masstodon 0.15

Investigate mass spectra for chemical substances, especially ETD products.

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)