Mapping protein-protein interactions in complexes is a tough job. We can go one of two ways with it:
1) The relative way: When I pull down proteins under condition A and under condition B, I see relative upregulation of this protein, so it must be associated
and
2) The crosslinking way: Under these conditions I throw in a crosslinking compound, then pull everything down, digest and identify the crosslinked peptides.
Both are hard, but the relative way is a good bit simpler from the data processing perspective. Analysis of crosslinked MS/MS spectra? Thats hard. There are some nice approaches like XComb and StavroX/MeroX. SIM-XL is a new one. If you wonder why you might want to try a different piece of software, look at this result output (click to Zoom!)
Um....how frickin' cool is that?!?!?
Its a GUI driven interface with all sorts of cool graphical maps to help make sense of your crosslinked data. It'll accept all sorts of MS/MS converted data files (and if you've got the MSFileReader installed, it'll directly read Thermo .RAW files!) and its even possible to map your data against spatial constraint data obtained from 3D protein structures to see if what you are seeing is possible at the biological level!
You can check out the SIM-XL website here.
And you can find the original paper by Lima et al., here.
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