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

Description Usage Arguments Value Examples

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

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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

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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.