protViz (version 0.7.9)

centroid: 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)

Value

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

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.

Author

Christian Panse and Jonas Grossmann, April 2020

Details

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

See Also

• MSnbase functions-Spectrum.R

• https://proteowizard.sourceforge.io/

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)