Investigate mass spectra for chemical substances, especially ETD products.
Project description
masstodon
Your Python3 module for investigating the Electron Transfer Dissociation in Mass Spectrometry, and more generally finding stuff in the mass spectrum.
Prerequisites
Python3
Installation
The package can be installed directly from the Python Package Index:
pip install masstodon
Otherwise, download this github repo, use the default branch, and install the software with:
pip install .
from the folder containing setup.py.
This will let you import masstodon
simply by
import masstodon
Running
After installation, you can use masstodon
as a library (support of CLI and web-based user-interface in progress).
Importing data. You can analyze individual mass spectra with masstodon
. This might very well be individual scans of an Orbitrap, or a general mass spectrum. The easiest way to import the mass spectrum is to present a plain ASCII file with m/z and intensity values in each row, separated by tab or some other whitespace sign.
m = masstodon_single(mz, intensity, fasta, q,
min_mz_diff = infinity,
modifications = modifications,
orbitrap = False,
threshold = threshold,
isotopic_coverage = isotopic_coverage,
min_prob = min_prob,
std_cnt = std_cnt)
Project details
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