pIR

An R package to analyze the isoelectric point of peptides and proteins based on experimental values and predicted using different functions. The package provides a statistical framework to analyze the correlation between predicted and expected values, and it can be used in other contexts.

Installation

First, we need to install devtools:

install.packages("devtools")
library(devtools)

Then we just call:

install_github("bigbio/pIR")
library(pIR)

Examples

# Other different pKSets that can be selected: rodwell, emboss, lehninger, grimsley, patrickios, DtaSelect

library(pIR)
seq <- "GLPRKILCAIAKKKGKCKGPLKLVCKC"
pI <- pIIterative(sequence = seq, pkSetMethod = "solomon")
print(pI)

# The result will be 10.526


# Computing all pI values using Iterative method.

sequence <- "AADCEVEQWDSDEPIPAK"
pIvalues <- computeAllIterativeValues(seq = sequence)

# The result will be...

pIvalues
#            method values
# 1         solomon 3.4161
# 2         rodwell 3.3749
# 3          emboss 3.5322
# 4       lehninger 3.3711
# 5        grimsley 3.3012
# 6      patrickios 3.4220
# 7       DtaSelect 3.7848
# 8        toseland 3.3571
# 9       thurlkill 3.4784
# 10 nozaki_tanford 3.6445

How to cite

Audain, E., Ramos, Y., Hermjakob, H., Flower, D. R., & Perez-Riverol, Y. (2015). Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences. Bioinformatics, btv674. article

Perez-Riverol, Y., Audain, E., Millan, A., Ramos, Y., Sanchez, A., Vizcaíno, J. A., ... & González, L. J. (2012). Isoelectric point optimization using peptide descriptors and support vector machines. Journal of proteomics, 75(7), 2269-2274. article

This library has been used in

• Ramos, Y., Gutierrez, E., Machado, Y., Sánchez, A., Castellanos-Serra, L., González, L.J., Fernández-de-Cossio, J., Pérez-Riverol, Y., Betancourt, L., Gil, J. and Padrón, G., 2008. Proteomics based on peptide fractionation by SDS-free PAGE. Journal of proteome research, 7(6), pp.2427-2434. article

• Ramos, Y., Garcia, Y., Pérez‐Riverol, Y., Leyva, A., Padrón, G., Sánchez, A., Castellanos‐Serra, L., González, L.J. and Besada, V., 2011. Peptide fractionation by acid pH SDS‐free electrophoresis. Electrophoresis, 32(11), pp.1323-1326. article