In the "return"(?) of MS crosslinking (? cause, did it ever leave? probably not, but there was definitely a point where we all avoided it whenever possible) a familiar name kind of faded into the background. StavRoX (non MS-cleavable) and MeroX (MS-cleavable) also never went away, but other newer software gained a lot of ground with new concepts. This new study shows that the software team didn't let these new improvements pass by un noticed
Earlier this year(? I lose track of time easily) Rappsilber lab demonstrated that monoisotopic precursor selection (MIPS or "Peptide match") doesn't work very well for crosslinked peptides and they adjusted for it in their software.
MeroX now does the same.
A couple of studies have shown that XlinkX can really handle global level eukaryote crosslinking data. Improvements in MeroX 2.0 can now search entire organisms as well! (They demonstrate by finding over 1,000 crosslinks in fruit flies)
I'll be honest, I don't entirely entirely understand false discovery rate (FDR) applications in crosslinking and how/why these differ and why the traditional stuff doesn't work right, but it appears that Sinz lab has developed a crosslink specific FDR. With so many published software packages fading into obscurity, it's always great to see one refreshed by a team paying attention to all the ways they can make their software better. It's all available at StaVroX.com
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