Have you looked at your output report from Proteome Discoverer -- or even MaxQuant and said something like "Wow, it would be awesome if I could easily get some super advanced statistics on all this quan without having to work very hard?"
If so -- I've got GREAT news for you -- and it's called ProteoSign! You can check it out in this nice open paper here.
These authors want to supply you with great differential statistics in a fast, simple and free web interface. They set up a nice little server online somewhere that you can access directly here.
At this point, ProteoSign appears set up for supporting PD 1.4 and a couple versions of MaxQuant only -- but -- since it is taking the text file output from PD -- I think that it would be able to take data from the new versions as well -- heck, I think if you matched the formatting ProteoSign requires you could put in data from any proteomic software with quantification (but I haven't tried yet).
If you are someone like me who loves to just start dumping data into a program before you read any instructions at all -- you'll be very impressed with the speed of the server interface -- you can make a lot of very large and embarrassingly uninformed mistakes about how the whole thing works. If you are persistent with this strategy (there is some value to pressure testing an online resource, right? Please don't take this as my encouragement to not read the instructions. I was just really excited to try it out!) you can accidentally hover over very nice instructions that will tell you what you should be doing that will make you feel dumb and teach you how to use the software at the same time!
Some statistical tools like ANOVA and PCA and volcano plots are coming to PD 2.2, but if you are using PD 1.4 and want to keep using it -- here are those tools. There are features in ProteoSign that don't have analogues in the upcoming PD version, such as the (really cool) replicate scatterplot as well.
I really appreciate the work the authors put in here. They looked at two pieces of software with thousands of users around the world and thought -- "hey, let's add a bunch of tools to them and make it really easy for users to get and use those tools!" Stuff like this explains: 1) Why this is the coolest field in all of science 2) Why this field continues to advance at the amazing pace that it is.
Disclaimer: Yes, I know there are several downstream statistical tools for MaxQuant. The emphasis of this post was -- great statistics without having to really learn anything!
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