Fragmentation of Polyfunctional Compounds Recorded Using Automated High-Throughput Desorption Electrospray Ionization

Abstract

Using desorption electrospray ionization (DESI) as part of an automated high-throughput system, tandem mass spectra of the compounds in a pharmaceutical library were recorded in the positive mode under standardized conditions. Quality control filtering yielded an MS/MS library of 16 662 spectra. Fragmentation of subsets of the compounds in the library chosen to contain a single instance of a particular functional group (amide, piperazine, sulfonamide) was predicted by experts, and the results were compared with the experimental data. Expert performance was good to excellent for all the cases evaluated. Substituents on the functional groups were found to exert important secondary control over the fragmentation, with the main effect observed being product ion stabilization by aromatic substitution, which was consistent across the different groups evaluated. These substituent effects are generally explicable in terms of standard physical organic chemistry considerations of product ion stability as controlling fragmentation. A somewhat unexpected feature was the incidence of homolytic cleavages, driven by the stability of substituted amine radical cations. The findings of this study are intended to lay the groundwork for machine learning approaches to performing MS/ MS spectrum → structure and structure → MS/MS spectrum operations on the same experimental data set. The effort involved and the success achieved in computer-aided interpretation, now underway, will be compared with the expert performance as described here.

Desorption Electrospray Ionization Mass Spectrometry Assay for Label‐Free Characterization of SULT2B1b Enzyme Kinetics

“…High‐throughput DESI‐MS analysis was carried out using the Purdue Make It system. Hardware, software, and operation of the system have been previously described [22,23,32,43] . Briefly, 50 nL samples are directly spotted from 384‐well plates onto DESI plates using a Biomek i7 fluid handling workstation (Beckman Coulter, Indianapolis, IN, USA) equipped with a 50‐nL floating slotted 384‐pin tool (V&P Scientific, San Diego, CA, USA).…”

“…In all experiments, the deposited amount of steroid sulfate on each spot was less than 1 ng, and even this was not completely sampled. Using custom software, DESI-MS analysis was performed automatically in a spot-to-spot manner, [23,43] with an effective analysis time of ~400 ms per spot.…”

“…Hardware, software, and operation of the system have been previously described. [22,23,32,43] Briefly, 50 nL samples are directly spotted from 384-well plates onto DESI plates using a Biomek i7 fluid handling workstation (Beckman Coulter, Indianapolis, IN, USA) equipped with a 50-nL floating slotted 384-pin tool (V&P Scientific, San Diego, CA, USA). Up to 6,144 samples can be spotted on a single DESI plate, with center-to-center distances of ca.…”

Applications of ambient ionization mass spectrometry in 2021: An annual review

“…Recently, Le et al. used a high‐throughput DESI system coupled with collision‐induced dissociation for the rapid generation of MS/MS data for a large set of compounds 163 . Thousands of pharmaceutically relevant small molecules were analysed, resulting in the production of over 16 000 high‐quality MS/MS spectra.…”

A Deep-Learning Proteomic-Scale Approach for Drug Design

“…The same can be inferred for downregulated genes and inhibition/antagonism. In addition, we are exploring the use of high-throughput robotic systems such as DESI-MS to generate large-scale interaction and activity data [82][83][84][85][86][87][88][89][90]. CANDO thus enables and illustrates the benefit of combining heterogeneous sources (gene, as well as protein expression, protein pathway databases, high-throughput binding, and activity data) to create novel types of interaction signatures/networks to produce design objectives that tackle complex indications.…”