Monday, October 5, 2015

First impressions of the free LFQ node from OpenMS

Over the weekend I got to finally toy around with one of the cool free nodes from the Kohlbacher lab that we can install into Proteome Discoverer 2.0.  The LFQ is short for "Label Free Quan" and the nodes are freely available to download for anybody here.   Now, before I go forward I should probably reiterate something that is on that page. These are 2nd party nodes and these won't be supported by Thermo's Proteome Discoverer team. Questions should be directed to the node developers. Fortunately, they seem quite straight forward!

Here are some early impressions of the nodes.

1) They are easy to install. Download the file from SourceForge, make sure all Proteome Discoverer versions on the PC are closed and run the file.  When you reopen, the nodes are there!

2) The node developer's even have workflows ready for us! There is a Processing Workflow and Consensus Workflow. Which is great! Cause, honestly, I wouldn't have thought to set them up as above....

3) Interesting note.  SequestHT and Percolator are mandatory. Gotta have 'em or you won't go anywhere, it seems.

4) LFQProfiler appears to multithread.

Windows performance loggers are always kind of hard to interpret, but all 8 cores on this desktop appeared to be doing something when the LFQ Profiler kicked in.  In the consensus you can actually tell that LFQ node how many cores it is allowed to use!  On other runs, it looked like I was maybe only using 4 cores, but this really isn't a good measurement.

5) Disclaimer here: I've got like 10 versions of Proteome and Compound Discoverer on my desktop because I have been alpha/beta testing them for years. I've got some versions that are locked down for different projects so my working environment is probably sub-ideal. But... I'm gonna be honest here, and I'm likely doing something wrong, but I'm finding the node a little difficult to integrate into my workflows, in an odd way. I keep getting "Execution failed" in my Administration tabs, but the failed workflow can be opened and looks just fine. I do have to unhide my Intensity but the numbers are here and it looks like it ran real fast!

So...first impressions. The LFQ node installs easy, has convenient pre-made workflows (additional downloads required) and seems to run fast. More analysis required to see how it works, but its Sunday and this is all the PD I think I'll do today!

UPDATE: 12/2/15.  Downloaded the LFQ nodes and they are AWESOME!!!


  1. I also tried on to run PD2.0-OpenMS workflow, everytime processing workflow looks good and successful. But everytime I got "Execution Failed" error at the end. The result can be opened as well, but there are no quantifications! Is it because it is not published? How do you think?

  2. Yeah, I get the same thing in regards to the execution. but you can get the intensities, you just need to "unhide" them. (at least in my case)

  3. Is it possible to integrate OpenMS node with Byonic identification? I tried to add them in one workflow, but I also got "Execution Failes" error. I still could open the result, but no quantification panel. How can I "unhide" the quantitation result? Thank you.