Compound Management: From Storage to Assay-Ready Plates in One Integrated Workflow

Every screening decision depends on the quality of the compounds being tested. SPT Labtech helps drug discovery teams preserve compound integrity, maximize recovery from valuable compound libraries, and maintain complete traceability throughout the compound lifecycle.

<0.3 µL

Dead volume: mosquito® maximizes recovery from precious compound stocks

6 sec

Cherry-pick cycle time with mosquito® X1

-20°C

Sealed storage: comPOUND® protects compound integrity under dry air/N₂

150 racks

Unattended processing with comSTACKER 2

OVERVIEW

What is Compound Management?

What is Compound Management?

Compound management is the process of maintaining chemical libraries and preparing compounds for drug discovery screening. It encompasses the entire lifecycle of a screening library, from long-term storage of compounds (typically in DMSO at -20ºC under an inert atmosphere) through tracking, retrieval, transfer, dilution, and assay preparation. The goal is to ensure that every compound is delivered to an experiment with its identity, concentration, and integrity preserved.

Because screening data is only as reliable as the compounds being tested, effective compound management is critical throughout drug discovery. Degradation, concentration errors, sample loss, and cross-contamination can compromise results and lead to incorrect decisions downstream.

Building a connected compound management workflow

As compound collections grow and screening operations become increasingly distributed, manual handoffs between storage, sample handling, and assay preparation can create bottlenecks, increase risk, and reduce efficiency. SPT Labtech combines automated storage (comPACT and comPOUND), automated sample transfer (connect), and nanoliter liquid handling (mosquito) into a single integrated workflow. Together, these technologies help scientists move compounds efficiently from storage to screening while preserving integrity, maximizing recovery, and maintaining complete traceability.

COMPOUND MANAGEMENT WORKFLOW

1
Compound Storage
Sealed at -20°C
comPOUND
2
Retrieval
Automated Pneumatic picking
comPOUND
3
Transfer
To liquid handling
connect
4
Hit Confirmation and Characterization
Reformat, dilute, dispense, replicate
mosquito
5
Hit Picking
Cherry-pick confirmed hits
mosquito X1

FEATURED PLATFORMS

Three Instruments, One Integrated Compound Management Solution

comPOUND product card
comPOUND®
Storage & Retrieval

Modular automated compound storage at -20°C to ambient. Hermetically sealed chamber under dry air or nitrogen. Pneumatic cherry-picking for fast individual vial retrieval. Scalable modular design - expand capacity without replacing the system.

Typical applications
Sample Management
Key Specifications
  • -20°C to ambient
  • Sealed chamber
  • Pneumatic picking
  • Modular & scalable
  • comSTACKER 2
Mosquito LV product card
mosquito®
Nanoliter Liquid Handling

Designed for compound management workflows, mosquito instruments deliver precise nanoliter transfers with minimal sample loss and zero carry-over between compounds.

Typical applications
Miniaturized screening workflows Dose-response studies Cherry-picking Medicinal Chemistry
Key Specifications
  • 25 nL – 5 µL (LV) or 500 nL - 5 µL (HV)
  • Multi- or single-channel
  • 100% DMSO-compatible
  • Dead volumes as low as 0.3 µL
  • Rapid plate reformatting across 96-, 384- and 1,536-well formats
  • Cherry-picking in 6 seconds per compound
connect product card(1)
connect
Sample Transfer Network

Automated sample and data transfer network connecting storage systems, liquid handlers, and analytical instruments. Eliminates manual sample transport between instruments. Tracks every sample through the compound management workflow with full provenance data.

Typical applications
Sample Transport
Key Specifications
  • Instrument integration
  • Full sample tracking
  • Automated transport

Hear from comPOUND users

comPOUND for us invaluable, as we demand a quick reliable service. we get walk away time added by having compound either store or pick vials. These are all ready for the end user, so are kept at the perfect storage temperature. we also get 100% accuracy, which cannot get replicated with human use.

MR Glen - Abcam PLC

comPOUND user(5)

We've been using comPOUND for almost 5 years, and the high-density storage and rapid retrieval system are game changers for our lab. The customer service has always been fantastic. They were responsive and helpful throughout the setup process and continue to provide excellent support whenever needed. Highly recommend this product!

Ratnadeep Bhattacharjee - Corteva Agriscience

comPOUND user(6)

This equipment is very effective for compound management. The original purchase of two modules was expanded to 3 then 4 in a seamless manner. A D2 variant of the store was added some time later for a different sample set. The modularity and scalability of the kit was necessary for a small-medium compound management facility like ours.

David Camp - Griffith University

comPOUND user(5)

REAL-WORLD IMPLEMENTATION

Lundbeck: Integrated Compound Management at Pharmaceutical Scale

Lundbeck, a global pharmaceutical company specializing in brain diseases, implemented SPT Labtech's complete compound management solution to support their drug discovery screening operations.

Lundbeck's compounds are stored in multiple linked -20°C comPOUND repositories, with access to these compounds managed using SPT Labtech's connect system. Compounds are transferred to screening-ready plates using mosquito LV. The implementation delivered significant operational improvements: processes are better defined, compounds are now in frozen storage in dry DMSO, vial cherry-picking is 10-fold faster than the previous manual process, and minimal sample volumes are available for all internal customers.

The entire screening community at Lundbeck has access to mother/working plates in a screening-ready format, with the ability to rapidly process compound requests. Complete sample traceability is maintained through the comPOUND database and connect system, providing visibility of storage format, volume, location, transaction history, and freeze-thaw cycles for every sample.

10×
Faster compound retrieval vs previous manual process
150
Racks of tubes processed unattended
<0.3 µL
Dead volume - mosquito maximizes compound recovery
Full tracking
Every sample: format, volume, location, freeze-thaw history

Watch our interview with Ludovic Otterbein, Head of Sample Management at Lundbeck:

Explore the evolution of comPOUND over 25 years

From the first demonstration to the public in 1999, all the way to how it is today. Explore the interactive timeline of comPOUND with us as we dive into its evolution from a disruptive technology to an industry standard sample management solution.

 

compound timeline post-landscape (1)

 

KEY CHALLENGES

Why Compound Management Demands Integrated Automation

Compound integrity during storage
Compound integrity during storage

Compounds in DMSO degrade through moisture absorption, oxidation, and repeated freeze-thaw cycles. comPOUND stores individual vials in a hermetically sealed, temperature-controlled chamber under dry air or nitrogen, minimizing degradation mechanisms and preserving compound integrity for years. Individual vial retrieval means only the needed compound is exposed - the rest of the library stays sealed. 

Precious compound conservation
Precious compound conservation

Compounds are expensive and often available only in limited quantities. Every microliter lost to dead volume is material that cannot be screened or progressed. With dead volumes as low as 0.3 µL per well, the lowest available in any compound management liquid handler, mosquito maximizes recovery from valuable compound stocks while supporting nanoliter-scale transfers for dilution series generation and assay-ready plate preparation. A full dose-response dilution curve can be prepared from less than 1 µL of stock compound. 

Cross-contamination in compound transfers
Cross-contamination in compound transfers

A single compound contaminant at nanoliter scale can generate false positives in sensitive screening assay. mosquito uses disposable micropipettes with individual pistons for every transfer, eliminating carry-over risk between samples. This is not a wash-and-reuse approach, It is a guaranteed-new-tip approach for every compound contact. 

Turnaround time for screening requests
Turnaround time for screening requests

Screening teams need assay-ready plates within hours, not days. Manual compound retrieval, reformatting, and dilution create bottlenecks that delay screening campaigns. The comPOUND + connect + mosquito workflow automates the entire path from compound library to screening plate, with comSTACKER 2 enabling walkaway operation for up to 150 racks without manual intervention. 

Sample tracking and provenance
Sample tracking and provenance

Regulatory and scientific rigor require complete tracking of every compound: what was stored, when, at what concentration, how many freeze-thaw cycles, where it went, and what was done with it. comPOUND's database and connect's transfer tracking provide full sample provenance, from initial receipt through every storage, retrieval, and liquid handling event. 

Scaling compound libraries
Scaling compound libraries

As compound libraries grow from thousands to hundreds of thousands of entries, manual management becomes impossible. comPOUND's modular architecture allows capacity to scale up without replacing the system, simply add modules. mosquito complements this scalability by delivering consistent low-volume dispensing performance across screening workflows of any scale, from small studies to campaigns supporting libraries of 500,000+ compounds.

WORKFLOW AUTOMATION

How comPOUND, mosquito & connect Map to Each Compound Management Step

Workflow Stage Task SPT Labtech Product Key Capability
Compound Storage Long-term storage of compound library vials at -20°C under dry/inert atmosphere  Hermetically sealed chamber; individual vial storage; dry air or nitrogen; -20°C to ambient; scalable modular design
Cherry-Pick Retrieval Retrieving specific vials from the compound library on demand  Pneumatic cherry-picking; fast individual vial access without disturbing the rest of the library; full tracking 
Sample Transfer Moving retrieved compounds from storage to liquid handling instruments  Automated sample and data transfer network; eliminates manual transport; full provenance tracking at every step 
Hit Confirmation and Characterization Compound pick-up, plate reformatting, serial dilutions and assay-ready plate preparation

 

DMSO-compatible nanoliter pipetting; ultra-low dead volumes; rapid plate replication
Hit Picking Cherry-picking confirmed hits for follow-up screening, profiling, and optimization Programmable single-channel access to any well in any plate; rapid pick cycle; CSV Worklists; Cherry Picker II integration 

FREQUENTLY ASKED QUESTIONS

Compound Management with SPT Labtech: Common Questions

Compound management is the systematic storage, tracking, retrieval, and liquid handling of chemical compound libraries for drug discovery. As compound libraries grow in size and screening demands increase, laboratories face increasing operational complexity. Manual processes can introduce compound degradation, cross-contamination, volume inaccuracies, and tracking gaps that affect both data quality and efficiency. SPT Labtech's integrated solution: comPOUND for storage and retrieval, mosquito for miniaturised assay setup, and connect for sample transfer and tracking, addresses these challenges through a connected, automated workflow. This ensures compounds are available in the right format, at the right time, for screening and characterization studies.

comPOUND is SPT Labtech's modular automated compound storage and retrieval system. It stores individual vials in a hermetically sealed chamber under dry air or nitrogen atmosphere, protecting compounds from moisture absorption, oxidation, and degradation. A unique high-density carousel architecture maximizes storage capacity, while pneumatic cherry-picking retrieves individual vials without disturbing the rest of the library. The modular design allows storage capacity to be expanded incrementally by adding modules rather than replacing the system. Accessories include comSTACKER 2 for unattended processing of up to 150 racks, and connect for remote storage, retrieval, and tracking of 2D barcoded tubes across up to 4 linked comPOUND systems.

All mosquito instruments use positive displacement pipetting, enabling DMSO compound stocks to be transferred with the same accuracy and precision as aqueous solutions, without the need to create or optimize liquid classes. Each disposable micropipette contains its own piston in direct contact with the liquid, eliminating the effects of viscosity, surface tension, and vapor pressure that can impact air-displacement systems. Compounds are transferred directly from standard source plates, avoiding the specialized labware required by acoustic or pressure-driven dispensers. Disposable micropipettes also eliminate carry-over between compounds, helping maintain data quality throughout screening workflows.

When compounds are available only in small quantities, the ability to generate high-quality data depends on minimizing source volume requirements and transfer losses while maximizing the number of experiments that can be performed from each stock. mosquito can generate serial dilutions, dose-response curves, and assay-ready plates directly from source wells containing less than 1 µL of compound stock. Support for assay miniaturization in 384- and 1,536-well formats further reduces compound consumption while increasing throughput, enabling more screening data, concentration points, and follow-up studies to be generated from the same amount of material.

Complete sample provenance requires every storage, retrieval, transfer, and liquid handling event to be recorded and linked throughout the workflow. SPT Labtech combines comPOUND for compound storage and retrieval with connect for sample and data transfer, creating a continuous record of compound identity, location, volume, storage conditions, and transaction history. This enables laboratories to track every compound from long-term storage through downstream screening workflows, supporting regulatory compliance, reproducibility, and informed decision-making.

Compound management provides the foundation for reliable hit validation and characterization studies. Compounds must be stored, retrieved, prepared, and tested with their identity, concentration, and integrity preserved. Poor storage conditions, concentration errors, sample loss, or cross-contamination can compromise potency measurements and lead prioritization decisions. Automated storage and retrieval systems such as comPOUND, combined with reproducible low-volume assay preparation, help ensure that dose-response and characterization data reflect true biological activity while maximizing the value of limited compound stocks.

Turnaround time is often limited by handoffs between storage, transfer, and liquid handling systems. Integrating these steps into a single workflow reduces manual intervention and helps compounds move efficiently from storage to screening format. In an SPT Labtech workflow, comPOUND automates compound storage and retrieval, connect manages sample and data transfer, and mosquito supports miniaturized screening workflows, from compound selection and dose-response studies to assay preparation. By eliminating workflow bottlenecks and manual transfers, screening-ready plates can be generated more quickly and consistently.

Lundbeck, a global pharmaceutical company focused on brain diseases, implemented SPT Labtech's complete compound management solution. Compounds are stored in multiple linked comPOUND repositories at -20°C, with access and workflow coordination managed through connect. mosquito X1 enables rapid compound cherry-picking, while mosquito LV supports low-volume assay preparation. The implementation delivered full compound integrity protection through frozen dry DMSO storage, reproducible and well-defined processes, 10-fold faster compound retrieval compared with the previous manual process, minimal compound consumption, and complete transaction tracking for every compound.

Yes. Whether managing a few thousand compounds or an enterprise-scale collection, the integrated platform grows with your needs while preserving workflow continuity and sample traceability. Laboratories can start with comPACT for smaller collections and follow a clear upgrade path to the modular comPOUND platform as storage requirements increase. connect accommodates additional storage and liquid handling systems as throughput demands grow, while mosquito provides a flexible platform for miniaturized screening workflows that scale seamlessly from small studies to large screening campaigns without changes to methods or instrumentation.

References


  1. Developing and Embedding In-House Compound Management within Artios. https://go.sptlabtech.com/slas-2025-artios-poster 
  2. Miniaturized serial dilution of compounds: essential for ultrahigh throughput screening (uHTS) drug discovery. https://go.sptlabtech.com/miniaturized-serial-dilution-of-compounds 
  3. Drug Discovery World. Compound Storage Evolution: Unlocking the Right Combination (SPT Labtech case study). https://www.ddw-online.com/media/32/winter-2007-compound-storage.pdf 
  4. SelectScience - comPOUND Product Reviews: modular -20°C compound storage and retrieval. https://www.selectscience.net/product/compound
  5. Larson JE, Hardy PB, Schomburg NK, et al. Development of a high-throughput TR-FRET screening assay for a fast-cycling KRAS mutant. SLAS Discovery. 2023 Jan 1; 28 (1): 39-47. https://doi.org/10.1016/j.slasd.2022.12.001  
  6. An Y, Lim J, Glavatskikh M, et al. In silico fragment-based discovery of CIB1-directed anti-tumor agents by FRASE-bot. Nature Communications. 2024 Jul 2; 15 (1): 5564. https://doi.org/10.1038/s41467-024-49892-9 

Ready to transform your compound management?

Our compound management specialists can design an integrated solution, from comPOUND storage through mosquito liquid handling, tailored to your library size, throughput, and screening workflow.