Need a step by step protocol to break out the microchannels and 96-well plates for TMT proteomics? Maybe you should check out SimPLIT.
What is cool here is how this group is prepping tons of cell culture proteomics in 96-well plates with labeling, offline fractionation (by HPLC) and repooling and running TMT (on a Fusion).
This feels like a study that came together out of a lot of replication and thinking about how to streamline sample prep to the maximum possible efficiency.
One cool thing here is how they're getting their cells lysed with a 8-horn sonicator thing. I've never seen one of these that could sonicate more than one sample at a time and it took me a bit to find it.
If I have a criticism of this study, it is that it kind of feels like overkill on the LCMS side. 12x pooled fractions at 150min gradients (30 hours) is starting to seem like a lot to me, 30 hours means that instrument operating 24-7 will complete 292 18-plexes per calendar year. For showing off how great your method is from a number of proteins quantified perspective, this is a great setup and I'm sure that shortening the gradient length or cutting out the 2D fractionation would work great for a lot of projects!
For real, though, great study, great data, cool new acronym!
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