Proteomics Sandbox

release type access

  • Operating System:

  • Terminal:

  • Shell:

  • Editor:

  • Package Manager:

  • Programming Language:

  • Utility:

The Proteomics Sandbox is a platform optimized for software applications used in proteomics. The app is deployed as a virtual desktop environment.

Software tools

The following software packages are available:

  • FragPipe:

    • Automated peptide and protein identification and quantification using the MSFragger search engine.

    • Supports the identification of arbitrary PTMs.

    • Includes additional tools for post-processing and visualization of search results.

  • MaxQuant:

    • Comprehensive software suite for proteomics data analysis.

    • Includes protein and peptide identification, quantification, and visualization of spectral matches.

    • Features an advanced search engine and a user-friendly graphical interface.

  • PDV:

    • Visualization tool for spectral matches, particularly those obtained from MSFragger searches.

    • Allows users to inspect and evaluate the quality of the matches.

    • Supports annotation and customization of plots.

  • SearchGUI:

    • User-friendly interface for performing peptide searches using multiple search engines (e.g. MSFragger, X!Tandem, OMSSA).

    • Supports a wide range of search options and post-processing features.

  • PeptideShaker:

    • Tool for visualizing and analyzing the results of peptide searches performed with SearchGUI.

    • Includes features for filtering, annotation, and visualization of results.

    • Supports integration with other proteomics databases and software.