Standard compound normalizer¶
Description¶
Info
The internal standard normalizer is now part of the Intensity normalizer to apply all normalization steps in a sequence.
Applies an internal standard compound correction to each feature individually, accounting for extraction efficiency and matrix effects within a sample. Internal standard features must be present in the detected samples. User can select one or multiple internal standard features, which must be present in all raw data files. Then feature height (and area) of each feature is normalized by either the nearest standard or a weighted contribution of all standards.
In case a weighted contribution is used, the contributions of all standards are weighted by distance. The distance of the standard feature to the feature being normalized is calculated as
where \(MZvsRT_{Balance}\) is a multiplier of m/z difference set by m/z vs RT balance parameter
Feature lists must be aligned prior to normalization.
Parameters¶
Standard compounds¶
List of features to use as internal standards. Each selected feature provides a reference point at its (m/z, RT) position for correction.
Normalization type¶
How the correction factor is derived from the available internal standards:
- Nearest: uses the single IS compound with the shortest distance (in m/z–RT space) to the feature being normalized.
- Weighted: uses a distance-weighted average over all IS compounds; features that are very close to a standard (distance = 0) are averaged directly.
m/z vs RT balance¶
Multiplier applied to the m/z difference when computing the distance between a feature and an internal standard. Increase this value to weight m/z similarity more heavily relative to RT similarity.
Reference samples¶
Sample types whose IS signal is used to build the correction model. Non-reference samples are corrected by interpolating between the nearest reference samples in acquisition order. It is best to add the same internal standards to all samples, but this option allows using internal standards from standard injections like QCs to interpolate changes to other samples.
Require all standards¶
When enabled, normalization fails if any selected IS compound is missing from a raw file. Disable to proceed with available standards when some may be absent in certain samples.