NPvis is a versatile interactive visualizer for tandem mass spectra (MS/MS) fragmentation of Natural Products (NPs). NPvis can work with compounds of an arbitrary chemical structure including all classes of NPs. The tool accepts as input molecules in popular chemical formats such as SMILES and MDL MOL as well as MS/MS data in common formats like mzML and MGF. NPvis allows users to match any annotated experimental peak to the corresponding chemical structure fragmentation. Our tool is embedded into the output of widely used in silico identification tools at the GNPS web platform. In contrast to proteomics MS/MS visualization tools, NPvis support structures with non-linear structure (e.g. cyclic, branched), containing non-standard amino acids as well as non-peptidic residues.


NPvis is a work-in-progress (WIP) project. We are doing our best to deliver it to you as soon as possible. Stay tuned!
Currently, you can try some of the NPvis functionality in the Dereplicator/VarQuest workflow at GNPS or check out a few examples below.

Examples of output

  1. Surugamide-783 identified in MSV000078604 dataset.
  2. Surugamide-769 identified in MSV000078604 dataset.
  3. Pristinamycin-733 identified in MSV000078604 dataset.
  4. Venepeptide-2138 identified in MSV000078839 dataset.
  5. Venepeptide-2154 identified in MSV000078839 dataset.
  6. Wollamide-1017 identified in MSV000078604 dataset.
  7. WS9326C-1036 identified in MSV000078604 dataset.
  8. Massetolide-1252 identified in MSV000079450 dataset.


NPvis is implemented in JavaScript/JQuery (visualization) and Python (preprocessing). The visualization part is based on Lorikeet, an MS/MS visualizer for proteomics. NP fragmentations are predicted with NPDtools utilities.


An NPvis poster was presented at the Lomonosov-2021 conference (19-23 April 2021, online on Twitter and in the BigBluButton server of FBB, MSU).