Glossary
Retention time alignment
Alignment is what lets many separate injections be compared as one study. Without it, a feature at a given time in one sample is not necessarily the same molecule in the next.
Definition
Retention time alignment is the process of correcting for shifts in when a compound elutes so the same feature can be matched across samples. Elution times move between injections because of column aging, temperature, mobile phase, and pressure. Alignment estimates and removes these shifts, either by warping each sample toward a reference or by modeling movement across the whole cohort, so that a feature detected in different runs is recognized as one entity. It is a prerequisite for building a feature table where every column refers to the same analyte in every sample.
Worked example
In practice
If a compound drifts from ninety to ninety four seconds over a long study, alignment ensures it is treated as one feature rather than two, so its intensities are compared correctly across samples.
What matters
Where this makes a difference
Why comparison needs it
A feature table assumes each column is one analyte across all samples. Elution drift breaks that assumption, so alignment is what makes cross sample comparison valid at all.
Reference warping versus cohort models
Warping to a single reference works when drift is small and anchors are abundant. Large heterogeneous cohorts do better with a model that uses all injections as mutual references.
Alignment and missing values
Many apparent missing values are alignment failures rather than true absence. Correct alignment recovers them, which changes the shape of the table and the statistics that follow.
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