Similarly to the mass detection step in the MZmine workflow, detect mass filters out low intensity signals. Here, you can opt to detect masses by the raw ion intensity (ion counts), or normalize the spectra to the most abundant ion, and detect as an intensity percentage of that ion. The default is set to include all ions that are at least 1% of the most abundant ion.
Arguments
- spec
a data frame containing the MS/MS spectra.
- normalize
a boolean indicating if the MS/MS spectra is normalized by the base peak before proceeding to filter out low intensity signal (normalize = TRUE), if normalize = FALSE the user has to provide the minimum ion count.
- min_int
a integer with the minimum ion intensity
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
# 26731 ion signals
dim(ProcA2_raw)
#> [1] 24249 6
# Detecting masses with the normalized spectra and ions with
# intensities greater than 5%
ProcA2_detected <- detect_mass(ProcA2_raw, normalize = TRUE, min_int = 5)
dim(ProcA2_detected)
#> [1] 40 6