How does alignment work in Progenesis LC-MS?

In Progenesis LC-MS one run is chosen as the alignment reference and all other runs have their retention times aligned to the reference. This allows us to correct for any drift in retention time. This gives adjusted retention times which are equivalent across all runs. Then we can create a single set of peptide ion outlines which are shared by all runs.

Alignment is driven by the placement of landmarks called "alignment vectors". Each vector connects the location of a particular peptide ion on the reference run with the location of the same ion on the run being aligned. Alignment can be performed automatically , or vectors can be placed manually. Once the vectors are placed they are used to calculate a non-linear mapping between the retention times of the reference run and those of the run being aligned.