I think my expectations are typical for what I expect from the good people of the world making free software and proteomics tools.
I just want:
1) Completely new ideas that are way better than the old ones.
2) Ultra powerful algorithms that use resources I couldn't possibly get or use elsewhere.
3) It all bundled in a way that will only take me like 45 seconds to install.
4) It to be intuitive enough that I don't have to read anything to use all this power.
All the perfectly reasonable expectations we all have for our bioinformagicians out there.
We know that chemically modifying a peptide with a PTM shifts it's retention time. How? That depends on the modification. Phosphopeptides generally come out earlier (you probably lost a significant number of them if you used a PepMap trap column.), but what about the other ones? That's one of the problems you need DeepLC for. Loads of application here, but I've gotta move fast today.
You can get the program from this Github!
Super easy installation and it only has 8 settings! Tons of new power for me in exchange for exactly zero effort on my part?