centroid: Centroid a spectrum acquired in profile mode
In protViz: Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

centroid

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

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)

protViz documentation built on Feb. 16, 2023, 9:45 p.m.