See Retention Time Alignment principles if needed.
Required condition to run the Retention Time Alignment algorithm:
If above condition is respected, then follow these steps:
Algorithms→Retention Time→Retention Time Alignment
MS Identifications→Context→Algorithms→Retention Time→Retention Time Alignment
On top of the dialog, are displayed the following information:
Retention time panel
Duration (min): analysis time in minutes
Delay (min): delay in minutes
Don't take into account outliers: check this box if you want the algorithm to skip species with predicted retention time far from the others.
Deviation threshold (%): if the above checkbox is selected, enter a thresh expressed in percentage. 100% represents the average absolute deviation (between RT & predicted RT). For example, a value of 200% means that species with predicted RT far about 200% from the average deviation are excluded from the calculation.
Grouping method panel
Average: average the RT values to compute the representative RT value of a species group
Median: use median to compute the representative RT value of a species group
Cross-product: use cross-product to compute the representative RT values of a species group
Combined: use median & cross-product to compute the representative RT value of a species group
Best score: use average to compute the representative RT value of a species group
Use memory tuning: if NOT selected, the process will be faster but memory consuming. If selected, the process will be a little bit slower but memory efficient.
When alignment process is finished, the following dialog message appears:
Each aligned identification has two new properties):
slope: slope of the linear regression
intercept: intercept of the linear regression
reference: reference user context
You can access your identification properties either from identifications under your user context, or the under the appropriate search contexts. If you look at the identification properties just after running the Retention Time Alignment algorithm, it may not refresh immediatly.
To apply alignment coefficients on species, you need to Recompute Retention Time.
During alignment process, retention time are predicted using an external utility and stored in peptide properties (peptides belonging to the reference context). These values are NOT the final recomputed retention times, they are only used by the retention time alignment algorithm.