peptagram visualizes the comparison of peptide coverage across proteomics experiments.

It even lets you compare peptides from different search engines.

The visualization is generated as an HTML5 visualization, which is:

  • executable: runs on any modern webbrowser
  • cross-platform: everyone has a webbrowser
  • self-contained: just zip directory and send by email
  • publishable: installable on any server, even on Dropbox

If you would rather examine spectra in detail, try peptide-shaker or PepXMLViewer.


peptagram consists of a set of python scripts that converts proteomics data into an HTML5 visualisation (Chrome, Safari, Firefox).

peptagram requries python 2.7. If your system does not have it, you should download python.

Download and unzip the package from

For developers: to use peptagram as a python module, you should:

> pip install peptagram

Or download the package and run:

> python install

peptagram has two python dependencies:

  1. pymzml to read .mzML files
  2. uniprot to get protein sequences from

To install them with the python package installer pip:

> pip install pymzml uniprot

Make Peptagrams

Visualization Generation - describes how to generate peptagrams.

Use Peptagrams

Visualization Help - describes all the features of a peptagram.

Extend New Peptagrams

Programming API - describes how to automate the generation of peptagrams and how to develop your own parsers for it.