This repository contains the scripts to reproduce the experiments and analyse the results for the manuscript:

"Joint structural annotation of small molecules using liquid chromatography retention order and tandem mass spectrometry data",

Eric Bach, Emma L. Schymanski and Juho Rousu, 2022

If you wish to re-produce our results please follow the instructions given below. All our experiments where performed using Linux as operating system and Python (version 3.8 and 3.9 are supported). Other operating systems are not officially supported. Detailed software requirements are given alongside the reproducibility instructions.

The first step for any of the following reproducibility tasks is to clone this repository:

clone https://github.com/aalto-ics-kepaco/lcms2struct_exp/
cd lcms2struct_exp

The raw outputs of the LC-MS²Struct for the experiments presented in the manuscript are available on Zenodo. Download both tar-files and unpack them in the repository's root directory.

• ALLDATA: https://zenodo.org/record/6451016
• ONLYSTEREO: https://zenodo.org/record/6037629

Detailed instructions how to re-produce the figures of the manuscript can be found here.

If you wish to re-run our experiments, you will have to install the LC-MS²Struct library, which provides an implementation of the presented Structured Support Vector Machine (SSVM). Furthermore, you will have to download our MassBank database containing all features, candidate sets, etc. from Zenodo. Detailed instructions are given here.

If you wish to re-build the MassBank DB used in our experiments, please follow the instructions given here

The repository is organized in different subdirectories those content is described in the following.

• misc_scripts: Contains a script to extract different MassBank database statistics
• run_scripts: Contains all scripts needed to re-run our experiments
• results_raw: Contains the "raw" result files as produces by our experimental scripts (download from Zenodo)
• results_processed: Contains the result files as used to produce the figures in our manuscript, e.g. aggregated max-margins, comparison methods, ... (download from Zenodo)
• ssvm_evaluation: Script generating the figures from the data (library)

Use the citation information of you want to reference our work:

@article {Bach2022,
  author = {Bach, Eric and Schymanski, Emma L. and Rousu, Juho},
  title = {Joint structural annotation of small molecules using liquid chromatography retention order and tandem mass spectrometry data},
  elocation-id = {2022.02.11.480137},
  year = {2022},
  doi = {10.1101/2022.02.11.480137}, 
  publisher = {Cold Spring Harbor Laboratory},
  URL = {https://www.biorxiv.org/content/early/2022/04/27/2022.02.11.480137},
  eprint = {https://www.biorxiv.org/content/early/2022/04/27/2022.02.11.480137.full.pdf},
  journal = {bioRxiv}
}

Software citation: