specL (version 1.6.2)

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).

Details

t.b.d.

See Also

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

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

Examples

# example of table iv [PMID:15238601]
  lapply(c("SCHTAVGR", "SCHTGLGR", "EDLIAYLK"), ssrc)
  
  
    Rc <- list()
    Rc[['W']] <- 11.0; 
    Rc[['F']] <- 10.5; 
    Rc[['L']] <- 9.6; 
    Rc[['I']] <- 8.4; 
    Rc[['M']] <- 5.8; 
    Rc[['V']] <- 5.0; 
    Rc[['Y']] <- 4.0; 
    Rc[['A']] <- 0.8; 
    Rc[['T']] <- 0.4; 
    Rc[['P']] <- 0.2; 
    Rc[['E']] <- 0.0; 
    Rc[['D']] <- -0.5; 
    Rc[['C']] <- -0.8; 
    Rc[['S']] <- -0.8; 
    Rc[['Q']] <- -0.9; 
    Rc[['G']] <- -0.9; 
    Rc[['N']] <- -1.2; 
    Rc[['R']] <- -1.3; 
    Rc[['H']] <- -1.3; 
    Rc[['K']] <- -1.9; 

    RcNt <- lapply(Rc, function(x){sum(unlist(Rc))/20 - x})
    
    ssrc <- unlist(lapply(peptideStd, function(x){ssrc(x$peptideSequence)}))
    rt <- unlist(lapply(peptideStd, function(x){x$rt}))

    plot(ssrc, rt) 
    abline(ssrc.lm <- lm(rt ~ ssrc), col='red'); 
    legend("topleft", paste("spearman", round(cor(ssrc, rt, method='spearman'),2)))