Modern mass spectrometry for synthetic biology and structure-based discovery of natural products

Abstract

Covering: up to 2016In this highlight, we describe the current landscape for dereplication and discovery of natural products based on the measurement of the intact mass by LC-MS. Often it is assumed that because better mass accuracy (provided by higher resolution mass spectrometers) is necessary for absolute chemical formula determination (≤1 part-per-million), that it is also necessary for dereplication of natural products. However, the average ability to dereplicate tapers off at ∼10 ppm, with modest improvement gained from better mass accuracy when querying focused databases of natural products. We also highlight some recent examples of how these platforms are applied to synthetic biology, and recent methods for dereplication and correlation of substructures using tandem MS data. We also offer this highlight to serve as a brief primer for those entering the field of mass spectrometry-based natural products discovery.

Fig. 1

A comparison of two different workflows for natural products discovery. Structure-based discovery (bottom) emphasizes the use of spectrometric data early in the pipeline to quickly dereplicate known compounds and scaffolds, allowing researchers to save resources and focus on unknown compounds.

Fig. 2

With a lower mass error (i.e., better mass accuracy), the observed mass of a compound will dereplicate to a fewer number of candidate compounds in a database of 35,215 natural products (Antibase was used here). On average, there is only a 4.7% gain in dereplication ability by increasing mass accuracy from 10 to 1 ppm.

Fig. 3

As mass accuracy increases, the number of compounds in the database that can be unambiguously dereplicated based on measurement of the intact mass increases drastically by going from 100 to 10 ppm, aga in to a lesser extent from 10 ppm to 1 ppm, and barely from 1 to 0.1 ppm.

Fig. 4

By selectively fragmenting a natural product, MS² can provide unique structural details that can assist dereplication.

Fig 5

A dereplication pipeline for natural products discovery. This pipeline takes advantage of the incredible amount of structural information that can be gleaned from LC-MS, especially when accurate mass (1-5 ppm) and MS² data are used together.