Top down proteomics is pretty cool, and the way that we all eventually want to go but a major drawback is that we can't quantify proteomic changes at that level, right? Wrong!
In this new paper from Ioanna Ntai et al., out of the Kelleher lab, we get the description of global identification and quantitation of proteins from top down. And it's automated. How'd they do it? I'm obviously tempted to say magic software (too bad they aren't a lab that makes their software commercially available sometimes, right?!), but the experimental design is really cool as well.
They started with a normal yeast background and spiked in some known standards as proof-of-principle. They followed up with a cool yeast vs. yeast knockout strain and pulled out known proteins to shift when this gene is deleted. Xtract was used for deconvolution, which essentially limited the upper level of the proteins to be quantified to around 30kDa and everything was backed up with cool statistics.
If you are interested in top down, I highly recommend this paper. There is a poster at ASMS as well. The App says tomorrow from 10:30 to 2:30; poster 157.
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