In-Silico Align controls how Byos handles retention time (RT) windows when using an in-silico peptide list. When a user provides an in-silico CSV, a single set of start and end times are defined per peptide. Because retention times can drift between samples, In-Silico Align allows the software to shift those time windows to better capture the target peak in each sample.
In-Silico Align refers to the alignment of chromatograms between samples, not the alignment of the in-silico information itself. It shifts the input RT windows from the CSV to account for chromatographic drift across samples.
Where to Find This Setting
As of Byos/Byosphere 5.11, tis feature is controlled directly within the workflow. Options are available in the Quant (Byologic) workflow node, replacing the need to configure this manually via advanced commands in most cases.
Align In-Silico Peptides
Determines whether the RT windows from the in silico CSV are applied uniformly to all samples, or shifted to track peak drift.
| Setting | Behavior |
|---|---|
| Yes | The algorithm shifts the input RT windows to capture peaks that drift from the times in the CSV |
| No | The RT boundaries from the CSV are applied as-is to all samples |
Tolerance Determination
Controls how the alignment tolerance is calculated.
| Setting | Behavior |
|---|---|
| Automatic | The software determines the appropriate tolerance, using the TimeWarp object to calculate dynamic shifts between samples. Works well in most cases. |
| Manual | The user specifies a fixed tolerance value. Useful when automatic determination is not performing as expected. |
Alignment Tolerance (minutes)
Specifies the maximum amount (in minutes) by which the RT window can shift. Only relevant when Align In Silico Peptides is set to Yes.
- Setting this to 0.0 is equivalent to setting Align In Silico Peptides to No — the CSV boundaries will be applied to all samples without adjustment.