/spectral_denoising

this is the repository for publication contents for spectral denoising paper

Primary LanguageJupyter Notebook

Spectral Denoising and Denoising search

Description

This repository contains all necessary code for Spectral Denoising and Denoising Search, as well as codes for generating figures in mansucript: "Denoising Search doubles the numbelof metabolite and exposome annotations inhuman plasma using an Orbitrap Astral massspectrometer".

Goal

  1. remove noise ions in MS/MS spectra based on elemental-formula information;

  2. Improve high confidence compound annotations based on denoised spectra

Data

All related experiemental data can be found on google drive: (https://drive.google.com/drive/folders/1xSKtLqNXukj6V8qP9c_e5MAbmbDLg2Ml?usp=sharing)

Usage

The algorithm was developed in a conda environment with Python 3.8. A yaml file will be provided shortly for compiling necessary dependencies.

Basic usage can be found in: sample_notebook.ipynb Demo data can be found in: /sample_data