genSwathIonLib: Spectrum library generator for SWATH analysis
In specL: specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics

Description Usage Arguments Details Value Author(s) See Also Examples

This function generates an ion library for SWATH analysis. It takes a R data object which contains a peak list. The R data object can be generated using the read.bibliospec function.

    genSwathIonLib(data, 
        data.fit = data,
        mascotIonScoreCutOFF=20,
        proteinIDPattern='',
        max.mZ.Da.error = 0.1,
        ignoreMascotIonScore = TRUE,
        topN = 10,
        fragmentIonMzRange = c(300, 1800),
        fragmentIonRange = c(4, 100),
        fragmentIonFUN = .defaultSwathFragmentIon,
        iRT = specL::iRTpeptides,
        AminoAcids = protViz::AA,
        breaks=NULL,
        NORMALIZE=.normalize_rt)

`data`	data set containing mZ and peptide sequence.
`mascotIonScoreCutOFF`	a value for filtering the specs.
`proteinIDPattern`	a filter for protein.
`max.mZ.Da.error`	the mZ error in Dalton on ms2 level.
`ignoreMascotIonScore`	Boolean if mascot score is considered or not.
`topN`	returns the most `N` intense fragment ion only.
`fragmentIonMzRange`	mZ range filter of fragment ion.
`fragmentIonRange`	range filter of the number of identified fragment ion which are assigned in the spectrum library set in `fragmentIonTyp`. Use this option to generate a library with a minimum of five transitions for all peptides using `c(5,100)`, all peptides where at least not five transmissions found were omitted.
`fragmentIonFUN`	`function (b, y)` which derives all requested fragment ion out a given tuple of `b` and `y` ion. If the parameter is not specified the method uses an internal function similar as the example below.
`iRT`	optional table which contains iRT peptides. If an iRT table is provided (default) a `lm` is applied to normalize the rt in `data`. See also `?iRT`. A necessary condition is that `data` contains at least two iRT peptides.
`AminoAcids`	a list containing of 1-letter code and mono-isotopic mass of the amino acids. Default uses the `protViz::AA` data set.
`data.fit`	data set containing mZ and peptide sequence which is used for normalizing rt using a linear model `lm(formula = rt ~ aggregateInputRT * fileName, data)`. The rt aggregation for the model uses `median`.
`breaks`	provides a vector of SWATH windows. If q1 (precursor mass) and q3 (fragment ion) fall into the same SWATH window the fragment ion is ignored in the resulting ion library. The follwing code shows an example `breaks=seq(400, 2000, by=25)`.
`NORMALIZE`	is a `function(data, data.fit, iRT, plot=FALSE)` normalizing the rt. The default is a internal R helper function using `lm`.

The function is the main contribution of the specL package. It generates the spectra library used in a SWATH analysis workflow out of a mass spectrometric measurement.

genSwathIonLib uses the core functions protViz::findNN, protViz::fragmentIon, and protViz::aa2mass.

The input is read by using read.bibliospec function of this package and passed by the data function parameter. If no BiblioSpec files are available also Mascot DAT files can be read using scripts contained in the protViz package exec folder.

If the protein information is lost you can benefit for the specL::annotate.protein_id.Rd method.

The function first appear in the protViz 0.1.45 package. It has been removed in protViz 0.2.6 to avoid package dependencies.

The output is a data structure defined as specLSet object. The generic method ionlibrary returns a list of specL objects, specLSet also stores the input and normalized retention times.

Christian Panse, Christian Trachsel, and Jonas Grossmann 2012, 2013, 2014, 2016

The S4 class definition: showClass("specL") showClass("specLSet")

and the package vignette file. vignette('specL')

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

        b1_ <- (b )
        y1_ <- (y ) 

        b2_ <- (b + Hydrogen) / 2
        y2_ <- (y + Hydrogen) / 2 

        b3_ <- (b + 2 * Hydrogen) / 3
        y3_ <- (y + 2 * Hydrogen) / 3

        return( cbind(b1_, y1_, b2_, y2_, b3_, y3_) )
    }

    peptideStd.ionLib <- genSwathIonLib(data=peptideStd, 
        data.fit=peptideStd.redundant, 
        fragmentIonFUN=myFragmentIon)
        
        
    summary(peptideStd.ionLib)


    idx<-40

    op <- par(mfrow = c(2,1))

    plot(peptideStd.ionLib)

    text(rt.input(peptideStd.ionLib)[idx],
        rt.normalized(peptideStd.ionLib)[idx],
        "X", cex=1.5)

    plot(ionlibrary(peptideStd.ionLib)[[idx]])


    ## Not run: 
        write.spectronaut(peptideStd.ionLib, 
            file="peptideStd.ionLib.csv")
   
## End(Not run)