Basis Species Comparison

This vignette from the R package canprot shows projections of protein composition made using two sets of basis species. Using the CHNOS basis species (CO₂, NH₃, H₂S, H₂O, O₂), the plots show that n̅_H2O and n̅_O2, i.e. the number of H₂O and O₂ in the formation per residue of the proteins from basis species, are both moderately correlated with Z_C (average oxidation state of carbon). Using the QEC basis species (glutamine, glutamic acid, cysteine, H₂O, O₂), we find that n̅_O2 is strongly correlated with Z_C, but n̅_H2O shows very little correlation. Accordingly, the QEC basis more clearly exposes two compositional variables – oxidation state and hydration state – in proteomic data.

First, load the canprot and CHNOSZ packages.

library(canprot)
library(CHNOSZ)

Here we define some labels used in the plot.

nH2Olab <- expression(bar(italic(n))[H[2] * O])
nO2lab <- expression(bar(italic(n))[O[2]])
ZClab <- expression(italic(Z)[C])
QEClab <- CHNOSZ::syslab(c("glutamine", "glutamic acid", "cysteine", "H2O", "O2"))
CHNOSlab <- CHNOSZ::syslab(c("CO2", "NH3", "H2S", "H2O", "O2"))

Next, get the amino acid compositions of all proteins in the UniProt human proteome and calculate the protein formulas and Z_C. Note that Z_C is a sum of elemental ratios and is independent of the choice of basis species.

aa <- get("human_base", canprot)
protein.formula <- CHNOSZ::protein.formula(aa)
ZC <- CHNOSZ::ZC(protein.formula)

Now set up the figure and plot the per-residue compositions of the proteins projected into different sets of basis species.

par(mfrow = c(2, 2))
par(mar = c(4, 4, 2.5, 1))
par(cex = 1.1)
par(mgp = c(2.5, 1, 0))
for(basis in c("QEC", "CHNOS")) {
  CHNOSZ::basis(basis)
  protein.basis <- CHNOSZ::protein.basis(aa)
  protein.length <- CHNOSZ::protein.length(aa)
  residue.basis <- protein.basis / protein.length
  smoothScatter(ZC, residue.basis[, "O2"], xlab = ZClab, ylab = nO2lab)
  smoothScatter(ZC, residue.basis[, "H2O"], xlab = ZClab, ylab = nH2Olab)
  if(basis=="QEC") mtext(QEClab, outer = TRUE, cex = 1.2, line = -1.5)
  if(basis=="CHNOS") mtext(CHNOSlab, outer = TRUE, cex = 1.2, line = -15)
}

This figure has been published as Figure S1 of Dick, 2017 (Chemical composition and the potential for proteomic transformation in cancer, hypoxia, and hyperosmotic stress. PeerJ 5:e3421).