I've been wanting to talk about this one for months!!! Unfortunately, I do have a day job and there are rules I have to follow to keep that day job, so I held my tongue until I found out I was finally allowed to talk about it this week.
At HUPO I got to see Pinnacle. Pinnacle is software specifically meant for all you translational people out there. I know, there is a ton of software out there, but I'm going to argue that you ought to demo this one if:
1) You have so many clinical samples (especially high resolution ones) that you can't process them in anything like a reasonable amount of time
2) You are doing label free quantification
3) You are doing data-independent analysis (DIA, pSMART, WiSIMDIA)
4) You just want to use a piece of software that is graphically pretty.
This software is fast. Sick fast. It-shouldn't-possibly-be-this-fast FAST. Put in HUNDREDS of Q Exactive Raw files -- targeted, untargeted, DIA, whatever -- and watch it pull the data out in minutes.
Wonder what the data quality is like? Just look at color and shape of the icons on the left (click on the pic above to zoom in) and get a feel for the quality OR look to the right of the peptide sequence where you ACTUALLY SEE THE INTEGRATED PEAKS. Sorry to shout, but how cool is that? "Wow, that is crazy upregulated! Should I investigate it? Nope, that is obviously just a poor integration. Better readjust that integration right now". In real time. Without changing the settings and reprocessing the data. Just fixing that peak. Click, click, done.
Pinnacle has a bunch of other functions. Its a thorough software package and you purchase the modules that you need for your work. You can also download a free trial version here that lets you process one dataset and see what I'm talking about.
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