This function normalizes raw spectra by converting from raw intensities, to 0-100% relative intensity based on the most intense ion. This function also remove low intensity signals based on minimum cutoff. The default cutoff is 1% and the spectra is normalized.
Arguments
- spec
a data frame produced by
import_mzxml()function.- min_int
an integer, minimum intensity. If spectra is normalized, this values should be in a 0-100 range. If the spectra is not not normalized, this value must be ion count.
Examples
# Importing the Spectrum of Procyanidin A2 in negative ionization mode
# and 20 eV as the collision energy
ProcA2_file <- system.file("extdata",
"ProcyanidinA2_neg_20eV.mzXML",
package = "MS2extract"
)
# Region of interest table (rt in seconds)
ProcA2_data <- data.frame(
Formula = "C30H24O12", Ionization_mode = "Negative",
min_rt = 163, max_rt = 180
)
ProcA2_raw <- import_mzxml(ProcA2_file, ProcA2_data)
#> • Processing: ProcyanidinA2_neg_20eV.mzXML
#> • Found 1 CE value: 20
#> • Remember to match CE velues in spec_metadata when exporting your library
#> • m/z range given 10 ppm: 575.11376 and 575.12526
# Check raw intensities
# Ranges: 1.125 851439.500
range(ProcA2_raw$intensity)
#> [1] 1.125 851439.500
ProcA2_norm <- normalize_spec(ProcA2_raw)
# Ranges: 2 100
range(ProcA2_norm$intensity)
#> [1] 2 100