R: Compute Parent Ion Mass of a Peptide Sequence

parentIonMass {protViz} | R Documentation

## Compute Parent Ion Mass of a Peptide Sequence

### Description

It computes the parent ion mass of a vector of peptide sequences. The weights of the amino acids and the C-Term are hard coded in the C function. Important: The precursor mass is calculated with an additional proton, so to speak the singly charged precursor!

### Usage

        parentIonMass(sequence, fixmod, NTerm)

### Arguments

`sequence` | peptide sequence encoded as character sequence using the 20 amino acid letters.
`fixmod` | a double vector of length 26 defining the amino acid mass.
`NTerm` | a double value defining the weight of the NTerm.

### Details

The `parentIonMass` function reqires one argument `secuence`.

### Author(s)

Christian Panse 2006

### Examples

            fetuin<-list( sequence=c('MK', 'SFVLLFCLAQLWGCHSIPLDPVAGYK',
            'EPACDDPDTEQAALAAVDYINK',
            'HLPR', 'GYK', 'HTLNQIDSVK', 'VWPR',
            'RPTGEVYDIEIDTLETTCHVLDPTPLANCSVR',
            'QQTQHAVEGDCDIHVLK', 'QDGQFSVLFTK',
            'CDSSPDSAEDVR', 'K', 'LCPDCPLLAPLNDSR',
            'VVHAVEVALATFNAESNGSYLQLVEISR',
            'AQFVPLPVSVSVEFAVAATDCIAK',
            'EVVDPTK', 'CNLLAEK', 'QYGFCK',
            'GSVIQK', 'ALGGEDVR',
            'VTCTLFQTQPVIPQPQPDGAEAEAPSAVPDAAGPTPSAAGPPVASVVVGPSVVAVPLPLHR',
            'AHYDLR', 'HTFSGVASVESSSGEAFHVGK',
            'TPIVGQPSIPGGPVR', 'LCPGR', 'IR', 'YFK', 'I'),
            description=
                "FETUA_BOVIN Alpha-2-HS-glycoprotein ")

            plot(peptideMass<-parentIonMass(sequence=fetuin$sequence),
                sub=list(fetuin$description, cex=0.75),
                main="tryptic digested peptides")

            AA<-c(71.037114, 114.534940, 160.030649, 115.026943, 129.042593, 147.068414,
                57.021464, 137.058912, 113.084064, 0.000000, 128.094963, 113.084064,
                131.040485, 114.042927, 0.000000, 97.052764, 128.058578, 156.101111,
                87.032028, 101.047679, 150.953630, 99.068414, 186.079313, 111.000000,
                163.063329, 128.550590)

            parentIonMass(c("ELVIS", "ELVISK"), fixmod=AA)

[Package protViz version 0.2.45 Index]