Mnova Gears – MS Scan (Starting Guide)

Importance of the Topic

A robust and automated workflow for extracting and quantifying mass spectra and chromatograms from large LC–MS datasets is critical in metabolomics and related fields. Manual processing in vendor software can be time-consuming and error-prone when handling multiple samples or long target mass lists. MS Scan 1.0, as a Mnova Gears plugin, addresses these challenges by streamlining batch processing of total ion current (TIC) files, enabling reliable, high-throughput data extraction and reporting.

Objectives and Study Overview

This document serves as a starting guide for configuring and running the MS Scan plugin within the Mnova Gears environment. It explains the end-to-end workflow—from initial software preferences to result review—aimed at guiding users through:

• Setting up input data sources
• Configuring processing and analysis parameters
• Generating and reviewing automated reports

Applied Instrumentation

The MS Scan workflow leverages the following tools:

• Mnova software (Mestrelab Research) for LC–MS data handling
• Mnova Gears platform for automated scripting and batch execution
• MS Scan 1.0 plugin for mass spectrum extraction and chromatogram quantification
• TIC (total ion current) data files from LC–MS instruments

Methodology

The workflow consists of five main stages:

1. Preferences Setup: Adjust Mnova saving options and mass analysis tolerances to minimize file size and define mass tolerance settings.
2. Input Selection: Point Gears to disk directories or databases and apply file masks to automatically detect relevant LC–MS experiment files.
3. Processing Scripts: Optionally upload custom processing scripts to standardize baseline correction, smoothing, or other preprocessing steps.
4. Plugin Configuration: Define up to three retention‐time windows, set minimum relative abundance and area thresholds, and select output variables (e.g., RT, m/z, relative area, peak height).
5. Design and Output: Choose report templates or scripts and designate output folders for saving CSV, HTML, Mnova, or PDF results.

Main Results and Discussion

Upon execution, MS Scan produces:

• CSV files summarizing each extracted chromatogram peak with columns for m/z, retention time, total relative area, relative area, absolute area, and relative height.
• HTML reports that mirror the CSV content and offer interactive table sorting, column selection, and export options.
• Mnova documents containing the extracted‐ion chromatograms and spectra for visual review.

The batch processing significantly reduces manual intervention and ensures consistent application of thresholds across samples. The HTML viewer allows users to inspect individual peaks, adjust display parameters, and save updates back to the results folder.

Benefits and Practical Applications

This approach offers:

• High-throughput analysis suitable for large metabolomics or QA/QC studies.
• Customizable thresholds and retention-time windows for targeted compound monitoring.
• Integrated reporting formats that facilitate data sharing and regulatory compliance.
• Ease of reprocessing when method parameters need adjustment.

Future Trends and Opportunities

As LC–MS datasets grow in size and complexity, future developments may include:

• Machine-learning algorithms to predict optimal extraction parameters.
• Real-time processing integration during data acquisition.
• Enhanced compatibility with multi-omics data fusion tools.
• Cloud-based deployment for collaborative analysis across laboratories.

Conclusion

MS Scan 1.0 within the Mnova Gears framework provides an efficient, reproducible solution for batch extraction and quantification of mass spectrometric data. By automating key steps and offering versatile reporting options, it streamlines metabolomics workflows and supports large-scale studies.

Reference

No specific literature references were provided in the source document.