Targeted and untargeted LC-MS copepodamide datasets for marine and freshwater copepods

This repository contains the datasets, analysis code and output generated and used in the scientific article titled "Mass spectroscopy reveals compositional differences in copepodamides from limnic and marine copepods" published in Scientific Reports (https://doi.org/10.1038/s41598-024-53247-1). Detailed information about the datasets are available in the README.txt. The source dataset created from the sampling effort, with targeted liquid chromatography coupled mass spectrometry (LC-MS) data, taxonomic information of individual copepods, their length measurements, estimated biomass etc is available in Masterfile_targeted_data_final.xlsx. The source dataset for precursor LC-MS scan data is available in Precursor_data_Deisotoped.xlsx. The resulting analysis data frames (last sheet in each .xlsx file) are available as separate .csv files (Arnoldt_targeted_analysis_data.csv & Arnoldt_targeted_analysis_data.xlsx). These files are denoted "Supplementary Data. 2" and "Supplementary Data. 1" respectively in the main article. Data files Chromatography.csv and zooplankton_composition_bulk.csv are used to create chromatograph line plots (Figures 3a & 3b in the article) and one of the supplementary figures (S1), respectively. A R-markdown file (Arnoldt_R_Code.Rmd) with the code to analyse and visualise all data, and its html-output file (Arnoldt_R_Code_Output.html) are also available here. The markdown files uses the four csv-files described in the paragraph above to generate all analyses and figures. The output (.html) file is denoted "Supplementary Code" in the main article.