Two new smart strategies for raw spectra -- Alphabet and pClean!

Oh no. Are those Greek letters on spectra? Did someone write the draft of this paper using R? Do I have a hunch it is really smart but I absolutely have no idea what is going on? Are we just looking for patterns in all the chaos of MS/MS data? What a great idea! Can I explain it better than this? Nope.

If spectral bioinformagics are your thing, maybe you should just check this one out yourself -- patterns in de novo is the theme.

And this is not the same thing at all -- but just happens to be in the most recent JPR as well, and something I think most of us have wondered about -- could we denoise some of the junk out of spectra ahead of time?

I know people who are still using Proteome Discoverer 1.4 in large part because they can use the (now defunct? or entirely incorporated into MSAmanda only?) MS2Spectrum processor (pd-nodes.org) prior to their Mascot searches. pClean is an R package that has much of this same functionality but goes a little bit further with it's fancy network stuff AND even if that isn't useful (there's no way I have the capability to judge) -- pClean can remove fragments that come from your TMT or iTRAQ tag that your search engine can't utilize properly in making assignments! That is certainly useful!

You can get pClean at this GitHub.