DESI Plate-Based High-Throughput Screening (HTS)

Accelerating drug discovery with ambient ionization mass spectrometry — direct analysis from multiwell plates at sub-second throughput.

DESI Plate-Based HTS (Desorption Electrospray Ionization Mass Spectrometry High-Throughput Screening) is an ambient ionization technique that enables direct, label-free MS analysis of samples directly from standard multiwell plates without chromatographic separation. With demonstrated throughput exceeding one sample per second, DESI plate-based HTS provides an ultra-rapid, cost-effective alternative to conventional LC-MS-based screening for reaction optimization, enzyme activity assays, and label-free bioassay readouts in drug discovery workflows.

At Creative Proteomics, our MassTarget™ DESI Plate-Based HTS platform integrates automated liquid handling, robotic plate positioning, and high-resolution mass spectrometry to deliver high-quality screening data with minimal sample preparation and rapid turnaround.

Key Advantages:

Ultra-high throughput (>1 sample/sec) — direct DESI analysis from 96/384/1536-well plates
No chromatography — eliminates LC separation, reducing run time and solvent consumption
Label-free detection — no fluorescent tags, no reporter assays, no immobilisation
Ambient ionization — analysis under open-air conditions, compatible with native assay buffers
Minimal sample preparation — direct analysis from reaction mixtures without workup

Submit Your DESI HTS Project View sample requirements

DESI plate-based high-throughput screening platform featuring DESI ionization spray from multiwell plate to mass spectrometer inlet for direct analysis.

What Is DESI Plate-Based HTS How It Works Applications Technology Comparison Sample Deliverables FAQ

What Is DESI Plate-Based HTS?

Desorption Electrospray Ionization (DESI) is an ambient ionization technique introduced by Cooks and colleagues at Purdue University. In DESI, a fine spray of charged solvent droplets is directed at a sample surface, where the impact desorbs and ionizes analytes, which are then transferred into the mass spectrometer inlet for detection. When coupled with automated plate positioning, DESI enables direct analysis of samples in multiwell plates — a configuration we call DESI Plate-Based HTS.

Unlike conventional LC-MS-based screening, which requires minutes per sample for chromatographic separation, DESI plate-based HTS analyzes each sample in less than one second directly from the assay plate. The technique is label-free, operates under ambient conditions, and requires no sample derivatisation, matrix application, or SPE cartridge consumables. These characteristics make it particularly attractive for high-throughput applications where speed and simplicity are critical.

DESI plate-based HTS has been successfully applied to a broad range of drug discovery workflows, including reaction screening and optimization, enzyme activity assays and inhibition studies, label-free binding detection, and direct-to-biology screening of unpurified synthetic mixtures. For complementary approaches, we also offer RapidFire MS and MALDI-TOF HTS as part of our integrated HT-MS screening portfolio.

Key Benefits of DESI Plate-Based HTS

Sub-second throughput

Each sample is analyzed in under one second directly from the multiwell plate, enabling screening campaigns of thousands of samples per day without LC bottlenecks.

Zero consumable cost

No SPE cartridges, no LC columns, no matrix, no derivatisation reagents — the only consumable is the spray solvent, making per-sample cost extremely low.

Native assay conditions

DESI operates under ambient, open-air conditions and is compatible with native assay buffers, preserving enzyme activity and native binding interactions.

Broad analyte compatibility

Small molecules, peptides, lipids, natural products, and reaction intermediates can all be detected directly from the assay plate without method re-optimization.

How DESI Plate-Based HTS Works

Our DESI plate-based HTS workflow follows a streamlined, automated process designed to minimize hands-on time and maximize data quality.

Sample Plate Preparation

Samples are prepared in standard multiwell plates (96, 384, or 1536-well format) using automated liquid handling. No special sample preparation or matrix application is required.

Automated Plate Loading

The prepared plate is loaded onto the DESI stage with robotic XY positioning for precise well-to-well movement. Plate alignment and calibration are performed automatically.

DESI Ionization and MS Detection

Charged solvent droplets are directed at each well, desorbing and ionising analytes in under one second per well. Ions are transferred into the mass spectrometer for high-resolution analysis.

Data Processing and Hit Calling

Raw mass spectra are processed using automated peak detection and alignment. Hits are identified based on predefined criteria and compiled into ranked hit lists.

Deliverables

We provide a comprehensive data package including raw mass spectra, processed peak lists, hit ranking tables, and optional custom data visualizations.

Key Applications of DESI Plate-Based HTS

DESI plate-based HTS is applicable across a broad range of drug discovery workflows, from early reaction screening to downstream binding validation.

Reaction Screening and Optimization

Rapid evaluation of reaction conditions — solvent, temperature, catalyst, stoichiometry — directly from the multiwell plate without workup. Ideal for accelerating SAR studies, late-stage functionalization screening, and route scouting in medicinal chemistry.

Enzyme Activity Assays and Inhibition Studies

Label-free enzyme assays using DESI-MS for cytochrome P450s, kinases, proteases, and transferases. Direct MS readout provides substrate consumption and product formation kinetics without fluorogenic substrates. IC50 determination and inhibition mode analysis supported.

Label-Free Binding and Bioassay Readouts

Detect non-covalent binding events directly from the assay matrix, complementing established affinity selection methods. Particularly advantageous for targets where functional assays are unavailable or label-dependent artefacts are a concern.

Direct-to-Biology Screening

Crude reaction mixtures analyzed directly without purification, enabling ultra-rapid triage of synthetic products. Eliminates purification bottlenecks and reduces cycle time from synthesis to screening data.

DESI Plate-Based HTS vs. Alternative HT-MS Technologies

Technology	Core Principle	Throughput	Sample Prep	Best For
DESI Plate-Based HTS	Ambient ionization from multiwell plates	>1 sample/sec	Minimal (none required)	Reaction screening, enzyme assays, label-free bioassays
RapidFire 400 (Agilent)	Online SPE-MS with autosampler	~10-15 sec/sample	Minimal	Quantitative analysis, ADME screening, PK
Acoustic Ejection MS (Sciex Echo MS)	Acoustic droplet ejection + ESI	~1 sample/sec	Minimal	High-throughput label-free screening
MALDI-TOF	Laser desorption from matrix co-crystals	~1 sample/sec	Matrix application required	High-mass analytes, imaging, peptide screening
Conventional LC-MS	LC separation + ESI-MS	2-10 min/sample	Filtration/centrifugation	Quantitative analysis, complex mixtures, metabolite ID

Sample Requirements

Sample Type	Required Amount	Concentration	Format	Notes
Enzyme Assay Mix	5–50 µL per well	Substrate: 1–100 µM; Enzyme: 0.1–10 nM	96/384/1536-well plate	MS-compatible buffer (no glycerol, low detergent)
Reaction Mixture	5–50 µL per well	Product ≥ 1 µM preferable	96/384/1536-well plate	Analyze directly without workup
Compound Library	1–10 mM stock in DMSO	10–100 µM final assay concentration	96/384/1536-well plate	Solubility check recommended
Binding Assay	10–50 µL per well	Target: 0.1–10 µM; Ligand: 1–100 µM	384/1536-well plate	Native buffer preferred

General Guidelines:

Avoid non-volatile buffers (phosphate, HEPES at high concentration) where possible
Glycerol concentrations should be kept below 5% (v/v)
Detergents (Triton, Tween) should be kept below 0.1% (v/v)
Samples should be free of particulates to avoid spray instability
For enzyme assays, provide substrate K_m and enzyme concentration if available

For detailed sample submission guidance, refer to our comprehensive HT-MS screening service page and sample requirements documentation. Our team consults on plate layout design, including control placement, replicate allocation, and concentration response formatting for IC50 studies. We also support integration with enzyme activity and mechanism studies for downstream hit characterization.

Deliverables

Raw mass spectra for each well position
Processed peak lists with accurate mass identification
Hit ranking table with intensity or binding enrichment metrics
Reaction conversion plots (for enzyme assays)
Optional: IC50 curves, inhibition mode analysis
Custom data visualisation upon request

Representative DESI HTS Demo Data

DESI HTS throughput comparison bar chart showing samples per hour for DESI plate-based HTS versus RapidFire MS, acoustic ejection MS, MALDI-TOF, and conventional LC-MS.

Throughput comparison: DESI HTS vs. alternative HT-MS platforms

FAQ

Frequently Asked Questions

Q: How does DESI plate-based HTS differ from conventional LC-MS screening?

DESI analyzes samples directly from the multiwell plate without LC separation, achieving throughput of more than one sample per second compared to 2–10 minutes per sample for LC-MS. This makes DESI ideal for high-volume screening campaigns where absolute quantitation is not required.

Q: What types of assays are compatible with DESI plate-based HTS?

DESI HTS is compatible with enzyme activity assays, reaction screening and optimization, label-free binding detection, and direct-to-biology screening of crude reaction mixtures. The technique performs best for assays where relative signal changes are sufficient for hit calling.

Q: What throughput can I expect from DESI plate-based HTS?

Our DESI HTS platform achieves throughput exceeding one sample per second, equivalent to more than 3,000 samples per hour. A full 384-well plate can be analyzed in approximately 5–7 minutes.

Q: Do I need special plates for DESI analysis?

DESI HTS can be performed using standard polystyrene or polypropylene multiwell plates (96, 384, or 1536-well). No special surface treatment or conductive coating is required.

Q: Can DESI detect weak or low-abundance signals?

With high-resolution mass spectrometry, DESI HTS can detect analytes at low micromolar to sub-micromolar concentrations, depending on the ionization efficiency of the analyte and the complexity of the sample matrix.

Q: How does DESI plate-based HTS compare with RapidFire or acoustic ejection MS?

All three technologies offer high throughput compared to conventional LC-MS. DESI offers the unique advantages of zero consumable cost, ambient ionization, and compatibility with standard multiwell plates without modification.

References

Shepherd RA, Fihn CA, Tabag AJ, McKinnie SMK, Sanchez LM. 'Need for speed: high throughput' — mass spectrometry approaches for high-throughput directed evolution screening of natural product enzymes. Nat Prod Rep. 2025;42(6):1037-1054. doi:10.1039/d4np00053f. https://doi.org/10.1039/d4np00053f
Zhang W, Chiang S, Li Z, et al. Automated high-throughput system combining small-scale synthesis with bioassays and reaction screening. SLAS Technol. 2021;26(6):607-618. doi:10.1177/24726303211047839. https://doi.org/10.1177/24726303211047839
Ghosh J, Morato NM, Feng Y, Cooks RG. High-throughput drug derivatization and bioassay by desorption electrospray ionization mass spectrometry. ChemPlusChem. 2025;90(6):e202500164. doi:10.1002/cplu.202500164. https://doi.org/10.1002/cplu.202500164
Prudent R, Annis DA, Dandliker PJ, et al. Exploring new targets and chemical space with affinity selection-mass spectrometry. Nat Rev Chem. 2021;5:62-71. doi:10.1038/s41570-020-00229-2. https://www.nature.com/articles/s41570-020-00229-2

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Share your screening objectives and assay requirements — our scientists will design a tailored DESI plate-based HTS strategy for your discovery program.

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For research use only. Not for use in diagnostic procedures. Creative Proteomics provides DESI plate-based HTS services exclusively for research and development purposes. Results are not intended for clinical diagnosis or medical decision-making.

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