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.
Really really well. Definitely try out this software.