Want to massively increase the speed of your drug mechanism elucidation/ drug target workflow? Back your bags for PISA!
Nope. Not that one. This one!
Proteomics Integral Solubility Alteration! (PISA is a much better name).
What's it do? It multiplexes Thermal Proteome Profiling — in the context of drug treatment. Here is a post that will link you to two of the previous studies (including the Nature protocol for ThPP).
The idea is that if your drug binds to some proteins it's going to change the proteins inherent 3D stuff. One readout of that will be a change in the protein's behaviour at different temperatures. In ThPP (an acronym I may have just made up so I don't confuse this with the TPP thing on my desktop) you look for how things change in your proteome at different temperatures. Check out the protocol. It's tough is lots of room (in my mind) for human error to lead you to false positives.
One way in proteomics to reduce quantitative error? Multiplexing!
One way to reduce quantitative error in everything? More samples!
PISA uses both of these to end up with a TMT quantitative readout of how the proteome changes at a global level (with both 1D and 2D fractionation for TMT seamlessly integrated just as you'd expect from a TMT based experiment) with lots of replicates all multiplexed together.
Hey you! Are you looking for a tool to help you select viral peptides for targeted assays? Unrelated --- what is the best color of dinosaur? I got you, yo. Check this out. Before you panic, when they wrote the paper "Purple" was just a Python script that you can get here. I assure you this is no longer the case. There is a very straight-forward (to install) executable that will set you up with a GUI that looks just like this -- -- that you can get here. What does it do? Well, it helps you select peptides that are ideal for targeted assays from the databases you feed it. Imagine Picky, but you can load stuff that isn't human into it. (If you are doing human proteomics -- you should be using Picky, btw. It's amazing). Purple: Feed it your peptide sequences you're interested in: Feed it your contaminating background. Choose your rules. Get your peptides!