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Retention Time Alignment
Here are the major steps followed by the Retention Time algorithm:
Collect species from the reference User context and predict their retention time using an external utility
For each identification gathered under the reference User context do:
Collect species to align from the identification
Constitute several pair groups between collected reference species & species to align. A pair group contains 2 groups of species having same sequence & calculated mass (group1 has species from reference User context and group2 has species to align from identifications).
Compute one (or several) representative value(s) for group1 & group2 for each pair group
Compute linear regression between representative values
Store linear regression coefficients
In more details…
Species Retention Time of the reference UserContext are predicted with
NETPrediction v2.2.3378 utility using Kangas method (click
here for more details). NETPrediction utility only uses species
sequences to predict a Normalized Elution Time (NET) value. First, a list of '
reference' species is built with the below criteria, then the corresponding sequences are exported in order to be used by the NETPrediction utility:
The reference species list doesn't contain any species with PTMs
If several species exist with redundant sequences, the best score species is retained
All the final child species, i.e. species in identifications, are collected.