1  Quick Start

1.1 Installation

To install the IsoPairFinder package, you can use the following command in R:

# intall public packages
if (!require(devtools)){
    install.packages("devtools")
}

if (!require(BiocManager)){
    install.packages("BiocManager")
}

# Required packages
required_pkgs <- c("dplyr","tidyr","readr", "stringr", "tibble", "purrr",
                   "ggplot2", "igraph", "pbapply", "Rdisop", "randomForest", "pryr", 
                   "magrittr", "rmarkdown", "caret", "writexl", "ggrepel", "crayon", 
                   "data.table", "mzR", "Rdisop", "grid", "gridExtra", "RaMS", "knitr",
                   "rcdk")
BiocManager::install(required_pkgs)
devtools::install_github("JustinZZW/SpectraTools2")
devtools::install_github("DoddLab/MassToolsMjhelf")

# install.packages("IsoPairFinder")
devtools::install_github("DoddLab/IsoPairFinder")

1.2 Demo data

The demo data belong to the uric acid catabolism pathway study1. Briefly, we cultured wild-type and mutant strains (hyuA mutant in the demo data) of C. sporogenes in the presence of either unlabeled uric acid or its [13C5]-labeled isotopolog (detailed study design can be found Chapter 4).

The demo data can be downloaded here. The downloaded data contains below files (Figure 1.1). Please refer to Chapter 2 for the detailed requirements of the data format for the step-by-step data preparation (xcms - Section 2.1, msdial - Section 2.2, mzmine - Section 2.3, tidymass - Section 2.4).

Figure 1.1: The screenshot of the demo data.

1.3 Run script

The basic use of IsoPairFinder is simply running the R script as below:

# run the IsoPairFinder workflow
library(tidyverse)
library(IsoPairFinder)

# analysis of HyuA (Mutant) 
find_intemidates(peak_table_unlabel = 'peak_table_C12.csv',
                 peak_table_label = 'peak_table_C13.csv',
                 sample_info = 'sample_info.csv',
                 path = '~/Project/00_Uric_Acid_project/Data/20250817_submit_test/',
                 polarity = 'positive',
                 control_group = c("WT"),
                 case_group = c('MUTANT'),
                 mz_tol = 10,
                 rt_tol = 0.05,
                 p_value_cutoff = 0.05,
                 p_adjust = TRUE,
                 fold_change_cutoff = 20,
                 is_recognize_adducts = TRUE)

Please refer to Section 3.2 for the explains of parameters.

1.4 Output

After running, a new folder “00_tracer_result” will be created. It contains several files, including “tracer_pair_result.xlsx” and several PDF files. In the tab of the XLSX file, we could find the identified ion pair results between the unlabeled and labeled groups (Figure 1.2). The detailed explanations of each file can be found in Section 3.3.

Figure 1.2: Overview of results.