I'm currently (well -- not right this second -- each run is only like 12 minutes -- but...) comparing a protein or 3 under both reduced (acidic conditions) and native (non acidic -- tried like
A minor problem is that there is exactly one computer with software that can handle deconvolution of native proteins in our building.
WooHoo! Thank you Deseree Reid et al., for this awesome free deconvolution software that is exactly what I need!
I was kinda bummed because the paper leads you to a download link to the software that looks like you have to use Python to use it (which isn't so much of a bummer since a guy in my lab is a Python expert) BUT then I found this link that leads you to a GUI!!
This is what it looks like in action --
See all these things it does? It has features that are not present in our commercial package -- including some things that I really wish that it did.
Now -- you do have to get the data into the correct format first -- from the manual (which is online here)
Okay -- so that's a lot of words and I don't know what most of them are. FORTUNATELY -- all this AMAZING software is looking for is a text file to deconvolute. That I can handle.
You can make Xcalibur do that for you. First, find your ugly protein peak (you don't get to see mine -- the peak is like 3 minutes wide -- it's essentially just a desalting column)
Then go to Excel and paste it!
Whoa! How cool is that? The RAW file doesn't start at exactly 2,000 (m/z)!! You'll have to believe me, but it doesn't stop at exactly 6,000 either! Quads get kind of wobbly at that kind of range, right? Makes sense to me.
Now you can make that into the text file and load it. Okay -- actually -- I'm having some trouble with the formatting on it. While my first suspicion is that this was designed for a TOF and the fact I have mass accuracy is probably the issue -- it might be the header format. It's a Saturday night and I've still got to do some sample prep so I'm going to worry about this later.
Even better? You can just directly paste the clipboard in.
It's even better than I thought!! Check this out.
Okay -- this will clearly need some optimization -- but with no use of the manual and I've got a nice peak out of this software on my first shot. For perspective, I don't know how to set the parking brake in the car I got in December. I just don't park on hills.
It was probably dumb to start with an unknown (that appears to suffer from some degradation with in-source collision energy at 90eV) so I put in one of my QC proteins. Check out this cool output deconvolution plot!
The protein should be 42,882 -- this trippy output requires some finagling (which appears to be a word?) but the software looks spot on and I haven't scratched the surface of what I can do with this awesome new tool I now have!