calculateOldIsotopePool {pulsedSilac} | R Documentation |
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.
calculateOldIsotopePool(x, ...) ## S4 method for signature 'SilacPeptideExperiment' calculateOldIsotopePool(x, newIsotopeAssayName, mixIsotopeAssayName) ## S4 method for signature 'SilacProteomicsExperiment' calculateOldIsotopePool(x, newIsotopeAssayName, mixIsotopeAssayName)
x |
A |
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Unused. |
newIsotopeAssayName |
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mixIsotopeAssayName |
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A SilacPeptideExperiment
or SilacProteomicsExperiment
with a peptide assay entry named "oldIsotopePool".
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')