ASMS Data Curation Pipeline

This repository contains a Python-based data curation pipeline for processing Affinity Selection Mass Spectrometry (ASMS) datasets. The pipeline prepares data for machine learning by performing cleaning, labeling, and fingerprint extraction.

Main Features

• Splits protein-specific data into separate files
• Detects and filters out anomalous entries
• Handles isomer corrections
• Adds negative samples from a master list
• Generates binary labels for machine learning
• Extracts chemical fingerprints (e.g., ECFP4, FCFP6, MACCS)
• Saves curated data in both CSV and Parquet formats

Data Inputs

The pipeline expects two input folders at the dataset root (the path given via --path, or the parent of the current working directory if --path is omitted). For instructions on how to run the pipeline, see USAGE.md.

RawData/

One or more ASMS results CSV files, for example ASMS_results_2_all.csv. Each row is a compound–protein measurement with target/non-target intensities, replicates, pool info, and protein metadata. Every CSV in this folder is processed.

MasterLists/

Excel files describing the compound libraries used in the screen. This folder must contain:

• MasterList_Information.xlsx (required). Maps each raw-data CSV to its corresponding master list. Must have two columns:

  • FileName — the filename of a CSV in RawData/ (e.g. ASMS_results_2_all.csv)
  • MaterListName — the base name (no extension) of the matching master list .xlsx file in MasterLists/

• One .xlsx per master list referenced above (e.g. Chemdiv+Chiral6k_15k.xlsx, Chemdiv_9k.xlsx). Each must contain at least a SMILES column; it's used to draw negative samples for the model.

Sample Data

For reference, the repo includes two small placeholder folders:

• RawData_sample/
• MasterLists_sample/

These show the expected file layout and naming. They are not picked up by the pipeline automatically — Main.py only reads from RawData/ and MasterLists/. To use them, either:

1. Rename the folders by dropping the _sample suffix:

   Rename-Item RawData_sample RawData
   Rename-Item MasterLists_sample MasterLists

2. Or copy/move the sample files into your own RawData/ and MasterLists/ folders.

Your real RawData/, MasterLists/, and the generated ProcessedData/ are all gitignored — only the _sample versions are tracked in this repo.