JSpectraViewer:

Metabolomics, lipidomics, exposomics and natural product (NP) chemistry use a variety of analytical chemistry techniques to detect or identify small molecules. These include nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry (MS), ultraviolet (UV), infrared (IR) and infrared ion (IRIS) spectroscopy. As a result, most of the “raw” data generated for these small- molecule omics research activities is in the form of spectral data. Just like structural data, spectral data needs to be visualized to be understood or interpreted. Unfortunately, most spectral visualization software available today is of the stand-alone, commercial variety. Furthermore, completely different spectral visualization tools must be used to view different types (MS vs. NMR vs. IR vs. IRIS vs. UV) of spectra. Very few freely available, stand-alone or web-based tools exist for spectral visualization or annotation (refs JSpecView, COLMAR, SpeckTackle). Those that do exist are quite limited in their capabilities and are typically designed for viewing a single type of spectral data. This makes it both difficult and expensive to share, exchange or visualize small molecule spectral data. This paucity of spectral visualization tools has been a real hindrance to the field of small molecule omics research as it severely limits the capabilities of metabolomics, lipidomics, exposomics and natural product databases or webservers. JSpectraViewer has been developed as part of the NP-MRD (Natural Products Magnetic Resonance Database) project, enabling the visualization and analysis of various spectral datatypes, including NMR, LC-MS, EI-MS, IR, and UV/Vis spectra. The library has been in use for several years for various web-based applications such as HMDB, GC-AutoFit, and However, a fully repackaged version is now available for public use under the alias "jsv2" (JSpectraViewer version 2) on Node Package Manager (npm).

NP-MRD Project:

The NP-MRD is a freely available cloud-based, user-friendly, FAIR electronic database. NP-MRD accepts NMR data and associated metadata from newly undertaken NP studies. The NP-MRD accepts raw (time domain data, processed spectra, assigned chemical shifts, J-couplings, RDCs, etc.), and meta-data (structures, sources, methods, taxonomy, geospatial data, etc) from natural products ranging from purifiedsubstances to crude extracts, in all major solvents. The NP-MRD includes NPs such as vitamins, minerals, and probiotics aswell as small molecules derived from plants, fungi, bacteria, marine organisms, or animals. The NP-MRD accepts, converts,and stores all major vendor NMR formats and all major NMR data exchange formats from all common NMR experiments as well asnew/uncommon NMR experiments or data sets. The NP-MRD has an intuitive user interface for spectra/structure deposition, retrieval,search, and analysis. Data deposition is fast (less than 5 min/per spectrum), easy and intuitive, and aided by online assignment andonline spectra/structure visualization tools. Structure and assignment validation reports are generated within 5 minutes ofdeposition and value-added data reports are provided to users within 24 hours of deposition, including high-quality DFT calculationsof chemical shifts for a deposited structure. Data integrity and data quality are ensured by extensive curation efforts and theuse of an objective ranking scale for all deposited data.

Please cite:

JSpectraViewer: A web-based interactive visualization tool for metabolomics research. Sukanta Saha, Jason Grant, Mark Berjanskii, Eponine Oler, Vasuk Gautam, Harrison Peters, David S Wishart