R package: proteinRuler

Guillaume Voisinne 2022 - 09 - 27

R Package : proteinRuler

Compute protein abundance from protein intensities using the ‘protein ruler’ methodology (See article by Wisniewski et. al).

Install

Install the package from github using devtools:

devtools::install_github("VoisinneG/proteinRuler")
library(proteinRuler)

Examples

Import a dataset containing protein intensities and protein IDs and compute protein abundances :

data("proteinGroups_CD4_Tcells")
res <- proteinRuler(proteinGroups_CD4_Tcells, DNA_mass_per_cell = 5.5209e-12, show_progress = FALSE)

## Getting annotations from UniProt...

names(res)

## [1] "copy_number" "summary"     "annotations"

print(res$summary)

##             column median_Intensity sum_Intensity sum_Intensity_histones
## 1   Intensity WT_0        369090000  2.206908e+13           512146984000
## 2 Intensity WT_030        338910000  1.994321e+13           456856460100
## 3 Intensity WT_120        294340000  1.662875e+13           506685089500
## 4 Intensity WT_300        280020000  1.612613e+13           366101939300
## 5 Intensity WT_600        262470000  1.448206e+13           342576488300
##   percentage_mass_histones protein_mass_per_cell_pg
## 1                 2.320654                 237.9028
## 2                 2.290787                 241.0045
## 3                 3.047043                 181.1888
## 4                 2.270241                 243.1856
## 5                 2.365524                 233.3902

Plot copy number distribution :

cond <- "CopyNumber_WT_0"
hist(log10(res$copy_number[[cond]]), main = "", xlab = paste(cond, "(log10)"), col = rgb(1,0,0,0.25))