HI skyline team,
We are confused about the protocol to do the retention time alignment between run-to-run of DIA data.
We searched methods in the skyline website, but we can only find the iRT calibration protocol.
We follow the iRT calibration steps as illustrated in the attached file. However, we think that the iRT calibration is used for time prediction of MRM. Is it right?
If we want to do retention time alignment in DIA data by using our added peptides or endogenous protein digests, is there any detail protocol for us to follow step-by-step?



Best,

Chen