centroid: Centroid a spectrum acquired in profile mode

In protViz: Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

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

• 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)

protViz documentation built on May 29, 2024, 8:21 a.m.