protViz (version 0.7.9)

parentIonMass: 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.

Author

Christian Panse 2006

Details

The parentIonMass function reqires one argument secuence.

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)