rescaleForTop3,MSnSet,MSnSet-method {synapter} | R Documentation

## Rescale for TOP3

### Description

This method rescales the intensity values of an `MSnSet` object to be suiteable for TOP3 quantification.

### Usage

    ## S4 method for signature 'MSnSet,MSnSet'
    rescaleForTop3(before, after, saturationThreshold,
    onlyForSaturatedRuns=TRUE, ...)

### Arguments

`before` | An `MSnSet` object before requantification.
`after` | The same `MSnSet` object as `before` but after requantification.
`saturationThreshold` | `double`, intensity of an ion (isotope of a given charge state) at which saturation is starting to occur.
`onlyForSaturatedRuns` | `logical`, rescale just runs where at least one isotope is affected by saturation.
`...` | further arguments passed to internal functions. Currently ignored.

### Details

If an `MSnSet` object was requantified using the `method="sum"` requantification method (see `requantify,MSnSet-method`) TOP3 is not valid anymore because the most abundant proteins are penalised by removing high intensity isotopes.

To overcome this `rescaleForTop3` takes the proportion `isotope/sum(isotopes` for each requantified peptide and calculates a correction factor by comparing these proportions against the unsaturated isotopes before requantification. The new rescale intensity values of the isotopes are the mean correction factor multiplied with the corrected intensity values (see https://github.com/lgatto/synapter/issues/39#issuecomment-207987278 for the complete explanation/discussion).

### Value

`MSnSet` where the `assayData` are requantified.

### Author(s)

Sebastian Gibb mail@sebastiangibb.de and Pavel Shliaha

### References

See discussion on github: https://github.com/lgatto/synapter/issues/39

### See Also

MSnSet documentation: `MSnSet` https://github.com/lgatto/synapter/issues/39#issuecomment-207987278

[Package synapter version 2.4.1 Index]