Skip to content

Adding colour to mass spectra: Charge Determination Analysis (CHARDA) assigns charge state to every ion peak

Notifications You must be signed in to change notification settings

Yaroslav-Lyutvinskiy/CHARDA

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

35 Commits
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

To reproduce article data analysis click the button below and run all the cells in opened Google Colab notebook.

Open In Colab

CHARDA

CHARDA - Charge Determination Analysis Yaroslav Lyutvinskiy, Amir Ata Saei, Yury Tsybin, Roman Zubarev

Traditionally, mass spectrometry (MS) output is the ion abundance plotted versus ionic mass-to-charge ratio m/z. While employing only commercially available equipment, Charge Determination Analysis (CHARDA) adds a third dimension to MS, estimating for individual peaks their charge states z, starting from z=1, and colour-coding z in m/z spectra. CHARDA combines the analysis of transient decay in Fourier transform (FT) MS with interrogation of mass defects. Being applied to individual isotopic peaks in a complex protein MS/MS dataset, CHARDA facilitates charge state deconvolution of large ionic species in crowded regions, estimating z even in the absence of isotopic distribution (e.g., for monoisotopic mass spectra). CHARDA is fast, robust and consistent with conventional FT MS and FT MS/MS data acquisition procedures. An effective charge resolution Rz≥6 is obtained, with potential for further improvements.

This code is published for article https://chemrxiv.org/engage/chemrxiv/article-details/613a227265db1e3f14b1ab27

"Adding colour to mass spectra: Charge Determination Analysis (CHARDA) assigns charge state to every ion peak"

Currently the article is under review.

Code of CHARDA project is presented in two flawors:

  1. /CHARDA-pytorch-colab.ipynb - version of CHARDA intended to run in standard colab environment.
  2. /code/CHARDA.ipynb file - version of CHARDA to run in dedicated docker container

Also /code folder containg binaries of publicly available software hardklor (https://proteome.gs.washington.edu/software/hardklor/) working as deisotoping algoritm for CHARDA.

The notebook /CHARDA-pytorch-colab.ipynb is self-sufficient and takes about 1 hour to complete in standard Google Colab environment with GPU acceleration (as of 4 apr 2023).

Charda can be run both on Linux and windows platforms, however setup for Linux platform is easier to reproduce. Corresponding docker file is located in /environment folder.

Data files for CHARDA were zipped to pass 50Mb limit of github upload. You should unzip them before use.

About

Adding colour to mass spectra: Charge Determination Analysis (CHARDA) assigns charge state to every ion peak

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published