Thursday, October 18, 2012

Byonic -- 1st impressions

I have a few extremely interesting RAW files that I was given a while back that I have ran against nearly every software package on the planet.  They are interesting because they are from a mixture of human proteins and the proteins from an organism with an extremely unstable genome.  These two files are what I measure all software packages by.  The samples are identical, with the exception that the MS/MS was collected with CID/ion trap in the first and HCD/Orbitrap in the second
Yesterday I finally had time to run these samples in Byonic.  The results are extremely impressive.  Extremely.  My primary protein of interest in this sample is an large membrane protein primarily composed of large variable regions which are expressed on the cell surface.  The first challenge is that membrane proteins are hard to ionize/fragment/sequence in an MS experiment. The second challenge is the high level of variability.
Using Sequest on the CID sample with the proper cutoffs will give you 10 peptides from this protein.  Adding mascot will give you 2 additional peptides that Sequest does not.  Running the same sample with no modifications, except for carbamidomethylation of cysteines, in Byonic returns 15 peptides.  With zero modifications, the search is fast.  I can't give you a good metric as I currently only have Byonic functional on a 32 Bit Win 7 machine with 3.5 GB of hard drive space. I'll have better metrics after running this on my server, where I have benchmarked processing times for various software packages running this sample.
The real advantage is when this sample is re-ran incorporating the 'wild card' search which allows for variations within a user-set mass range.  I used the default cut-offs of -40 and +200 Da.
The rerun added 7 unique peptides that all appear to have suffered 1 amino acid substitution!  So I've moved from 12 peptides in Sequest + Mascot to 22 peptides from my protein of interest, as well as a lead in point to the modifications that this particular parasite has undergone.
Another big advantage to Byonic is your report.  When the processing is complete, you get an Excel spreadsheet with 3 pages:  1) A summary 2) Your spectra/peptide report 3) Your nicely summarized protein report.

The summary contains a plot of your precursor mass errors and the distribution of your protein scores and other useful information as shown above.  The spectra and protein reports are easily searched, well organized, and contain all the right information.
I may post more after further study, but I just want to leave you here with this suggestion:  Contact Protein Metric and check out this software.  I think you will be impressed!

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