Sunday, June 10, 2018

ProteomeTools takes on 21 different PTMs!!

Spectral libraries are coming back with a vengeance. Check out this great new study in press at MCP!

What were their limitations again?

1) The libraries weren't big enough?

2) Integrating library search into normal workflows wasn't straight forward?

3) There aren't enough PTM libraries?

1) ProteomeTools has already dropped 400,000 synthetic human peptides through their site and through collaborations with institutions like NIST. A LOT more are coming. Couple this with the MASSIVE's new libraries and the treasure trove at NIST?

2) More on this later, I think. But more and more of our normal software workflows are becoming spectral library compatible. Mascot supports them now (right?). I've seen two mentions of spectral libraries in MaxQuant in the literature, so that's coming and all the DIA software is ready to go for libraries of all kinds.

3) NIST has had a huge human phospho library for years, sounds like MASSIVE has a ton now as well -- but ---

This team synthesized a ton of peptides with weird PTMs on them!! I'm sure they have or will release the libraries -- but what might be more important right now is that the RAW files are available via ProteomeXchange now (PXD009449, here)

Is that really a crotonylated lysine you're looking at? Ever seen one before? (I'd never even heard of it until recently...) sure would help if you could download a couple RAW files with real ones in them and find out they look like this in HCD, right?

Better image from the RAW file itself (yeah -- that 152.107 is in virtually every MS/MS spectra -- you know, just checking...):

This paper is an absolute treasure -- if you're European you probably know that Andromeda can make use of these diagnostic ions in the scoring algorithm. So...if 92% of all crotonylated lysines made a 152.1070 fragment ion, Andromeda can take that into account and help you weed out the false cool is that?!?  I just went through PD and even in the text editor interface for modifications in MSAmanda 2.0 I don't seem to have the ability to do that at all...(you can, however, get MSAmanda to preferentially score you new neutral loss masses, but it requires some finagling to get it right. Can't guarantee I've got it, but you edit those here in the Administration).

Wow -- as soon as I think this paper has stopped giving -- there is more stuff. If you're interested in any sort of weird PTMs -- this study should be on your desk. It'll be handy when it's formatted, but it's worth cutting 45 pages out of a tree right now --

HOLY COW --- The very last figure of the supplemental info casually shows you how to resolve one of the single hardest things I could ever think of trying to work with -- there are different neutral loss patterns whether a peptide is symmetrically or asymmetrically dimethylated....the more I think about that the more I'm certain I probably couldn't manually sequence that without this information....but -- could I go back into the settings above and feed MSAmanda this information and get it and PtmRS to use this information to resolve these correctly?

I can't believe how great this study is.  I don't use this .gif lightly...

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