calculateOldIsotopePool: Estimates the fraction of old isotope for each time point

In marcpaga/pulsedSilac: Analysis of pulsed-SILAC quantitative proteomics data

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')

marcpaga/pulsedSilac documentation built on March 11, 2020, 8:49 p.m.