R: Sequence Specific Retention Calculator

ssrc {protViz} | R Documentation

## 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).

### Author(s)

Christian Panse, Christian Trachsel 2015

### 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

      # example of table iv [PMID:15238601]
      lapply(c("SCHTAVGR", "SCHTGLGR", "EDLIAYLK"), ssrc)

      plot(sapply(as.character(iRTpeptides$peptide), ssrc) ~  iRTpeptides$rt)

[Package protViz version 0.6.8 Index]