Saturday, December 9, 2017

What are the best open Linux Proteomics tools?

I run into this question a lot and I'm surprised I haven't thought to work on a post like this before.

Linux is a family of alternative (and mostly free) operating systems. I tried really hard during grad school to live my life with these -- primarily because I was broke -- but also because I had this strong anti-corporate thing (I appear to have misplaced that along the way...).  This experiment failed dramatically. The versions I tried just couldn't support my crappy hardware and I wasn't smart enough to install/alter my own drivers to make them work.

These operating systems have come a LOOONG way since then -- are still mostly free -- and when universities build supercomputing complexes this is what they're going to use (or UNIX, but we'll ignore that).

Quick note on these, however, I've got to mess with one quite a lot recently. These huge "cloud cluster" computers have unbelievable numbers of processing cores and threads available. However, the architecture of these processors might be very different from the desktop ones that we're more familiar with. I was first allotted 8 cores for Proteome Discoverer 1.4 and 2.1 that worked within a simulated Windows environment. It was SO slow. I complained and they gave me 16, then 32, and it still wasn't as fast as my old 8 core desktop. I got bored and did something else. Really it might be that software needs to be designed specifically for these things to work optimally on them....

And that's a lot of words leading up to  -- what proteomics programs can I install on Linux!?!
In no particular order:

#1 SearchGUI!  

I <3 SearchGUI. You know all those command line search engines everyone talks about in the literature? SearchGUI make them all work in one simple, easy interface. You can then bring all the results together in PeptideShaker.  I would make #2 the denovoGUI -- but it has now been integrated into SearchGUI so it only gets 1 entry.  You can get it here.

#2 OpenMS!

I've only installed the great OpenMS package in Windows. It is a full integrated environment for mass spectrometry with quantification and identification for proteomics and metabolomics. There may be some extra steps to get it installed in your Linux environment. Fortunately, those instructions are here.

Now, it is probably worth noting that you can really make any Windows program work in a Linux environment by creating a simulated Windows environment within the Linux system. This is what I was doing with Proteome Discoverer, but the performance was too much of a problem. This really might have been that I didn't know what I was doing...

This page is a resource that will help you set up MaxQuant working in the same way!

Heck, this guide will help you set up Proteome Discoverer (1.4) on Linux as well.  Please keep the limitations in mind.

There are other tools that will work in these environments as well, but I don't have hands-on with them personally:


The TransProteomic Pipeline!

And...of course you can install R and use R for Proteomics.

Many of the IMP tools (including MSAmanda) can be operated stand-alone in Linux

Please let me know what I've forgot, I'm sure there is a ton!

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