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Review

Data processing for high-throughput mass spectrometry in drug discovery

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Pages 815-825 | Received 25 Mar 2024, Accepted 08 May 2024, Published online: 24 May 2024

References

  • Vincent F, Nueda A, Lee J, et al. Phenotypic drug discovery: recent successes, lessons learned and new directions. Nat Rev Drug Discov. 2022;21(12):1–16. doi: 10.1038/s41573-022-00472-w
  • Korfmacher WA. Foundation review: principles and applications of LC-MS in new drug discovery. Drug Discov Today. 2005;10(20):1357–1367. doi: 10.1016/S1359-6446(05)03620-2
  • Shou WZ. Current status and future directions of high-throughput ADME screening in drug discovery. J Pharm Anal. 2020;10(3):201–208. doi: 10.1016/j.jpha.2020.05.004
  • Rentsch KM. Knowing the unknown–State of the art of LCMS in toxicology. Trac-Trend Anal Chem. 2016;84:88–93. doi: 10.1016/j.trac.2016.01.028
  • Xu RN, Fan L, Rieser MJ, et al. Recent advances in high-throughput quantitative bioanalysis by LC–MS/MS. J Pharm Biomed Anal. 2007;44(2):342–355. doi: 10.1016/j.jpba.2007.02.006
  • Kapinos B, Liu J, Piotrowski M, et al. Development of a high-performance, enterprise-level, multimode LC–MS/MS autosampler for drug discovery. Bioanalysis. 2017;9(21):1643–1654. doi: 10.4155/bio-2017-0149
  • Santanilla AB, Regalado EL, Pereira T, et al. Nanomole-scale high-throughput chemistry for the synthesis of complex molecules. Science. 2015;347(6217):49–53. doi: 10.1126/science.1259203
  • Liu C, Zhang H. High-throughput mass spectrometry in drug discovery. Hoboken, New Jersey: John Wiley & Sons; 2023.
  • Annis DA, Nickbarg E, Yang X, et al. Affinity selection-mass spectrometry screening techniques for small molecule drug discovery. Curr Opin Chem Biol. 2007;11(5):518–526. doi: 10.1016/j.cbpa.2007.07.011
  • Haslam C, Hellicar J, Dunn A, et al. The evolution of MALDI-TOF mass spectrometry toward ultra-high-throughput screening: 1536-well format and beyond. J Biomol Screen. 2016;21(2):176–186. doi: 10.1177/1087057115608605
  • Winter M, Ries R, Kleiner C, et al. Automated MALDI target preparation concept: providing ultra-high-throughput mass spectrometry–based screening for drug discovery. SLAS Technol. 2019;24(2):209–221. doi: 10.1177/2472630318791981
  • Krenkel H, Hartmane E, Piras C, et al. Advancing liquid atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry toward ultrahigh-throughput analysis. Anal Chem. 2020;92(4):2931–2936. doi: 10.1021/acs.analchem.9b05202
  • Vestal M, Li L, Dobrinskikh E, et al. Rapid MALDI‐TOF molecular imaging: instrument enhancements and their practical consequences. J Mass Spectrom. 2020;55(8):e4423. doi: 10.1002/jms.4423
  • O’Kane PT, Dudley QM, McMillan AK, et al. High-throughput mapping of CoA metabolites by SAMDI-MS to optimize the cell-free biosynthesis of HMG-CoA. Sci Adv. 2019;5(6):eaaw9180. doi: 10.1126/sciadv.aaw9180
  • Corr JJ, Kovarik P, Schneider BB, et al. Design considerations for high speed quantitative mass spectrometry with MALDI ionization. J Am Soc Mass Spectrom. 2006;17(8):1129–1141. doi: 10.1016/j.jasms.2006.04.026
  • Wu J, Hughes CS, Picard P, et al. High-throughput cytochrome P450 inhibition assays using laser diode thermal desorption-atmospheric pressure chemical ionization-tandem mass spectrometry. Anal Chem. 2007;79(12):4657–4665. doi: 10.1021/ac070221o
  • Yu S, Crawford E, Tice J, et al. Bioanalysis without sample cleanup or chromatography: the evaluation and initial implementation of direct analysis in real time ionization mass spectrometry for the quantification of drugs in biological matrixes. Anal Chem. 2009;81(1):193–202. doi: 10.1021/ac801734t
  • Sawicki JW, Bogdan AR, Searle PA, et al. Rapid analytical characterization of high-throughput chemistry screens utilizing desorption electrospray ionization mass spectrometry. React Chem Eng. 2019;4(9):1589–1594. doi: 10.1039/C9RE00054B
  • Morato NM, Holden DT, Cooks RG. High‐throughput label‐free enzymatic assays using desorption electrospray‐ionization mass spectrometry. Angew Chem Int Ed. 2020;59(46):20459–20464. doi: 10.1002/anie.202009598
  • Krenkel H, Brown J, Richardson K, et al. Ultrahigh-throughput sample analysis using liquid atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry. Anal Chem. 2022;94(10):4141–4145. doi: 10.1021/acs.analchem.1c05614
  • Pu F, Radosevich AJ, Sawicki JW, et al. High-throughput label-free biochemical assays using infrared matrix-assisted desorption electrospray ionization mass spectrometry. Anal Chem. 2021;93(17):6792–6800. doi: 10.1021/acs.analchem.1c00737
  • Radosevich AJ, Pu F, Chang-Yen D, et al. Ultrahigh-throughput direct sampling MS: Sampling at 22 Hz by infrared matrix-assisted desorption electrospray ionization mass spectrometry. Anal Chem. 2022;94(12):4913–4918. doi: 10.1021/acs.analchem.1c04605
  • Wei Z, Xie Z, Kuvelkar R, et al. High‐throughput bioassays using “dip‐and‐go” multiplexed electrospray mass spectrometry. Angew Chem Int Ed. 2019;58(49):17594–17598. doi: 10.1002/anie.201909047
  • Sinclair I, Bachman M, Addison D, et al. Acoustic mist ionization platform for direct and contactless ultrahigh-throughput mass spectrometry analysis of liquid samples. Anal Chem. 2019;91(6):3790–3794. doi: 10.1021/acs.analchem.9b00142
  • Sinclair I, Davies G, Semple H. Acoustic mist ionization mass spectrometry (AMI-MS) as a drug discovery platform. Expert Opin Drug Discov. 2019;14(7):609–617. doi: 10.1080/17460441.2019.1613369
  • Smith MJ, Ivanov DP, Weber RJ, et al. Acoustic mist ionization mass spectrometry for ultrahigh-throughput metabolomics screening. Anal Chem. 2021;93(26):9258–9266. doi: 10.1021/acs.analchem.1c01616
  • Liu C. Acoustic ejection mass spectrometry: fundamentals and applications in high-throughput drug discovery. Expert Opin Drug Discov. 2022 Jul 03;17(7):775–787. doi: 10.1080/17460441.2022.2084069
  • Liu C, Van Berkel GJ, Cox DM, et al. Operational modes and speed considerations of an acoustic droplet dispenser for mass spectrometry. Anal Chem. 2020;92(24):15818–15826. doi: 10.1021/acs.analchem.0c02999
  • Liu C, Van Berkel GJ, Kovarik P, et al. Fluid dynamics of the open port interface for high speed nanoliter volume sampling mass spectrometry. Anal Chem. 2021;93(24):8559–8567. doi: 10.1021/acs.analchem.1c01312
  • Zhang H, Liu C, Hua W, et al. Acoustic ejection mass spectrometry for high-throughput analysis. Anal Chem. 2021;93(31):10850–10861. doi: 10.1021/acs.analchem.1c01137
  • McLaren DG, Shah V, Wisniewski T, et al. High-throughput mass spectrometry for hit identification: Current landscape and future perspectives. SLAS Discov. 2021;26(2):168–191. doi: 10.1177/2472555220980696
  • Pu F, Knizner KT, Robey MT, et al. High-throughput deconvolution of intact protein mass spectra for the screening of covalent inhibitors. J Am Soc Mass Spectrom. 2022;33(12):2338–2341. doi: 10.1021/jasms.2c00273
  • Hu H, Singh AN, Lehnherr D, et al. Accelerating pharmaceutical process development with an acoustic droplet ejection-multiple reaction monitoring-mass spectrometry workflow. Anal Chem. 2024;96(3):1138–1146. doi: 10.1021/acs.analchem.3c04211
  • Liu C. Automated mass spectra comparison algorithm for high-throughput compound QC applications ASMS 2021. 2021;Philadelphia, PA.
  • DiRico KJ, Hua W, Liu C, et al. Ultra-high-throughput acoustic droplet ejection-open port interface-mass spectrometry for parallel medicinal chemistry. ACS Med Chem Lett. 2020;11(6):1101–1110. doi: 10.1021/acsmedchemlett.0c00066
  • Lin S, Dikler S, Blincoe WD, et al. Mapping the dark space of chemical reactions with extended nanomole synthesis and MALDI-TOF MS. Science. 2018;361(6402):eaar6236. doi: 10.1126/science.aar6236
  • Holland‐Moritz DA, Wismer MK, Mann BF, et al. Mass activated droplet sorting (MADS) enables high‐throughput screening of enzymatic reactions at nanoliter scale. Angewandte Chemie. 2020;59(11):4470–4477. doi: 10.1002/anie.201913203
  • Piras C, Hale OJ, Reynolds CK, et al. LAP-MALDI MS coupled with machine learning: an ambient mass spectrometry approach for high-throughput diagnostics. Chem Sci. 2022;13(6):1746–1758. doi: 10.1039/D1SC05171G
  • Piras C, Hale OJ, Reynolds CK, et al. Speciation and milk adulteration analysis by rapid ambient liquid MALDI mass spectrometry profiling using machine learning. Sci Rep. 2021;11(1):1–9. doi: 10.1038/s41598-021-82846-5
  • Luippold AH, Arnhold T, Jörg W, et al. An integrated platform for fully automated high-throughput LC–MS/MS analysis of in vitro metabolic stability assay samples. Int J Mass Spectrom. 2010;296(1–3):1–9. doi: 10.1016/j.ijms.2010.07.004
  • Wagner AD, Kolb JM, Özbal CC, et al. Ultrafast mass spectrometry based bioanalytical method for digoxin supporting an in vitro P‐glycoprotein (P‐gp) inhibition screen. Rapid Commun Mass Spectrom. 2011;25(9):1231–1240. doi: 10.1002/rcm.4984
  • Zacharias AO, Liu C, VanAernum ZL, et al. Ultrahigh-throughput intact protein analysis with acoustic ejection mass spectrometry. J Am Soc Mass Spectrom. 2022;34(1):4–9. doi: 10.1021/jasms.2c00276
  • Zhang J, Zhang Y, Liu C, et al. Acoustic ejection/full-scan mass spectrometry analysis for high-throughput compound quality control. SLAS Technol. 2021;26(2):178–188. doi: 10.1177/2472630320967625
  • Simon RP, Häbe TT, Ries R, et al. Acoustic ejection mass spectrometry: a fully automatable technology for high-throughput screening in drug discovery. SLAS Discov. 2021;26(8):961–973. doi: 10.1177/24725552211028135
  • Wen X, Liu C, Ghislain L, et al. Direct analysis from phase-separated liquid samples using ADE-OPI-MS: applicability to high-throughput screening for inhibitors of diacylglycerol acyltransferase 2. Anal Chem. 2021;93(15):6071–7079. doi: 10.1021/acs.analchem.0c04312
  • Ramanathan R, Jemal M, Ramagiri S, et al. It is time for a paradigm shift in drug discovery bioanalysis: from SRM to HRMS. J Mass Spectrom. 2011;46(6):595–601. doi: 10.1002/jms.1921
  • Zhang J, Liu C, Veiga C, et al. A full scan data review tool to match the speed of acoustic ejection mass spectrometry. LCGC North America. 2022;40(7):314–320. doi: 10.56530/lcgc.na.ib7278q3
  • Wen X. Ultra-high-throughput intact protein analysis for drug discovery using acoustic ejection mass spectrometry. ASMS 2023. 2023; Houston, TX.
  • Bachman M, Sinclair I, Ivanov D, et al. Information-rich high-throughput cellular assays using acoustic mist ionisation mass spectrometry. Analyst. 2021;146(1):315–321. doi: 10.1039/D0AN01519A
  • Kassel DB. Applications of high-throughput ADME in drug discovery. Curr Opin Chem Biol. 2004;8(3):339–345. doi: 10.1016/j.cbpa.2004.04.015
  • Song XS, Zhang J, Chen X, et al. Identification of DGAT2 inhibitors using mass spectrometry. J Biomol Screen. 2016;21(2):117–126. doi: 10.1177/1087057115607463
  • Jemal M. High‐throughput quantitative bioanalysis by LC/MS/MS. Biomed Chromatogr. 2000;14(6):422–429. doi: 10.1002/1099-0801(200010)14:6<422:AID-BMC25>3.0.CO;2-I
  • Zhang J-H, Chung TD, Oldenburg KR. A simple statistical parameter for use in evaluation and validation of high throughput screening assays. J Biomol Screen. 1999;4(2):67–73. doi: 10.1177/108705719900400206
  • Pu F, Radosevich AJ, Bruckner BG, et al. New platform for label-free, proximal cellular pharmacodynamic assays: identification of glutaminase inhibitors using infrared matrix-assisted laser desorption electrospray ionization mass spectrometry. ACS Chem Biol. 2023;18(4):942–948. doi: 10.1021/acschembio.3c00087
  • Boike L, Henning NJ, Nomura DK. Advances in covalent drug discovery. Nat Rev Drug Discov. 2022 Dec 01;21(12):881–898. doi: 10.1038/s41573-022-00542-z
  • Campuzano ID, San Miguel T, Rowe T, et al. High-throughput mass spectrometric analysis of covalent protein-inhibitor adducts for the discovery of irreversible inhibitors: a complete workflow. J Biomol Screen. 2016 Feb;21(2):136–144. doi: 10.1177/1087057115621288
  • Shin Y, Jeong JW, Wurz RP, et al. Discovery of N-(1-acryloylazetidin-3-yl)-2-(1H-indol-1-yl)acetamides as covalent inhibitors of KRAS(G12C). ACS Med Chem Lett. 2019 Sep;10(9):1302–1308. doi: 10.1021/acsmedchemlett.9b00258
  • Covey TR, Schneider BB, Javaheri H, et al. ESI, APCI, and MALDI A comparison of the central analytical figures of merit: sensitivity, reproducibility, and speed. In: Core BB, editor. Electrospray and MALDI Mass Spectrometry: Fundamentals, Instrumentation, Practicalities, and Biological Applications. Hoboken, New Jersey: Wiley; 2010.
  • Zhang K, Lin J, Lieu R, et al. High-throughput experimentation: where does mass spectrometry fit? 2019.
  • Ginsburg-Moraff C, Grob J, Chin K, et al. Integrated and automated high-throughput purification of libraries on microscale. SLAS Technol. 2022;27(6):350–360. doi: 10.1016/j.slast.2022.08.002
  • Logsdon DL, Li Y, Paschoal Sobreira TJ, et al. High-throughput screening of reductive amination reactions using desorption electrospray ionization mass spectrometry. Org Process Res Dev. 2020;24(9):1647–1657. doi: 10.1021/acs.oprd.0c00230
  • Sun AC, Steyer DJ, Allen AR, et al. A droplet microfluidic platform for high-throughput photochemical reaction discovery. Nat Commun. 2020;11(1):6202. doi: 10.1038/s41467-020-19926-z
  • Grainger R, Whibley S. A perspective on the analytical challenges encountered in high-throughput experimentation. Org Process Res Dev. 2021;25(3):354–364. doi: 10.1021/acs.oprd.0c00463
  • What’s new with chrom reaction optimization 1.1 2023. Available from: https://resources.mestrelab.com/whats-new-with-chrom-reaction-optimization-1-1/
  • Simon RP, Winter M, Kleiner C, et al. MALDI-TOF-based affinity selection mass spectrometry for automated screening of protein–ligand interactions at high throughput. SLAS Discov. 2021;26(1):44–57. doi: 10.1177/2472555220959266
  • Annis DA, Athanasopoulos J, Curran PJ, et al. An affinity selection–mass spectrometry method for the identification of small molecule ligands from self-encoded combinatorial libraries: Discovery of a novel antagonist of E. coli dihydrofolate reductase. Int J Mass Spectrom. 2004;238(2):77–83. doi: 10.1016/S1387-3806(04)00335-5
  • Flusberg DA, Rizvi NF, Kutilek V, et al. Identification of G-quadruplex-binding inhibitors of Myc expression through affinity selection–mass spectrometry. SLAS Discov. 2019;24(2):142–157. doi: 10.1177/2472555218796656
  • Rizvi NF, Santa Maria JP Jr, Nahvi A, et al. Targeting RNA with small molecules: identification of selective, RNA-binding small molecules occupying drug-like chemical space. SLAS Discov. 2020;25(4):384–396. doi: 10.1177/2472555219885373
  • O’Connell TN, Ramsay J, Rieth SF, et al. Solution-based indirect affinity selection mass spectrometry – a general tool for high-throughput screening of pharmaceutical compound libraries. Anal Chem. 2014 Aug 5;86(15):7413–7420. doi: 10.1021/ac500938y
  • Comess KM, Schurdak ME, Voorbach MJ, et al. An ultraefficient affinity-based high-throughout screening process: application to bacterial cell wall biosynthesis enzyme MurF. J Biomol Screen. 2006 Oct;11(7):743–754. doi: 10.1177/1087057106289971
  • Thomas O’Connell WH, Hui Zhang. Affinity selection mass spectrometry for Hit ID and early hit expansion. Pittsburg Conference; 2019.
  • Xu LL, Young A, Zhou A, et al. Machine learning in mass spectrometric analysis of DIA data. Proteomics. 2020;20(21–22):1900352. doi: 10.1002/pmic.201900352
  • Bilbao A, Munoz N, Kim J, et al. PeakDecoder enables machine learning-based metabolite annotation and accurate profiling in multidimensional mass spectrometry measurements. Nat Commun. 2023;14(1):2461. doi: 10.1038/s41467-023-37031-9
  • Eyke NS, Koscher BA, Jensen KF. Toward machine learning-enhanced high-throughput experimentation. Trend Chem. 2021;3(2):120–132. doi: 10.1016/j.trechm.2020.12.001

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