protViz (version 0.6.8)

ssrc: Sequence Specific Retention Calculator

Description

This function returns as output one hydrophobicity value for a given sequence of amino acids (tryptic peptide) which can be used to predict the retention times. The calculation is based on the method described in PMID:15238601.

Usage

ssrc(x, H=list())

Arguments

x

sequence of amino acids, e.g., x="ELIVSK"

H

A list of retention coefficients. The default is set to the values of PMID:15238601 table II column 2(Rc values).

References

Krokhin, O. V. et al. An improved model for prediction of retention times of tryptic peptides in ion pair reversed-phase HPLC: its application to protein peptide mapping by off-line HPLC-MALDI MS. Mol. Cell Proteomics 3, 908-919 (2004). http://www.ncbi.nlm.nih.gov/pubmed/15238601

See Also

• http://hs2.proteome.ca/SSRCalc/SSRCalcX.html

• iRTpeptides

Examples

# NOT RUN {
  # example of table iv [PMID:15238601]
  lapply(c("SCHTAVGR", "SCHTGLGR", "EDLIAYLK"), ssrc)
  
  plot(sapply(as.character(iRTpeptides$peptide), ssrc) ~  iRTpeptides$rt)
# }