Monday, September 21, 2026

diaTracer - my first impressions (diaPASEF data!)


I've been generally confused about the whole "FragPipe + DIA" thing for a while. What's the DIA-NN node doing there....? Why wouldn't I just run DIA-NN...? (for examples.)

When a new way to process DIA data showed up last year, I had my hands full and just didn't get around to it. I've got SpectroNaut, BPS and automatic command line DIA-NN (academic version). Why would I need anything else? 

What if you are an academic and someone set you up a very nice interface where they'll just load you up anything that will run in Linux? And you don't want to type stuff into a command line? And you don't want to convert your Bruker files? And you don't want to pay anything for it? And you don't want to mess around with making spectral libraries yourself? 

Enter diaTracer! So I'm checking it out vs the other tools and - HOT DAMN THIS THING IS FAST! 


Maybe you can't read the box above but diaTracer took 5 minutes and then everything else took about 5 minutes. That's super fast for these files!  

Also! 
1) I didn't really have to learn anything. I already know how to use FragPipe. (I did have to download FragPipe 24 and then look very hard for the diaTracer button) 
2) I didn't even give this search a lot of resources. I pointed at 2 random single cells, gave it 18 threads (parallelization)  and I have a report in 10.2 minutes? On diaPASEF data? I can't convert these 2 files to .HTRMS to upload into SpectroNaut this fast!  
3) I'll have to compare the results (or make someone smart and meticulous do it.....) I'm just eyeballing the DIA-NN data and they seem similar. 

WHAT??? And here is one of the proteins that I'm looking for! Oh. This might be super cool. 



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