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Accelerate Proteomics Research with Smart Automation

Written by | Published: 09.04.2025

Thermo Fisher’s Proteomics Software Solution streamlines complex proteomics workflows through automation, integrating data acquisition, analysis, and secure management. Combining Thermo Scientific Proteome Discoverer and Thermo Scientific Ardia Platform, it enables real-time processing, remote access, and flexible tool integration, reducing manual tasks, accelerating insights, and supporting high-throughput, collaborative research.

Proteomics software solution

Smart automation

Proteomics workflows generate large, complex datasets that require precision at every step—from sample preparation through LC-MS acquisition and data processing. As sample numbers rise and analytical depth increases, manual handling can introduce variability and consume valuable research time. Smart automation provides a way to simplify routine tasks, maintain reproducibility, and support high-throughput studies while giving researchers more time to focus on interpretation and discovery.

Ardia proteomics process: data collection through data processing

Frequently Asked Questions

The proteomics software solution is an integrated platform combining powerful mass spectrometry data analysis using the Thermo Scientific Proteome Discoverer software with centralized data management and processing by way of the Ardia Platform to automate data acquisition, analysis, and secure storage in a centralized, connected environment.

Yes. The solution allows real-time remote monitoring of data acquisition and processing, enabling collaboration and quick issue resolution without needing to be physically present.

  • The solution includes tools like TMT (Tandem Mass Tag) quantification, cross-linking analysis, and AI-powered algorithms such as CHIMERYS and INFERYS, supporting flexible, high-throughput proteomics workflows.

  • It centralizes data storage with automated backups and archiving, reducing the risk of data loss and ensuring secure, controlled access for collaboration without moving files outside your organization.

  • Yes. It’s designed as an open platform that supports multiple instruments and integrates with third-party software, allowing flexible workflows and easy data sharing across applications.

Smart Automation vs. Manual Approach

Workflow
Component

Manual Approach

Automated Approach

Data management

Fragmented storage; manual file movement

Centralized, automated, secure data transfer and processing

Data processing

Bottlenecks in multiplexed studies

Injection’s processing can begin immediately after acquisition

Operator access

Physical presence required

Remote monitoring of data processing and acquisition

High-throughput LC-MS Workflow Automation

High-throughput proteomics requires tightly coordinated acquisition and data processing. Automated LC-MS workflows streamline these activities by enabling continuous sample queues, standardized instrument methods, and automated data routing for processing. When used with software environments that manage both acquisition and analysis, automated LC-MS setups help keep high-volume studies moving without manual intervention between runs.

In high-throughput settings, automation supports:

  • Immediate processing of each injection as soon as data acquisition finishes
  • Reduced downtime between LC-MS runs
  • Support for multiplexed or large-cohort study designs
  • Centralized storage and compute resources for efficient data handling
  • Remote access for monitoring and collaboration

The future of proteomics is connected and automated.
The proteomics software solution brings automation, integration, and security together to streamline workflows, accelerate insights, and empower scalable, collaborative proteomics research.

Additional Resources

See what’s possible – Explore the Proteomics Software Solution or watch our recent webinar-Facilitating High-Throughput, Large Cohort Proteomic Analyses Using an Integrated Software Solution, to learn more

Visit us on LinkedIn: #Proteomics #ProteomicsSoftwareSolution #ArdiaPlatform #Automation

Written by:

Zoe Julian

Product Marketing Manager, Chromatography Software, Thermo Fisher Scientific

Zoe Julian is a Marketing Manager in the chromatography and mass spectrometry software division at Thermo Fisher Scientific. With over 12 years of experience in analytical science and scientific software, as well as professional experience in digital marketing, she creates customer-focused content that helps laboratories solve challenges, improve productivity, and streamline workflows. Her background in GC and GC-MS/(MS) organic environmental analysis gives her a practical understanding of the needs of scientists today.

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