Friday, April 29, 2016
ReACT -- Spectral library searching for crosslinked peptides
2 papers in a week is coincidence, right? 3 is something else...
So...in this very nice (paywalled) paper at JPR we see something a little different for determining protein-protein interactions for chemically cross-linked species.. This algorithm, REACT, has been described previously in FT-ICR studies out of Seattle. It is written in the "ion trap control language" which, to my small brain, makes it seem a little less than universally acceptable.
In this study they show that the algorithm can not only be used to analyze Q Exactive Plus data, but also that it (they seem surprised in the paper. I'm not! Q Exactive, FTW!) produces more and better data than the FT-ICR.
The gist of this program is that you generate spectral libraries representing your theoretically occurring cross-linked peptides and that is what you search your experimentally obtained MS/MS spectra against. In this way it is similar to the awesome XCOMB resource from the Goodlett lab. (Wow, I need to update my old links to this in the blog!)
XCOMB relies on a search algorithm like Sequest or Mascot to make the identifications. ReACT uses SpectraST. This is probably another application where spectral libraries will shine and hopefully we'll see ReACT bundled into something user friendly so we can try it out!