|Combining own DDA library with SWATH atlas library for DIA data||moe||2016-09-04|
I've read the Skyline iRT Retention Time Prediction tutorial but I wondered if I could get some help. I would like to combine an in-house DDA library (generated from a DDA experiment of depleted human plasma) with an external DDA library (e.g. Rosenberger library).
1) I've created my own human plasma DDA library using my own DDA experiment loaded into skyline via File - Import - Peptide Search
2) Additionally I've downloaded a custom library from SWATH Atlas (phl004_canonical_sall_osw.csv) from here https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetDIALibs, selected the proteins of interest (all proteins identified by Farrah et al in plasma) and generated a library in skyline via File - Import - Transition List
I now have the two libraries in skyline and I would like to align the retention times of both libraries to generate a more comprehensive library and get the most out of my DIA data.
If possible I aim to use ApoA1 to calibrate retention times of my own plasma DDA library and then use the calibrated retention times of ApoA1 and convert all retention times of the online SWATH atlas library.
Any help on how I can achieve this would be appreciated.