calculateOldIsotopePool {pulsedSilac} | R Documentation

## Estimates the fraction of old isotope for each time point

### Description

To estimate how much of the "old" isotope is being used in "new" proteins we can use the expression level of miss-cleaved peptides that contain a mix of isotopes (one old and one new) and miss-cleaved peptides that contain only new isotopes. This can be done using the following formula:

Which gives an idea of how much recyling (turnover understimation) is happening.

Both peptide types, mix of old/new isotope and two new isotopes, have to be found in a time point to calculate the fraction of old isotope.

### Usage

    calculateOldIsotopePool(x, ...)

    ## S4 method for signature 'SilacPeptideExperiment'
    calculateOldIsotopePool(x, newIsotopeAssayName, mixIsotopeAssayName)

    ## S4 method for signature 'SilacProteomicsExperiment'
    calculateOldIsotopePool(x, newIsotopeAssayName, mixIsotopeAssayName)

### Arguments

`x` | A `SilacPeptideExperiment` or `SilacProteomicsExperiment` object.
`...` | Unused.
`newIsotopeAssayName` | `character` indicating the assay that contains quantification data for miss-cleaved peptides with two new isotopes incorporated.
`mixIsotopeAssayName` | `character` indicating the assay that contains quantification data for miss-cleaved peptides with one old isotope and one new isotope incorporated.

### Value

A `SilacPeptideExperiment` or `SilacProteomicsExperiment` with a peptide assay entry named "oldIsotopePool".

### Examples

    data('wormsPE')
    data('recycleLightLysine')
    protPE <- ProtExp(wormsPE)
    missPE <- addMisscleavedPeptides(x = protPE,
                                     newdata = recycleLightLysine,
                                     idColPept = 'Sequence',
                                     modCol = 'Modifications',
                                     dataCols = c(18:31))

    names(assays(missPE))[1:2] <- c('int_lys8lys8', 'int_lys8lys0')
    missPE <- calculateOldIsotopePool(x = missPE, 'int_lys8lys8', 'int_lys8lys0')

    plotDistributionAssay(missPE, assayName = 'oldIsotopePool')

[Package pulsedSilac version 1.9.1 Index]