ssrc {protViz} | R Documentation |
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.
ssrc(x, H=list())
x |
sequence of amino acids, e.g., |
H |
A list of retention coefficients. The default is set to the values of PMID:15238601 table II column 2(Rc values). |
Christian Panse, Christian Trachsel 2015
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
# example of table iv [PMID:15238601] lapply(c("SCHTAVGR", "SCHTGLGR", "EDLIAYLK"), ssrc) plot(sapply(as.character(iRTpeptides$peptide), ssrc) ~ iRTpeptides$rt)