ssrc: Sequence Specific Retention Calculator

In protViz: Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

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). \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1074/mcp.M400031-MCP200")}

See Also

• iRTpeptides

Examples

  # example of table iv [PMID:15238601]
  lapply(c("SCHTAVGR", "SCHTGLGR", "EDLIAYLK"), ssrc)
  
  plot(sapply(as.character(iRTpeptides$peptide), ssrc) ~  iRTpeptides$rt)

protViz documentation built on May 29, 2024, 8:21 a.m.