R: Centroid a spectrum acquired in profile mode

centroid {protViz} | R Documentation

## Centroid a spectrum acquired in profile mode

### Description

returns a centroid spectrum of a recorded profile mode spectrum.

### Usage

    centroid(mZ, intensity, tolppm=100, debug=FALSE)

### Arguments

`mZ` | Numerical vector of profile recorded data and sorted mZ values.
`intensity` | corresponding intensity values.
`tolppm` | maximal distance in Da between to profile mZ values. default is set to 100ppm.
`debug` | if true all peak profiles are plotted. default is false.

### Details

the method is tested on an Orbitrap Fusion Lumos FSN20242 data set.

### Value

returns a `data.frame` with a mZ and a intensity column.

### Note

thanks to Nienke Meekel and Andrea Brunner (kwrwater.nl) and Witold E. Wolski.

### Author(s)

Christian Panse and Jonas Grossmann, April 2020

### See Also

- MSnbase functions-Spectrum.R

- http://proteowizard.sourceforge.net/tools.shtml

- https://planetorbitrap.com/rawfilereader

### Examples

       # Orbitrap Fusion Lumos FSN20242
       # p2722/.../.../stds_pos_neg_MS_highconc_UVPD_50_300.raw
       # scan 1959
       # CC(C)(C)C(O)C(OC1=CC=C(Cl)C=C1)N1C=NC=N1	1
       # exact.mass 295.1088
       # FTMS + p ESI d Full ms2 296.1162@uvpd50.00

        p <- protViz:::.getProfileMS2()

        # determine eps
        plot((diff(p$mZ)) ~ p$mZ[2:length(p$mZ)], log='y');
        abline(h=0.1, col='red')
        points(p$mZ , 1E-4 * p$mZ, col='grey', type='l')
        abline(v=296.1162, col='cyan')

        op <- par(mfrow=c(2, 1))
        plot(p$mZ, p$intensity, type='h',
          main='profile', xlim=c(100,300))
        abline(v=296.1162, col='cyan')

        plot(centroid(p$mZ, p$intensity),type='h',
          main="centroid",xlim=c(100,300))
        par(op)

        op <- par(mfrow=c(2, 1), ask = TRUE)
            rv <- centroid(p$mZ, p$intensity, debug = TRUE)

[Package protViz version 0.6.8 Index]