Wednesday, April 6, 2016

Pattern lab -- A bunch of cool tools bundled in an easy GUI!

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."

Wrong answer!!!  

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 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...)
Spectral counting
XDScoring (for Phosphosites!)
Isobaric quantification
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!


  1. We have a user forum. PatternLab has been community driven; we strive to address feature requests. Should you run into any trouble using patternlab please do not hesitate in contacting us. (Paulo Costa Carvalho)

  2. I see your point on navigating through the various directories to define inputs using a directory browser. I never do it that way because, as you said, can be very tiresome. PatternLab accepts copying and pasting directory paths from the file explorer; this simplifies the process. note there is always a textbox were you can paste the path. As the other folders will be close by, the process of switching to fileexplorer and going to the next folder to obtain the path is simplified. Thanks for pointing this out. We will look forward in including a video on our website to show these little tricks.

  3. Paulo,
    Wow, thanks for the useful comments! It really is a nice and well thought-out piece of work!