addMisscleavedPeptides: Add miss-cleaved peptide expression levels for old isotope...

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 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 can be used to estimate amino acid recycling. To add this information a data.frame with the following information is required:

• A column with ids that can be mapped to the peptide rowData (not necessary for SilacProteinExperiment objects).

• A column indicating which isotope configuration the peptide has: two heavy isotopes, mix of light and heavy isotope, etc.

• A set of columns with peptide expression quantification. The number of columns should be the same, and in the same order, as the number of samples in the SilacProteinExperiment, SilacPeptideExperiment or SilacProteomicsExperiment.

Non-detected measurements should be NA.

Usage

addMisscleavedPeptides(x, ...)

## S4 method for signature 'SilacProteinExperiment'
addMisscleavedPeptides(x, newdata, modCol, dataCols, idColPept)

## S4 method for signature 'SilacPeptideExperiment'
addMisscleavedPeptides(x, newdata, modCol, dataCols, idColPept)

## S4 method for signature 'SilacProteomicsExperiment'
addMisscleavedPeptides(x, newdata, modCol, dataCols, idColPept)

Arguments

x	A SilacProteinExperiment, SilacPeptideExperiment or SilacProteomicsExperiment.
...	Unused.
newdata	a data.frame containing the data described in the description.
modCol	character or numeric indicating which column of newdata contains the peptide's isotope configuration.
dataCols	character or numeric vector indicating which columns of newdata contain the quantitative data. It should have the same length as the number of samples in x (ncol(x)). Samples should be in the same order.
idColPept	character indicating which column contains the ids that will be used in the merge with rowDataPept(x). The column in newdata should have the same name as in rowDataPept(x).

Value

A SilacPeptideExperiment or SilacProteomicsExperiment with new assay entries. If x is a SilacProteinExperiment then a SilacPeptideExperiment is returned.

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.