NP Analyst: An Open Online Platform for Compound Activity Mapping

Abstract

Few tools exist in natural products discovery to integrate biological screening and untargeted mass spectrometry data at the library scale. Previously, we reported Compound Activity Mapping as a strategy for predicting compound bioactivity profiles directly from primary screening results on extract libraries. We now present NP Analyst, an open online platform for Compound Activity Mapping that accepts bioassay data of almost any type, and is compatible with mass spectrometry data from major instrument manufacturers via the mzML format. In addition, NP Analyst will accept processed mass spectrometry data from the MZmine 2 and GNPS open-source platforms, making it a versatile tool for integration with existing discovery workflows. We demonstrate the utility of this new tool for both the dereplication of known compounds and the discovery of novel bioactive natural products using a challenging low-resolution antimicrobial bioassay data set. This new platform is available at .

Bioactive Natural Products Identification Using Automation of Molecular Networking Software

“…No additional overhead time for file import and export that require Internet access. 23 We have also detected as a limitation the need to manually remove reference masses from our feature quantification table (.csv file) before data integration and visualization when using LC-MS QTOF mass spectrometers. These types of mass spectrometers work using reference masses for accurate mass correction.…”

“…Compatible with classic molecular networking. Assists in the identification of known and unknown compounds by shape and demonstrating their biological activity at the same time. Filters nodes based on activity scores in molecular network view. Files are stored locally. No additional overhead time for file import and export that require Internet access …”

Artificial intelligence in microbial natural product drug discovery: current and emerging role

“…106 Further, a versatile, open-access platform NP Analyst was developed as a user friendly web-based infrastructure enabling NP community to analyze without the need for intense data processing. 107 Although in the past MN could only be done via the web with GNPS, now many off-line tools such as MZmine3.0, 86 MS-DIAL, 88 Metaboseek, 108 NetID 109 and commercial software like Compound Discoverer (Thermo Scientific) have the ability to perform MN without the online platform making it easier.…”

Data fusion discovery (DAFdiscovery) pipeline to aid compound annotation and bioactive compound discovery across diverse spectral data

“…Different approaches were suggested in the literature on how to integrate chemical data with bioassay results to reach bioactive compounds in early research stages. 6,7,8 Within these efforts, multivariate analysis (i.e., PCA, PLS-DA) of the chemical data of samples classified into active and inactive in a given bioassay is the straightforward method to follow. 9,10 NP Analyst is a recent tool developed as a webserver to integrate MS metabolomics data with a series of bioactivity assays such as antimicrobial panels.…”

“…9,10 NP Analyst is a recent tool developed as a webserver to integrate MS metabolomics data with a series of bioactivity assays such as antimicrobial panels. 7 Through NP Analyst users can integrate data from a big library of samples to prioritize those pointed out as promising; for instance, the parameter consistency of bioactivity of each MS features present. Developed by the same group (Linington Lab, SFU), MADByTE is a tool that searches for sharing TOCSY spin systems (in combination with HSQC peaks) from NMR data to create networks that can be used to visualize samples according to their characteristics and biological profiles.…”