parentIonMass: Compute Parent Ion Mass of a Peptide Sequence

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

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)

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