA on our TIMSTOF with extremely reproducible results (our daily QA is: 30 min LC gradient, 15 cm PepSep Reprosil C-18 1.7um with 3cm trap of same, "if 200 ng of K562 is less than 3,300 protein groups on FragPipe QC workflow, stop, something is wrong", which is altogether kind of insane, but when the system is freshly clean we come close to 4,000)

If you're thinking: "wait, is it as complex as that other cell line?" Check this out!  

5,000 N-linked glycopeptides?! That should be enough to QC your glycoproteomics workflow! 

As another option, NIST developed a liver homogenate lysate for proteomics. I don't think it's shipping yet, but it should go live soon. 

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