What does proteomics need more of? Easy pretty GUIs! This morning a friend sent me a link to a program he's been working with (and presumably likes...). In the instructions, the very first line is (no joking): "open your command prompt."
PatternLab might just be the complete opposite! It is super GUI driven and uses nice primary colors. Look, I don't require a search engine that could fit in at Toys R Us...but...it might be a preference and I'll take it over a C:/ (sorry, I know I sound like a slacker, but its 2016!)
(Typed "GUI meme" into Google. Was NOT disappointed)
AND you aren't necessarily giving up power here. This pretty interface has a ton of powerful tools in it including:
PepExplorer (de novo!?! haven't checked it yet...)
XDScoring (for Phosphosites!)
Integrated XIC extraction
You can also add in other external modules. SIM-XL (for crosslinking studies!) and something called Y.A.D.A. that appears to be a deconvoluter of some kind. I didn't have time to explore it yet. There is a lot in this interface.
And I got results without reading the instruction manual at all. Though, I suspect I'd get better data if I did read some of it. I was just a little unclear about the mass cutoffs and centering, but it spit out a protein table with a rational number of results and that is all the time I really have for it this morning.
If I had a criticism of the program, I'd say it could be easier to load files into it. You point it to folders rather than files and it doesn't seem to have a persistent memory. I have to start at MyComputer every time and hunt down my folder location. If your paths are as ridiculous as mine, it gets tiresome on search 2 or 3. I'd also say that Comet searches are a good bit slower than I'm used to seeing them through other interfaces, but they aren't that bad, just noting an observation. I started with a whole human cell lysate sample and had a data table in 20 minutes or so (filtering and data visualization are separate steps). Same dataset on PeptideShaker (just using Comet) is probably under 10 on my PC if I run the SearchGUI and have it automatically bump open PeptideShaker when its done. There might be a point where you can optimize threads and resources to speed it up (you'd need to read the manual for it. So this point might be totally moot.)
TL/DR: PatternLab is nice shotgun proteomics software with a ton of features and you probably already know how to use it. There are some tools that you can run through it (SIM-XL come to mind) that may not have a true equivalent.
You can read about it in Nature Protocols! here.
And you can check out the website and download the program here. (Final note: it is ridiculously easy to install!) If you want to load RAW files directly the MSFileReader needs to be installed on your PC, but chances are you already have it.
Edit: Definitely check out the comments below from one of the authors!