VarQuest

Description

VarQuest is a novel algorithm for the identification of PNP variants via database search of mass spectra, the first high-throughput mutation-tolerant PNP identification method capable of analyzing the entire GNPS infrastructure. VarQuest is based on Dereplicator source code, a method aimed at standard PNP identification.

How to run

You can try VarQuest online at the GNPS website (registration is needed but it is quick and simple). Our tool is embedded in the Dereplicator workflow (use “Search analogs” checkbox to enable VarQuest). See the documentation for details.

Also, we provide the command line version as part of the NPDtools package. Running instructions are specified in the README file (also available inside the package). The package is released under the Apache 2.0 License. The package includes sample mass spectra for a peptide (Surugamide) and a polyketide (Chalcomycin).

Download the latest NPDtools binaries (for 64-bit Linux or macOS)

News

VarQuest was presented at RECOMB 2018 in Paris (France) — highlight talk in Session 3.

VarQuest paper was published in Nature Microbiology volume 3, pages 319–327 (2018).

We publicly released the command line version of our tool, see download links above.

Our poster (B-363) was presented at ISMB/ECCB 2017 in Prague (Czech Republic).

Examples of VarQuest output

VarQuest identifications on various GNPS datasets visualized with NPvis:

  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.

Example of chemical structures database: PNPdatabase (5021 compounds in MOL V3000 format and the description file needed for VarQuest/Dereplicator).

List of 120 MassIVE accession numbers used in VarQuest benchmarking on the entire GNPS.

Contact

In case of any questions, suggestions, bug reports, please write to .

The tool is developed in collaboration with University of California, San Diego.

Publications

  2. Gurevich A. , Shlemov A., Mikheenko A. , Korobeynikov A. , Pevzner P. A. Identification of novel peptidic antibiotics via large scale scoring of mass spectra against natural products databases (poster), 2017
  3. Gurevich A. , Shlemov A., Mikheenko A. , Korobeynikov A. , Pevzner P. A. VarQuest: modification-tolerant identification of novel variants of peptidic antibiotics and other natural products. (poster), 2017