Mnova Gears – Affinity Screen (Starting Guide)

Importance of the Topic

The analysis of protein–ligand interactions is fundamental in drug discovery and proteomics. Affinity Selection Mass Spectrometry (AS-MS) enables high-throughput screening of compound libraries, but processing the resulting data involves multiple complex steps. Affinity Screen software automates key stages such as peak detection, assignment, scoring and reporting, significantly reducing analysis time and minimizing human error.

Objectives and Study Overview

This guide presents the workflow for Affinity Screen, detailing installation, data input, processing, plugin configuration, and result visualization. The goal is to enable users to efficiently detect and quantify bound versus unbound ligands in LC-MS experiments, group samples, calculate binding scores, and generate interactive, human-readable reports.

Methodology and Used Instrumentation

Affinity Screen operates within Mnova MSChrom (v≥15.0) and Mnova Gears (v≥2.5) environments. Key steps include:

• Input selection: automatic or manual detection of LC-MS files from disk directories.
• Compound metadata: importing CSV with SMILES, molecular formula or monoisotopic mass to generate extracted ion chromatograms (EICs).
• Processing scripts: optional custom preprocessing.
• Analysis plugin settings: defining role masks (reference, bound, unbound), EIC mass tolerance, peak detection parameters, isotope-based matching options, scoring functions (e.g., bound/unbound ratio), and hit thresholds.
• Quality controls: checks for molecular formula overlaps, multiple peaks, missing or unassigned peaks, and assignment failures with customizable flags.
• Output configuration: saving results as HTML, PDF, Mnova documents and CSV summaries.

Main Results and Discussion

Affinity Screen organizes results in an output folder containing: an HTML summary with key metrics and control charts; PDF and Mnova reports showing per-ligand EIC overlays and structures; and a CSV file with scores, statuses and flags. The Mnova Gears Results Viewer displays well-plate heat maps of hits, matches and ligand counts, and allows interactive review of individual ligand assignments and manual reassignment with on-the-fly recalculation.

Benefits and Practical Applications

Affinity Screen accelerates AS-MS data analysis by automating routine tasks, enhancing reproducibility and consistency. Interactive viewers and customizable reporting facilitate rapid hit triage in drug screening, fragment-based design, and biochemical assay development.

Future Trends and Opportunities

Emerging trends include integration with cloud-based databases for real-time experiment monitoring, advanced machine-learning models for peak deconvolution, and expansion to other affinity-based modalities such as SPR–MS hybrid workflows. Enhanced visualization dashboards and automated prioritization algorithms are expected to further streamline compound selection.

Conclusion

Affinity Screen within the Mnova Gears framework provides a comprehensive, user-friendly solution for AS-MS data analysis. Its robust automation, flexible quality control, and interactive review capabilities support high-throughput hit discovery and improve the efficiency of proteomics research.