Friday, September 21, 2012

Byonic -- A next generation search engine

This week I learned about Byonic, a 'next generation' search engine from Protein Metrics.  And what I heard is really exciting, but I'll back up a few steps.
Dynamic modifications are functional groups or post-translational modifications that may or may not be present in your proteome.  For example, when we are doing a phosphoproteomic study, we set +phospho as a dynamic modification that may, or may not, be on every serine, threonine and tyrosine in every protein in the proteome.  Every modification dramatically increases the matrix that your spectra are searched against, leading to an increase in search time.
Back when I was doing phosphoproteomics with Bioworks (Sequest), I expected that a full human proteome search would nearly triple in search time when I added the possibility of just the three phosphorylation states mentioned above.  While multi-core processors with multi-thread algorithms have cut this time, we are still practically limited in Sequest and Mascot to a small number of PTMs for the sake of time and bandwidth.
This is where Byonic steps in.  Byonic can look at hundreds of potential modifications.  How?  I don't know exactly, but I have a suspicion.  What if your reach engine ran through and identified every unmodified peptide.  Even on a single core Sequest with plenty of RAM, you could complete that search in minutes.  Then you took your identified peptides (you could use a very loose stringency) and you exported a FASTA file that only contained those proteins that might contain the peptides you probably ID'ed.  In this step you would very quickly reduce your database at least 10 fold, but most likely, several hundred fold.
With this reduced database, you could add dynamic modifications willy-nilly without causing your searches to run for days or weeks.

Again, I have no idea if this is how Byonic works!  This is simply a guess because it is the only way that I could think of to make a search of hundreds of dynamic mods fit into a reasonable amount of time.

Best part of this article?  You can download Byonic and try it for free for 30 days.  I'm going to dump a load of data into it this weekend.  You can find out more about Byonic and Protein Metric here.

Wednesday, September 19, 2012

New toy from PNNL: Protein Coverage Summarizer

Looking for a new way to visualize your protein sequence coverage?  Check out this free (and customizable) tool from PNNL.
Just don't forget to acknowledge them if you use it for a publication or grant!

Wednesday, September 12, 2012

Eksigent ekspert nanoLC 400 system

I don't really do a good job of keeping my disdain for Eksigent nano LCs to myself.  The absolutely horrid experience we had with the nanoLC 2D systems will keep me from ever recommending these silly gas-driven things, but I'm still on the email lists. I know, other people like them.  Just not me.  Anyway, here is a copy of the announcement:
Oh golly!  It is also SWATH compatible.  Can't wait to review a paper that used this setup!

Monday, September 10, 2012

Advion NanoMate

Last week I was introduced to the Advion NanoMate.  The NanoMate is a new type of ionization source.  Rather than using a single emitter, the NanoMate has a chip that can contain as many as 400 separate emitters worked into it.  I'm sure there are a number of uses for this device, but the lab I visited was using it primarily to maintain extremely high spray quality.  When the NanoMate detects that there is a problem with the emitter currently in use, the chip simply moves over to the next emitter.  This would be really useful if your samples are either extremely dirty, or extremely complex, and tend to rapidly foul emitters.

I don't know the limits of the NanoMate's compatibility, but it definitely compatible with the LTQ Orbitrap systems and the Q Exactive.  Although it does not run within Xcalibur, the two software packages were working together seemlessly on the two instruments that I observed.

The drawback of the device is that is considerably more expensive than any nanospray source I know of, and it doesn't appear at all trivial to operate due to the three dimensional aspects of moving a tiny emitter into and out of place all the time.  But if you are burning through hundreds of emitters, it might be worth looking into.  

New nodes for Proteome Discoverer

Just a quick note about something I learned while at BRIMS last week.  A joint effort from the Research Institute of Molecular Pathology and other groups through the Austrain Academy of Sciences has set up a site devoted to new nodes for Proteome Discoverer.  The aptly named site, PD-Nodes ( currently only has 2 new nodes, but promises further development.  The first is an improved version of Phospho-RS, our favorite phospho-site localization software.  The second is an MS2 Spectrum Processing Node for deconvolution of ions in MS2 spectra.
I've bookmarked this site and will check frequently to see what else pops up for us to use!