fragmentIons: Compute the b and y Fragment Ions of a Peptide Sequence

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

Compute the b and y Fragment Ions of a Peptide Sequence

Description

The function computes the fragment ions of a peptide sequence, according to the rules of fragmentation in a collision cell. It can be either CID fragmentation (collision-induced dissociation) or ETD (electron transfer dissociation) which are common in proteomics experiments. All are in a positive mode.

If multiple peptide sequences are given it returns a list of fragment ion table.

Usage

    fragmentIon(sequence, FUN, modified, modification, N_term, C_term)

Arguments

sequence	peptide sequence encoded as character sequence using the 20 amino acid letters or a double vector of amino acid weights.
FUN	the function to be applied to compute further ions. If no function is assigned fragmentIon will use defaultIon.
modified	a vector of interger containing the varmod id of the peptide position.
modification	a double vector of defining the varmod mass in Dalton.
N_term	N-Term mass in Dalton. Default is set to 1.007825.
C_term	C-Term mass in Dalton. Default is set to 17.002740.

Details

The fragment ions of a peptide can be computed following the rules proposed in PMID:6525415. Beside the b and y ions the FUN argument of fragmentIon defines which ions are computed. the default ions beeing computed are defined in the function defaultIon. The are no limits for defining other forms of fragment ions for ETD (c and z ions) CID (b and y ions).

NOTE: for simplicity, we have set a Carbamidomethyl (C) fixed modification with 160.030649 (Cysteine mono mass is 103.00919). The fixed modifications setting are not enabled in the package yet.

If only a vector of amino acids weights is given fragmentIon computes the ions series according to weights. If this case applies, the function returns only a list having one data frame.

Author(s)

Christian Panse, Bertran Gerrits 2006.

References

\Sexpr[results=rd]{tools:::Rd_expr_doi("10.1002/bms.1200111109")}

Protein Sequencing and Identification Using Tandem Mass Spectrometry, Michael Kinter and Nicholas E. Sherman, Wiley-Interscience; 1st edition (September 18, 2000)

See Also

first used in peakplot.

Examples

# Example 1
peptide.AA<-"KINHSFLR";

peptide.AA.weights <- c(128.09496,113.08406,114.04293,
    137.05891,87.03203,147.06841,113.08406,156.10111);

fragmentIon(peptide.AA);

fragmentIon(peptide.AA.weights);

HCD_Ion <- function(b, y){
    return(cbind(b = b, y = y))
}


ETD_Ion <- function(b, y){
    Hydrogen <- 1.007825
    Oxygen <- 15.994915
    Nitrogen <- 14.003074

    y_0 <- y - Oxygen - Hydrogen - Hydrogen
    c <- b + (Nitrogen + (3 * Hydrogen))
    z <- y - (Nitrogen + (3 * Hydrogen))

    return(cbind(y_0, c, z))
}

fragmentIon(peptide.AA, FUN = ETD_Ion)
        
peptides<-c('HTLNQIDSVK', 'ALGGEDVR', 'TPIVGQPSIPGGPVR')

pim <- parentIonMass(peptides)
fi <- fragmentIon(peptides)
(df <- as.data.frame(fi))

op <- par(mfrow=c(3,1)); 
for (i in 1:length(peptides)){
    plot(0, 0,
    xlab='m/Z',
    ylab='',
    xlim=range(c(fi[[i]]$b,fi[[i]]$y)),
    ylim=c(0,1),
    type='n',
    axes=FALSE,
    sub=paste(peptides[i], "/", pim[i], "Da"));
    box()
    axis(1, fi[[i]]$b, round(fi[[i]]$b,1), las=2)
    axis(1, fi[[i]]$y, round(fi[[i]]$y,1), las=2)

    pepSeq<-strsplit(peptides[i], "")
    axis(3,fi[[i]]$b, paste("b", row.names(fi[[i]]),sep=''),las=2)
    axis(3,fi[[i]]$y, paste("y", row.names(fi[[i]]),sep=''),las=2)

    text(fi[[i]]$b, rep(0.3, nchar(peptides[i])), 
    pepSeq[[1]],pos=3,cex=4, lwd=4, col="#aaaaaaaa")

    abline(v=fi[[i]]$b, col='red') 
    abline(v=fi[[i]]$y, col='blue',lwd=2)
}
par(op)


fi <- fragmentIon(c("ATSFYK","XGXFNAGVGK"))[[2]]
fi$b[1] + fi$y[9]
fi$b[2] + fi$y[8]


ION2C <- function(b, y){
    Hydrogen <- 1.007825
    Oxygen <- 15.994915
    Nitrogen <- 14.003074

    # yo <- fi$y - Oxygen - Hydrogen - Hydrogen
    c <- b + (Nitrogen + (3 * Hydrogen))
    z <- y - (Nitrogen + (3 * Hydrogen))
    
    # compute doubly charged fragment ions
    b2 <- (b + Hydrogen) / 2
    y2 <- (y + Hydrogen) / 2

    return(cbind(b, y, b2 ,y2))
}

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