Maybe, but I'm pretty sure they could easily write a paper describing say version 19 like Fragpipe or MaxQuant had done. I suspect they are just not bothered about a scientific publication.
Many passionate debates in lab about if (open source) software should have a publication ("just look at the code"), yet most closed source software never gets published and doesn't get critiqued for not being published.
That’s the curious thing about fragpipe (and others, but it’s the most notable), it isn’t open source.
So it appears that you need to describe the approach in at least algorithmic detail to get it published.
Maybe those commercial software tried and couldn’t publish without giving away their IP.
Comments
My guess is that it had something to do with it being a black box/closed source.
Any insights @spectronaut.bsky.social ?
It's pretty obscure for the main publication of the software, and doesn't go into software details, unlike DIA-NN, FragPipe...
So it appears that you need to describe the approach in at least algorithmic detail to get it published.
Maybe those commercial software tried and couldn’t publish without giving away their IP.
https://patents.google.com/patent/WO2022184406