FBMW with Cytoscape

Introduction to FBMN

The Feature-Based Molecular Networking (FBMN) is a computational method that bridges popular mass spectrometry data processing tools for LC-MS/MS and molecular networking analysis on GNPS. The tools supported are: MZmine2, OpenMS, MS-DIAL, MetaboScape, XCMS, and Progenesis QI.

The main documentation for Feature-Based Molecular Networking can be accessed here:

The documentation for Feature-Based Molecular Networking and Cytoscape is provided below.

Feature-Based Molecular Networking in Cytoscape

Cytoscape is an open source software platform used to visualize, analyze and annotate molecular networks from GNPS. Cytoscape is available for download from here. The instructions were created with Cytoscape 3.7, but should work for subsequent versions.

Shannon, P., et al. (2003). Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res, 13(11), 2498-2504. doi:10.1101/gr.1239303

Downloading Cytoscape Files from GNPS

The first step is to download the input file (.graphML file format) for import into Cytoscape. From the job status page in the Feature-Based Molecular Networking workflow, click on Download Cytoscape Data. Save and unzip the downloaded file.

Unzip the file and the resulting folder will look like this:

Importing Files from GNPS to Cytoscape

To import the network file into Cytoscape: * in Cytoscape click on Import Network from File System and then choose the .graphml file. * Alternatively, you can drag and drop the .graphml file into Cytoscape.

The imported network will be displayed in the main window. In the Control Panel (left panel), in the Network tab, rename the network with right-click and select Rename Network.

You can import the table file into Cytoscape, click on Import Table from File System and then choose into the “DB_result” folder the .csv file. Then, click on OK in the opened window.

Rotation of the Network

To rotate the entire molecular network choose the tab Layout and click on Node Layout tool. In the opened window, unclick the box Selected Only to rotate the entire network and move the blue bar to 90. You can also select specific subnetworks and rotate them by clicking the box Selected only.

Table Panel Visualization Data

For advance network visualisation and data analysis, you may click on Table Panel and select node or edge column information (network metadata) to be displayed. For example, in the Node Table, you can select the "Compound_name" (name of the spectral library match), the "parent mass" (precursor ion mass), the "RTconsensus" (retention time for the node), "MZErrorPPM" (ppm error with the spectral library match) and any attributes of interest in your in Node Table (node metadata).

Create a New Style

A style can be created by clicking on Create New Style and a style name can be specified (e.g. "High vs Low Plant Consumer"). The created style can be exported by going in the main menu to File > Export > Styles to File, or a previous style can be imported by clicking on Import > Style From File in the File section.

Edit the Style

Node Styling

Label

In the Control Panel (left panel), go to the Style tab. Within the Node sub-tab, the properties of the node style can be modified. For example, you can choose the precursor mass as node label for the molecular networks [you need to select Passthrough Mapping as the Mapping Type]. Go to Properties to display more style properties.

Size

In order to match the label size to the node size, go into Style panel, at Label Front Size option, select “SumPeakIntensity” or the “number of spectra” (as selected for node size) as Column and Continuous Mapping as _Mapping Typ_e. As described above, begin by setting the value for minimum and maximum node size value with the button Set Min and Max, then choose the same continuous mapping as used for the node size.

Pie charts

If you used a metadata table, the node table will contain group columns for each group specified in the metadata table. The group columns starts with "_GNPSGROUP__" and will consist of the mean (default and recommended) or summed intensity of the ion across the group's samples based on the MS1 feature table (LC-MS peak area). This group columns can be used to visualize groups as pie charts in the network.

To start visualizing pie charts on node for the groups, click on the left box (Def column) for the Image/Chart1 node property. Choose the Charts tab and select the Pie Chart Icon. Now, in the Data sub-tab, select the group columns you are interested in visualizing in the Select Columns box (e.g. "GNPSGROUP: Less_than 5" (low plant consumers) and "GNPSGROUP:More_than_30" (high plant consumers)). Click on Options (below Data) to choose colors for the Groups (groups are numerized based on their position in the Selected Columns box). Click Apply when you are done with your selection.

Edge Styling

Width

To aid in the visualization of individual node relatedness within a cluster, the cosine score is displayed as an edge. The cosine scores define similarity between two MS/MS spectra. Scores ranging from 0 (totally dissimilar) to 1 (identical). The edge thickness can be used to visualize the cosine score value between related nodes. For this we will use the cosine score based continuous mapping for the edge thickness. Go to the Style tab, and the Edge sub-tab. From the Width property drop down menu, select "cosine_score" for the Column and Continuous Mapping for the Mapping Type. Double click on the Continuous Mapping area of the menu to adjust the thickness of the edge. Click OK to apply the setting changes. Optimise the minimum and maximum value for the continuous mapping.

Mining information in the network

Sub-network creation

To separate one or multilple specific desired network(s), press “ctrl” or “command” (windows or MacOS, respectively) at the same time drag the mouse to select the network(s). Then, click on the symbol as shown below. Automatically, the sub-network is created. For going back to the main network, go into the Control Panel, select Network and then choose the main network.

The Cytoscape's toolbar can be used to search nodes or edge metadata (e.g., "shared name"). Note that this feature is very slow, especially with large network. The list of nodes in the Note Table will be updated. You can select nodes of interest, perform right-click for Select nodes and then click on the + magnifier in the main menu to perform a zoom on the selected node.

The Select function

The Select function can be used to create a selection of nodes and/or edges based on their metadata and/or network topology. Go to the Control Panel and click on Select tab. Then, click on the "+" button and choose between column, degree, or topology filter(s) to add different filter properties. The "x" button deletes the corresponding property. For each filter property, various options are provided depending on the column type (numeric column: is, is not, between; for string column: contains and does not contain. Here, we create annotation filter who selects nodes with a spectral library match with 10 ppm maximum error between precursor ions ("MZErrorPPM" from 0 to 10). By default, the filter should be automatically applied to the network, otherwise click on Apply. Below Filter tab, the number of nodes meeting the filter property variables (here 160 nodes) will be selected. These nodes are automatically selected and highlighted in yellow in the network.

Filters are very powerful network analysis tools that can be modified, saved and exported. To rename, remove, create a new filter, or other options, click on the right button beside the Filter list menu. The list of available Filters will appear in the top part of the panel.

For more details and options, follow this link.

Bypass mode for style property

A bypass could be applied on selected nodes and/or edged by going into the Style panel, and clicking on the Byp. _column for the property you want to change such as _Border paint and Border Width. For modifying or removing the bypass property, select the nodes concerned, click right and choose Remove Bypass or set Bypass option.

Drawing structure in nodes

The chemical structures can be visualized in the node using chemViz2 bioinformatics plugin for Cytoscape (http://www.cgl.ucsf.edu/cytoscape/chemViz/). First the chemViz2 plugin has to be installed. To do that, in the main menu, go to Apps tab then open App Manager. In the Install Apps click on chemViz2 and install it by clicking on the Install button. For more information about chemViz2, refer to the information available in the following chemViz2 website link.

Once installed, chemViz2 can be used to display chemical structures on nodes. First, you will have to verify that the chemViz2 is properly parameterized. Select Apps in the main menu, go to Cheminformatics Tools and click on Setting. In Attribute Settings, choose for the SMILES Attribute the node.Smiles value and/or for InCHI Attribute the node.INCHI value. Apply it by clicking on the OK button.

Finally, to draw structures in nodes, return to Apps and Cheminformatics Tools to go to Paint Structures and select on all nodes or on selected nodes. Visualize the results. If needed, create a dedicated style to facilitate structure visualization.

Video Tutorial FBMN and Cytoscape

Our tutorial on running a FBMN analysis on GNPS including a Cytoscape demo.

See our tutorial on using MZmine2 for FBMN analysis of a cohort from the [American Gut Project] (http://humanfoodproject.com/americangut/).

Page contributors

Melissa Esposito (UCSD), Irina Koester (SIO, UCSD), Christian Martin (INDICASAT), Louis Felix Nothias (UCSD).

Contribute to the Documentation

For informations/feature request, please open an "Issue" on the CCMS-UCSD/GNPSDocumentation GitHub repository.
To contribute directly to the GNPS documentation, fork the CCMS-UCSD/GNPSDocumentation repository, and make a "Pull Request".