There are a lot of MaxQuant fans out there.I was one once, for sure, and I keep meaning to check out the new versions. No question, it is powerful software!
My objections to the software are 1) Wow, that is a lot of buttons and settings and I have no idea what those are..and really, I don't have time to take a week of classes to figure out what they all do and 2) Wow, that output is really ugly.
We all have different strategies to get what we want. If you want to maintain your aura of the awesome mass spec wizard in the basement with your tools that no one in your department will ever really understand -- actually, most software will let you dazzle your ignorant collaborators with your unsurpassed brilliance --- but MaxQuant just might take the cake. (Just make sure you know what all 75 columns in that output sheet are when they ask! Or do the huffy frustrated genius thing, roll your eyes, storm out and go look them up.)
Do we have to trade power for ease of use? Not according to Tao Zhou et al., and their new work in PLOSone! Here they introduce the MaxReport GUI above.
You can download the GUI along with the source code (Python) and a CMD version of the program here.
Alright! That there is a rational number of buttons! And all I had to do was download, UnZip and run the .EXE to get an interface.
Okay, so what does it do? According to the authors its main mission is to: optimize the results of MaxQuant and to provide additional functions for protein N-terminal modifications, isobaric labeling quantification and descriptive statistical analyses
Yeah! Now, its worth noting that the current version is compatible with MaxQuant 1.2-1.5. What do we really get now out of the program? Well, we get some nice output graphics and summaries of the data.
Hey! Its one heck of a lot friendlier than the imposing Excel worksheet I tend to end up with. And biologists do love pie charts. What I'm seeing is some stuff that Perseus doesn't give me and something that is a whole lot friendlier than an Excel worksheet that goes out to column CQ. Does it really take MaxQuant and package it nicely for muggles? Not quite, but its certainly a step in the right direction!
Edit: The more I think about it, the more I like the ability to stack predicted isobaric tag quan info over the observed. That actually is a pretty nice touch. Not sure where I'd use it, but I haven't seen it before!
Edit 2: Stolen from this Tumblr
Hi Ben,
ReplyDeleteI agree that Maxquant/Perseus is tough to learn and understand (unless you just go by the default values). But what is your favourite program to use for, for instance, SILAC? Proteome Discoverer also lacks the statistical graphics output and we need to go into programs like Excel. I heard it's coming more in version 2.2 though.
Or do you have any other program which you rather use?
Best regards,
Marten.
Marten,
DeleteYeah...you're totally right all the way around. We're lacking a lot of statistical power in PD. And it is coming. If what is in Compound Discoverer 2.0 is any indication, PD 2.2 is going to be awesome. But in the meantime...I don't have good answers. I was lucky enough in my instrumentation days that my coworkers/collaborators were amazed enough with my mass spec wizardry that they didn't question the lack of stats. When it started to get important later, we passed the PSM lists and instensities off to a really good Bioinformatician who used BioConductor R packages to pull the stats together...or used Skyline or Pinpoint to extract the targets of highest interest from the RAW data.