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Flow Injection

# load libraries
library(isoorbi) # for Orbitrap functions
library(dplyr) # for data wrangling
library(ggplot2) # for data visualization

Data

Load data

# load and process data
data <- 
  # load file included in isoorbi package
  system.file(package = "isoorbi", "extdata", "testfile_flow.isox") |>
  orbi_read_isox() |>
  orbi_simplify_isox() |>
  # define data block where signal is stable (plateau)
  orbi_define_block_for_flow_injection(start_time.min = 0.1, end_time.min = 0.9) |>
  # flag extreme TICxIT values
  orbi_flag_outliers(agc_fold_cutoff = 2)
✔ [231ms] orbi_read_isox() loaded 6449 peaks for 1 compound (HSO4-) with 5
isotopocules (M0, 33S, 17O, 34S, and 18O) from testfile_flow.isox
✔ [2ms] orbi_simplify_isox() kept columns filepath, filename, scan.no,
time.min, compound, isotopocule, ions.incremental, tic, and it.ms
✔ [12ms] orbi_define_block_for_flow_injection() added a new block (0.1 to 0.9
min) to 3 files
✔ [8ms] orbi_flag_outliers() confirmed that none of the 1290 scans are outliers
based on 2 fold AGC cutoff, i.e. based on scans below 1/2 and above 2 times the
average number of ions tic * it.ms in the Orbitrap analyzer, in 6 data groups
(based on filename, block, and segment)

Calculations

Ratios

# basepeak & ratios
data_w_basepeak <- 
  data |>
  orbi_define_basepeak("M0")
✔ [51ms] orbi_define_basepeak() set M0 as the ratio denominator and calculated
5.16k ratio values for 4 isotopocules (33S, 17O, 34S, and 18O)
# ratio summaries
data_summary <- 
  data_w_basepeak |>
  orbi_summarize_results(ratio_method = "sum")
✔ [26ms] orbi_summarize_results() summarized ratios from 4.14k peak (excluding
0 flagged peaks; excluding 1.02k unused peaks) using the sum method and
grouping the data by filename, compound, basepeak, isotopocule, block,
sample_name, segment, data_group, and data_type

Figures

Visualize data

orbi_plot_raw_data(data, y = ions.incremental, y_scale = "log")
Ions of isotopocules in time
Ions of isotopocules in time

Raw ratios

data_w_basepeak |> orbi_plot_raw_data(y = ratio) 
Isotopocule ratios vs M0
Isotopocule ratios vs M0

Ratios for 18O

fig <- 
  data_summary |>
  filter(isotopocule == "18O") |>
  # plot
  ggplot() +
  aes(
    x = filename,
    y = ratio, ymin = ratio - ratio_sem, ymax = ratio + ratio_sem,
    color = filename, shape = filename
  ) +
  geom_pointrange() +
  scale_color_brewer(palette = "Dark2") +
  # theme definitions
  theme_bw() +
  theme(
    text = element_text(size = 16),
    panel.grid = element_blank()
  ) +
  # labels
  labs(
    y = expression("ratio ("^18*O/M0*")")
  )
fig
Isotopocule ratios 18O vs M0
Isotopocule ratios 18O vs M0

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.