Introduction

Overview

El-MAVEN, our open source LC-MS data processing engine is optimized for isotopomer labeling and untargeted metabolomic profiling experiments. You can view the mass spectra, align chromatograms, perform peak-feature detection and alignment for labeled and unlabeled MS data. FirstView enables you to have a first look at your data using basic visualizations to get preliminary insights.

Scope of the App

• Provides visualizations for both labeled and unlabeled data
• Provides visualizations on both raw and log₂ transformed intensities
• View intensity plot for each metabolite
• View Isotope plot for each metabolite in case of labeled data
• View heat map for the entire dataset

Figure 1. FirstView

Getting Started

User Input

There are two ways to upload files to FirstView:

El-MAVEN FirstView interface

It allows you to directly push El-MAVEN output to FirstView as shown in Figure 2.

Figure 2. El-MAVEN FirstView Interface

Application upload interface

To use FirstView from Polly, you only require the El-MAVEN Output file:

Figure 3. El-MAVEN Output FIle

Steps in data processing

• Upload data to FirstView
• Visualize the intensity plot for each metabolite
• Visualize the isotope plot for each metabolite
• Visualize the heat map for the entire dataset

Caveats

• The El-MAVEN output should be generated using a compound database
• For labeled data, the intensities in the Isotope Plot are NOT corrected for natural abundance
• Log₂ Transformation does not change the Isotope Plot
• For unlabeled data, the Isotope Plot section will be blank

Tutorial

Upload files

El-MAVEN FirstView Interface

Once you have derived a peak table containing the list of metabolites. You can click on the Polly Icon at the Menu Bar to export the data directly to PollyTM FirstView. Provide your Polly login credentials and a window will pop-up which allows you to select the peak table to be uploaded to FirstView. You can select the workspace from the list of your existing Polly Workspaces or choose to create a new one from this menu itself and then click on Upload. Once the files are uploaded, click on Go to FirstView and you would be redirected to FirstView.

Figure 4. El-MAVEN FirstView Interface

Application upload interface

Alternatively, select FirstView from the dashboard under the Metabolomics Data Tab.

Figure 5. Polly Dashboard

Create a New Workspace or choose the existing one from the drop down and provide the Name of the Session to be redirected to FirstView's upload page as shown in Figure 6.

Figure 6. Workspace selection

Figure 7. Upload page of FirstView

Upload your intensity file by either clicking on Browse or using the drag and drop functionality.

Visualization

The visualization interface provides the data summary (number of samples, groups and metabolites present in the uploaded data) and normalization on the left side whereas the rest of the interface provides the generated plots.

Intensity Plot

The Intensity Plot displays the intensity values either raw or log₂ transformed, for a given metabolite across all samples. For labeled data, the intensity for all isotopologues are displayed in different colors in stacked bar plots as illustrated in Figure 8. below.

Figure 8. Intensity Plot with raw intensities

Click on the drop down to visualize the intensity for a different metabolite.

Figure 9. Drop down to Intensity Plot with raw intensities

To see a normalized Intensity Plot, select the Log2 Transformed option in Normalization section. The plot would get updated to accommodate the normalized intensities.

Figure 10. Intensity Plot with normalized intensities

Isotope Plot

Click on Isotope Plot option beside Intensity Plot to see a fractional enrichment vs sample plot. The values seen are calculated as:

intensity of parent or isotopologue / sum (intensity of metabolite for a sample)

Figure 11. Isotope Plot with raw intensities

Heat map

Click on Heat map option beside Isotope Plot to open the heat map. Heat map is a graphical representation of data where the individual values contained in a matrix are represented as different colors corresponding to the intensity. Here, the heat map represents intensity value of each metabolite corresponding to the number of samples in the data.

Figure 12. Heat map with raw intensities

You can view this plot with both raw intensities and normalized intensities by choosing the desired normalization option from the left section of the page. Hovering over the plot will display the specific values.

Figure 13. Heat map with normalized intensities