This is an example for shot-noise analysis from Kantnerová et al. (2023).
# load and process data data <- # load file included in isoorbi package system.file(package = "isoorbi", "extdata", "testfile_shotnoise.isox") |> orbi_read_isox() |> # check data for satellite peaks orbi_flag_satellite_peaks() |> # make sure isotopocules are present in (almost) all scans, otherwise # shot noise analyses can be inaccurate orbi_flag_weak_isotopocules(min_percent = 90) |> # see if there are any AGC outliers orbi_flag_outliers(agc_fold_cutoff = 2)
This indicates that there were a few satellite peaks and weak isotopocules but no outliers.
Show the isotopocule coverage for the different amino acids, thus
highlighting which isotopocules were detected in which scans. Note that
2H was highlighted as weak for Alanine, Arginine, and Phenylalanine.
This is because of the high cutoff (90%) in
orbi_flag_weak_isotopocules() which is appropriate for
shot-noise analyses but simply for inspecting ratios it would be
reasonable to examine the 2H signal at least for Alanine.
data |> orbi_plot_isotopocule_coverage()
Show peaks that were flagged as satellite peaks.
data |> orbi_plot_satellite_peaks()
data |> orbi_plot_raw_data( isotopocules = "M0", y = intensity, y_scale = "log" )
data_w_bp |> orbi_plot_raw_data(y = ratio)
shot_noise |> orbi_plot_shot_noise()