Monday, December 7, 2015

Playing with the OpenMS Proteome Discoverer community nodes!

Hot diggity dog!

I got some samples and got to work playing with the OpenMS PD Community nodes for PD 2.0, which you can get here!  BTW, new and improved nodes are coming for PD 2.1!!!

Here is the processing setup. The LFQ nodes require Sequest and Percolator for now. I looked at my samples and picked a good retention time that made sense. The peaks were real nice so I used a typical retention time of 60 seconds.  I would have used a smaller window with other LFQ software, but this stuff is fast enough that I didn't really care.

Note:  In Spectrum selector "MS Order" MUST say "Any" or it won't work.

These are the settings I used for Consensus. It appears that you only need the two nodes on the right, but I don't see any problems when I use the other nodes. The data may not fully integrate, but it doesn't hurt the output. There is a dramatic difference in speed on my PC when I change the number of cores that the Profiler is allowed to use. If I give it 8 cores this thing is faaaaaassssttttt!!!!

Okay. Boring part over!  How's the data look?

Well, you get these sweet new tabs!  Quantified proteins/ quantified peptides and EVEN BETTER?!?!? Quantified features!!! You get quantification even if you didn't identify stuff.
"Hey, whats that thing that's upregulated 27-fold in the tumor?"  Well, sir/madam, that is your biomarker. Figure out what the heck it is now.

Okay. Sorry for all the scribbles. This isn't my data. This anonymous protein is present in all 12 samples analyzed. The files I put in are labeled in order of their "F" value in PD.  My first file is "Abundance number 1".

I can go into quantified peptides and/or features to see the individual quan values, or I can pop over to the PSM tab and see how the original MS1 intensities look.

Okay. But this is the real test. How do the values compare to the RAW intensity values and XIC areas?

 Really really well. Definitely try out this software.

1 comment:

  1. Hi Ben,

    I am not exactly sure what this rave is all about recently released openMS quantitation modules? I manually checked peptide XIC values for 3 charge states of the peptide with very good intensity and they were all 2-3 times off the values calculated manually by XCalibur, while already implemented PD very own Ion Area Detector is only 3% off of XCalibur manually calculated values. The same situation was repeated for other signals. And if openMS can not get peptide levels right then what are the chances of correct protein Label Free quantitation ? And it is not like those modules has a lot of parameters to adjust. So the question is if PD Ion Area Calculator does the job fabulously well whats the point of introducing additional modules, which I am not that sure undergone rigorous testing.