DirectLFQ - Super fast requantification of your processed data for some reason!

 

I'm more than a little confused about this, but I tell you what -- it is FAST!

I read the preprint sort of asleep early this morning, then this guy drove by my house with CRAZY LOUD BASS, like you could feel it in your chest sort of bass when I was bringing my trashcans in. I waved him down and told him I also love the Backstreet Boys and for some reason it made him really really mad. Apparently Backstreet is NOT back and I misidentified the artist. Surprised he could tell what he was playing, but that's okay. I was a little more alert after this discussion got really heated in a hurry, so I looked back through the paper.

I downloaded it (you can get the one-click GUI's here) and I ran it.

I pulled up 128 different mouse organs that I'd ran on a TIMSTOF in DDA format and processed with FragPipe 19.1 last week. I loaded the combined_ion.tsv file into DirectDIA and within about 60- 90 seconds it made me a new protein report. I didn't even have time to get distracted. 

Where I started to get confused is here -- I already have a protein report from FragPipe. When I compare them, they are pretty similar. DirectLFQ had about 10% more missing values at the protein level (low n) but the numbers do seem to line up reasonably well.

My big question is where this fits into my workflow? I don't really have tools here where I get PSM level quan and I don't get protein level quan. The paper doesn't illuminate it for me much. I do get it, the software definitely is fast, I just can't figure out when I'd use it? 

You can load DIA-NN data into it and MaxQuant data and there is a generic format uploader for whatever else you want to requantify. DIA-NN and MaxQuant both also make protein level quan reports. 

If I look at my Fragpipe log files the assembly of the PSM level quan data to protein level isn't exactly my limiting step either: 

It looks like this took about 2 minutes? 

Look, I'm not taking anything away from this. It is free software that runs on Linux, Mac, PC and it can take your PSM level quan data and make you a protein quan report. If you don't have that capability in your pipeline -- you do now!