Are you in one of those facilities (all of them...?) where you aren't allowed to install new software or updates on your PCs anytime you want? Do you wonder why you don't keep liquor in your desk when you realize your only option is to call your IT security guy? Are you currently considering the logistics of getting your own PowerPC and filling the ethernet and USB ports with hot glue so it is CLEARLY not a security risk to anyone and lug it around with you so you don't ever have to make that phone call again?
I am going to say without any hesitation at all that the new Metamorpheus with FlashLFQ is 100% worth interrupting your IT security person during his/her 35th straight hour of Dungeons and Dragons knockoff M.M.O.R.P.G. to come up and put his/her administrator password into your PC so you can install it. Yes, I know how long it takes to get Dorito(TM) crumbs out of your keyboard...yet again.... STILL WORTH IT.
Why? Because Metamorpheus can do almost everything now.
Crazy fast proteomic analysis
Scary accurate label free quan
Crosslink analysis (what!?! I haven't checked this part out yet)
Find just about any PTM and localize it before you've even reduced you RAW file to your peak picked list in other software (through the G-PTM-D) which, btw takes UniProt XML files (that contain the known PTMs -- you don't even have to unzip the files!)
The advancements in the LFQ -- FlashLFQ! -- were just described here. FlashLFQ may also work separately on it's own, but once I realized I just had to upgrade my Metamorpheus (which happened automatically...on my own PC of course, which I'm not carrying around with me...yet...)
Somehow -- MetaMorpheus does all this stuff without being an intimidating mess. It looks very straight forward and it even has a button that says
It's fast, too. I think I mentioned in my post about the G-PTM-D that it still took a few days to search every known modification against a human database. This is not the case with MetaMorpheus. I took 6 Orbitrap Fusion files (OT-OT) and searched with every modification in UniProt. My MaxDestroyer did this for about 30 minutes.
..and then it was done!
It uses very little RAM. You can change that and speed the search up massively if you turn off the function "conserve memory" -- this assumes you've got a lot of RAM and that your RAM is fast. 8GB of RAM on my old Proteome Destroyer was like half of it. On this one -- what is that? A tenth?
What do you get from this? If you aren't impressed that I searched 6 Fusion files with around 1200 dynamic modifications and did it in 30 minutes, you might not be on the right blog. Oh -- and I quantified everything as well with FlashLFQ.
You can get your output as XML that you can bring right into Perseus -- or open in Excel (it will complain) and interrogate your results with the Ctrl+F function.
Now...I think the paper is en route that fully describes this amazing software. Maybe if it is really hard for you to get software installed you should wait until you have the publication in your hands -- or maybe you're like me and you just want to search all your data so you can move on to the next project. In that case, maybe you should check out MetaMorpheus and tell that nerd in the basement to pause his campaign.... ;)
For more information on this amazing piece of free software you should check out the (hilarious! ) MetaMorpheus Wiki for more details.
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