Multiple Spectrum Alignment

Multiple Mass Spectral Alignment

MMSA is an interactive web-based tool that improves the interpretability of molecular networks by visualizing the detailed spectral alignment information of a molecular network component. It identifies shared fragment peaks (peak sets) across spectra, providing insights into the structural relationships within molecular families. MMSA’s interface allows users to explore and analyze the global alignment of molecular networks, enabling deeper insights into molecular relationships.

Access the tool here.

MMSA Web Interface Input Options

Task id and component number

Enter a GNPS2 task ID and component number to visualize alignments for a specific molecular network.

USI input

Input line-separated Universal Spectrum Identifiers (USIs) to define a custom molecular network.

MMSA Output

Visualizing the Spectral Alignment

After providing input, click the “Process and Save JSON” button to calculate alignments. Once processed, click “View Alignment” to display the interactive visualization.

Customizations

Users can specify the x-axis and y-axis limits to zoom in and focus on peaks of interest. The order of spectra displayed in the alignment can also be customized based on spectrum scan numbers. Note that changing the order does not affect the calculated spectral alignment.

Peak Sets

The default display is the top 3 largest peak sets highlighted in red, green, and blue.

Highlighted Peak Sets

Click on any peak to view the peaks that are in its set and the alignment information across spectra, including scan number, peak index, precursor m/z, peak m/z, and intensity.

Source Code

View the source code here.