We all know the Fusion is fast. Crazy fast. And we know that the Fusion has some FTICR level resolution capabilities (though much faster). What if the crazies out at the Thermo factory decided to re-approach DIA (sometimes called SWOTH, or something) and utilized all of the powers of the Fusion to negate all of my complaints about these approaches?
Well, you'd probably end up with this technique described in this application note. I cut the core experiment description about above. Here is the gist: you do SIM at 240,000 resolution (1/4 million!) and break it into 3 largish windows. So you start with the depth and sensitivity of a SIM scan. At the same time, you have the ion trap do little DIA experiments of 12 Da windows, so you have the specificity of tiny DIAs on top of the dynamic range and specificity of big window SIMs.
If you bring me data where you show me your peptide of interest resolved at 240,000 resolution, 99% of the time I'm going to say "sure, that's your peptide" if you can back it up with 8 fragment ions from your DIA (which is the default quan method that this method uses!!!!!) from the same freaking experiment, you've identified that ion without any shadow of a doubt.
This method will be a default template in the next release of the Fusion software.
Update 4/16/14: There appears to be a problem with the graphics on the link above. The original PDF of the application note is available on Planet Orbitrap.
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