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

Scripts to run the experiments and analysis for the publication "Joint structural annotation of small molecules using liquid chromatography retention order and tandem mass spectrometry data" by Bach et al.

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

Repository

Scripts to run the experiments and analysis for the publication "Joint structural annotation of small molecules using liquid chromatography retention order and tandem mass spectrometry data" by Bach et al.

https://github.com/aalto-ics-kepaco/lcms2struct_exp/blob/main/

# Experiments and result analysis scripts for the LC-MSStruct

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

## Reproducibility

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

### Manuscript figures

The raw outputs of the LC-MSStruct for the experiments presented in the manuscript are available on Zenodo. Download 
both [tar-files](https://en.wikipedia.org/wiki/Tar_(computing)) 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](results_processed/publication/massbank/ssvm_lib=v2__exp_ver=4/README.md). 

### Re-run the experiments

If you wish to re-run our experiments, you will have to install the [LC-MSStruct library](https://github.com/aalto-ics-kepaco/msms_rt_ssvm), 
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](https://zenodo.org/record/5854661).
Detailed instructions are given [here](run_scripts/README.md). 

### Re-building the MassBank DB

If you wish to re-build the MassBank DB used in our experiments, please follow the instructions given [here](data/README.md)

## Repository structure

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)

# Citation information

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

```bibtex
@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: 


[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7057255.svg)](https://doi.org/10.5281/zenodo.7057255)

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