About

NPvis is a versatile interactive visualizer for tandem mass spectra (MS/MS) fragmentation of Peptidic Natural Products (PNPs), that is ribosomally synthesized and post-translationally modified peptides (RiPPs) and nonribosomal peptides (NRPs). The tool takes as input a mass spectrum, e.g., in MGF or mzXML format, and a corresponding PNP chemical structure, e.g., as an MDL MOL file or SMILES string. NPvis annotates the match and allows users to interactively maps annotated spectrum peaks to the corresponding PNP fragments and to assess the match correctness.

NPvis accounts for the wide chemical diversity of PNPs that prevents the use of the existing proteomics visualizer.  In particular, the tool handles PNPs that have cyclic, branched, or more sophisticated structure, contain non-proteinogenic amino acids and complex post-translational modifications, include non-amide linkages of amino acids. Moreover, NPvis works even if the exact chemical structure of the matching PNP is unknown (the “PNP with modification” mode).

The tool is available online, as a standalone application, and as an embedding in the GNPS web platform (the Dereplicator/VarQuest workflow). We hope it will benefit the community by streamlining PNP MS/MS data analysis and validation. NPvis was developed within the RSF 20-74-00032 project.

Try it!

• (recommended) via web server (tested on Chrome, Firefox and Safari; instant results without registration! )
• via command-line (macOS & Linux only; consult with README)
• via GNPS Dereplicator/VarQuest workflow (you should register/log in first; consult with the documentation).
• .. or just test interactive examples below to grasp the concept!

Examples of output

• Web server (GET Requests!)
  • CCMSLIB00000839197 vs surugamide A (the “PNP with modification” mode)
  • CCMSLIB00000839197 vs surugamide B (the “PNP” mode, note the same spectrum but different PNP compared to above)
  • .. also you can always press the “Load Sample Data” and “Submit” buttons to get a sample output

• Static HTML files (generated via the command-line version)
  • Surugamide-769 identified in MSV000078604 dataset.
  • Venepeptide-2154 identified in MSV000078839 dataset.
  • Massetolide-1252 identified in MSV000079450 dataset.

• GNPS
  • Three significant PSMs identified by VarQuest in a sample run (press “View Annotation” to see the NPvis visualizations)

Implementation

NPvis is implemented in JavaScript/JQuery (visualization) and Python (preprocessing). The visualization part is based on Lorikeet, an MS/MS visualizer for proteomics. PNP fragmentations are predicted with NPDtools utilities. The web server is made with the Django Python web framework. The source code of both the web server and the console utility are in our GitHub repo.

Publications/Posters

An NPvis poster was presented at the Lomonosov-2021 conference (19–23 April 2021, Moscow/online), read the abstract here.

Kunyavskaya, Mikheenko, Gurevich. NPvis: an Interactive Visualizer of Peptidic Natural Product–MS/MS Matches. Metabolites, 2022

Plans

• Add advanced features of proteomics visualizers: account for neutral losses during the MS/MS peaks annotation, provide manual peak annotation
• Handle compounds without a peptidic backbone, such as polyketides and terpenes (use Dereplicator+ or more advanced fragmentation models)

Feedback, bug reports

If you have any questions or want to report a bug, please write to or post an issue on https://github.com/ablab/npvis/issues.