R: PTM MarkerFinder

PTM_MarkerFinder {protViz} | R Documentation

## PTM MarkerFinder

### Description

`PTM_MarkerFinder` is a fucntion to identify and validate spectra from peptides carrying post-translational modifications.

### Usage

    PTM_MarkerFinder(data,
        modification,
        modificationName,
        mZmarkerIons,
        minNumberIons=2,
        itol_ppm=10,
        minMarkerIntensityRatio=5,
        mgfFilename=-1,
        PEAKPLOT=TRUE
        )

    findMz(data, mZmarkerIons, itol_ppm = 10, minNumberIons = 2, minMarkerIntensityRatio = 10)

    ## S3 method for class 'psmSet'
    findMz(data, mZmarkerIons, itol_ppm, minNumberIons, minMarkerIntensityRatio)

    ## S3 method for class 'mascot'
    findMz(data, mZmarkerIons, itol_ppm = 10, minNumberIons = 2, minMarkerIntensityRatio = 10)

### Arguments

`data` | A list of spectra where each list element contains a list of `mZ, intensity` vectors. This object can be received by using the `mascotDat2RData.pl` perl script.
`modification` | A double vector containing the mono mass PTMs.
`modificationName` | A character vector containing the Name of the PTMs. This is the string which will show up in the peptide sequence in square brackets.
`mZmarkerIons` | The m/z patterns which should be searched.
`minNumberIons` | Minimal number of marker ions to be found for further analysis.
`itol_ppm` | The ion tolerance of the marker ions in ppm. default is set to 10ppm.
`minMarkerIntensityRatio` | The marker ions intencity percentage compared to the sum of all peak intensities.
`mgfFilename` | if a mgf(mascot generic file) filename is given, the function writes an mgf file containing only the ms2 having the `mZmarkerIons`.
`PEAKPLOT` | If this boolean is `FALSE` the `peakplot` function is not used.
`...` | passed

### Details

The function screens MS2 spectra for the presence of fragment ions specific Post Translational Modifications (PTMs). The function requires an R-object containing the mass spectrometric measurement, the peptide assignments, potential modification information, and a list of marker ions. The R-object can be retrieved right out of the Mascot Server search result dat files using a perl script `mascotDat2RData.pl` which is included in the package's `exec/` directory.

The functions iterates over each spectrum of the mass spectrometric measurement and searches for the as input provided marker ions. If a certain number of marker ions (default is, that two marker ions are required) are found and the maker ion intensity ratio is higher than a given threshold, the tandem mass spectrum is considered as HCD scan type and the corresponding ion series are drawn using the protViz:peakplot methode. Furthermore the function is searching for the corresponding ETD scan having the same peptide mass by screening the succeeding scans for ETD spectra. If such a spectrum is found the peptide spectrum assignment containing the c, z, and y ions is drawn. Note that the PTM MarkerFinder expects the ETD scan right after the HCD scan. If the MS protocol changes the PTM MarkerFinder methode has to be adapted.

For each HCD scan PTM MarkerFinder plots both HCD and ETD scans, a ppm error versus maker ion m/z scatter plot, a intensity versus marker ion m/z plot, and two pie charts where the relative and absolute maker ion intensity are shown.

As a summery report the function returns a table containing the following column attributes: "scans", "mZ", "markerIonMZ", "markerIonIntensity", "markerIonMzError", "markerIonPpmError", and "query" which can be used for statistics.

Furthermore, if `mgfFilename` is defined, a Mascot Generic File (MGF) is created containig the HCD scans (having the marker ions) and the corresponding ETD scans.

### Author(s)

Paolo Nanni, Peter Gehrig, Christian Panse 2011-2013;

### References

- Nanni P, Panse C, Gehrig P, Mueller S, Grossmann J, Schlapbach R.(2013), PTM MarkerFinder, a software tool to detect and validate spectra from peptides carrying post-translational modifications. Proteomics. 2013 Aug;13(15):2251-5. http://dx.doi.org/10.1002/pmic.201300036.

- `ADP_Ribose <- c(136.0618, 250.0935, 348.0704, 428.0367)` marker ions have been used in: Bilan V, Leutert M, Nanni P, Panse C, Hottiger MO. Combining Higher-Energy Collision Dissociation and Electron-Transfer/Higher-Energy Collision Dissociation Fragmentation in a Product-Dependent Manner Confidently Assigns Proteomewide ADP-Ribose Acceptor Sites, Anal. Chem., 2017, 89 (3), pp 1523-1530 https://doi.org/10.1021/acs.analchem.6b03365.

### See Also

`peakplot`

### Examples

        # some marker ions

        Glykan_MarkerIons <- c(109.02841, 127.03897, 145.04954, 163.06010, 325.11292)

        HexNAc_MarkerIons <- c(126.05495, 138.05495, 144.06552, 168.06552, 186.07608, 204.08665)

        # DOI: 10.1021/acs.analchem.6b03365
        # Anal Chem 2017 Feb 13;89(3):1523-1530. Epub 2017 Jan 13.
        ADP_Ribose <- c(136.0618, 250.0935, 348.0704, 428.0367)

        data(HexNAc)

        # prepare modification
        ptm.0 <- cbind(AA="-",
            mono=0.0, avg=0.0, desc="unmodified", unimodAccID=NA)

        ptm.1 <- cbind(AA='N',
              mono=317.122300, avg=NA, desc="HexNAc",
                      unimodAccID=2)

        ptm.2 <- cbind(AA='M',
                mono=147.035400, avg=NA, desc="Oxidation",
                        unimodAccID=1)

        m <- as.data.frame(rbind(ptm.0, ptm.1, ptm.2))

        s <- PTM_MarkerFinder(data=HexNAc, modification=m$mono,
            modificationName=m$desc,
            minMarkerIntensityRatio=3,
            itol_ppm=20,
            mZmarkerIons=HexNAc_MarkerIons)

        boxplot(s$markerIonIntensity ~ s$markerIonMZ,
            log='y',
            main='Summary plot: boxplot of marker ion intensities from all pPTM spectra',
            xlab='markerIon m/z',
            ylab='log10 based marker ion intensity')

        # export
        w <- reshape(s[,c(1,7,3,4)], direction='wide',
            timevar="markerIonMZ", idvar=c('scans','query'))

        write.table(w, file="HexNAc_PTM_markerFinder.csv",
            sep=',', row.names=FALSE,col.names=TRUE, quote=FALSE)

[Package protViz version 0.2.45 Index]