EncyclopeDIA (v-2.12.30) Manual
With a new EncyclopeDIA version coming out soon, I thought it would be a good time to share my manual for the last stable version. Once the new version comes out, I’ll put out an updated manual …let’s hope this occurs soon!
EncyclopeDIA v-2.12.30 manual link
What new features will be in the new version of EncylopeDIA? Well honestly, I have no clue, but I am hoping it includes:
Searching for alternative types of mass analyzers including ion traps and time of flight. While there still won’t be a good EncyclopeDIA search solution for the ion mobility spectra of TIMS TOF data, I believe the ability to search TOF data will be more easily incorporated in the GUI.
The ability to schedule PRMs from DIA experiments. I’m confident this feature will be in there!
Koina interface? This is a newer feature, as of the past few months, and its not super well tested, so I have no clue if this will make it into the stable release for library predictions.
A program that the Searle lab has unofficially named “Chromatogrinder,” which essentially allows for EncyclopeDIA’s peak picking algorithm to be used without full searches. This is useful in cases where I have wanted to assess if a list of chromatograms and decide whether to use them for a PRM or not. It’s quick and has no refinement ability like in Skyline, so when I have 500 peptides, I can get through assessing them in about 25-30 min. I can click through the peptides and click the left arrow to say “nope, not real” or the right arrow to say “yup, looks decent.” We’ve also been calling this a peptide dating app, or peptide tindr.
I guess we will find out the new features soon!