Another good reason to use Proteome Discoverer for Orbitrap data!

So this is another thing that, yes, is probably biased cause you know who I work for.  But if you've read anything I've written over the years, you know that I have been plugging this software for a long time, even back when I worked for other companies and government entities.
Anyway, I first heard back this summer that some open sourceware proteomics programs might be mishandling Orbitrap RAW data.  I only got the chance a few weeks ago to check it out.

Summary (and, as always, email me directly if you want the data):

Conversion of Orbitrap Elite data:
1.)  Mascot Distiller only does it correctly if peak picking is employed.  If you take results from the file, it does not grab the correct monoisotopic mass.
2.)  MM File Conversion 3 does not grab the high resolution monoisotopic mass
3.)  Neither does Mass matrix (both only use the pre-scan lower resolution mass)
4.)  The ProteoWizard and Transproteomic pipeline appear to use the correct mass, but the monoisotopic does not match ours exactly

Conversion of Q Exactive data
1)  I haven't had a chance to investigate the monoisotopic mass (part 2, later?) but this week I discovered that the ProteoWizard, while getting the correct monoisotopic, incorrectly centroids profile MS/MS spectra leading to massive confusion and processing crashes.

These are all good and very useful programs.  But if they aren't reading your RAW data correctly what is the point?  Thermo is so concerned about this problem that there is a free solution that has been around for quite a while.  If you aren't going to use Proteome Discoverer for processing your data, you can at least use the free demo version and the Daemon to convert your data to MGF or MZML or MZDATA before running your hard-earned data on these other processing programs.  You can download the Proteome Discoverer demo at the BRIMS software portal.  You can find tutorials on how to set up PD and the Daemon so it will still convert your data after the 60 day trial has ended (when it converts to the PD Viewer package) at Planet Orbitrap. You'll have to register (for free) at both sites for access to the downloadable content.