Create a carbon structure using the arrow keys to add a circle in the direction corresponding to the arrow. Once finished creating your structure click Add to Map to have the diagram appear on the Escher Map. The circles in the diagram can be clicked to indicate label, and can be moved across the Escher Map.
Remove carbon circles by clicking Remove Carbon and then clicking the circle you would like to remove
Add a label to the diagram by inserting text into the the input below and clicking Add Text Label. Click and drag the label to the desired location.
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This fragment contains nonsensical labeling likely due to improper peak integration or natural abundance correction. For assistance, go to section 10. Isotopologue Range Calculator in the Escher-Trace documentation.
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Baseline corrected MS data can be uploaded in CSV format. The proper CSV schema is located here. Additional information about the natural isotope correction in Escher-Trace can be found here.
Natural isotope abundance corrected data uploaded in CSV format. The proper CSV schema is located here
Previously saved workspaces will be in JSON format.
Entering time point information will allow access to kinetic line graphs of enrichment, abundance, and isotopologue labeling in the Escher-Trace menu as well as right-click menu of each graph. Enter a Condition Name and corresponding Time Point for each group. Enter the units of time in the input above the table. Apply changes by clicking Submit Form.
| Group | Condition Name | Time Point |
|---|
Rename a condition by changing the input next to the respective condition name. Apply changes by clicking Submit Form
| Current Condition Name | Updated Condition Name |
|---|
Select your normalizing experimental condition and/or metabolite if applicable, if not select 'N/A.' Enter relevant cell numbers or sample masses, if not applicable enter "1". All entered fields will be used to normalize metabolite abundances. Changes will be reflected in all abundance related graphs. Apply changes by clicking Submit Form. More information about how normalization calculations are performed can be found here.
| Condition to Normalize to: |
|---|
| Metabolite to Normalize to: |
|---|
| Conditions | Cell Number or Sample Mass |
|---|
Click and drag conditions to display to the To Graph list. Multiple conditions can be moved at the same time by first clicking them individually, turning them red, and then dragging them. Order them as you would like them to be displayed then click Submit
Click and drag conditions to display to the To Graph list. Multiple conditions can be moved at the same time by first clicking them individually, turning them red, and then dragging them. Order them as you would like them to be displayed then click Submit.
Data will be averaged across samples within user defined groups. To group samples, enter a group name (for example, (+)Drug) below and click Add Group. A new column heading will appear with the entered title. Samples can be added to groups by clicking and dragging them from File List to the group heading. Multiple samples can be selected simultaneously by clicking them individually, turning them red. After all desired groups and files have been ordered, click Submit Form.
Choose which metabolites will have data displayed on the Escher map by selecting them in the table. Only graphs for selected (checked) metabolites will be visible on the Escher Map. Apply changes by clicking Submit Form.
To limit the isotopologues which are included in all Escher-Trace graphs, select the maximum isotopologue to be displayed for each metabolite. The selected isotopologue limit is also used as the total number of possible labeling positions in the calculation of metabolite enrichments as described here. Apply changes by clicking Submit Form.
| Name | Isotopologue Limit |
|---|
Enter information of labeled standards used to quantify metabolite abundances. Select the isotopologue of the labeled standard and enter its concentration. Metabolite abundances will be quantified by taking the ratio of the unlabeled fraction (M0) over the labeling corresponding to the standard isotopologue and multiplying by the standard concentration. More information can be found here. Apply changes by clicking Submit Form.
| Name | Standard Isotopologue | Standard Concentration |
|---|
Click and drag conditions that will be included in the graph from Condition List to the To Graph list. Multiple conditions can be moved at the same time by first clicking them individually, turning them red, and then dragging them. Order them as you would like them to be displayed.
Select a Metabolite, Fragment, and Data Type you would like to include in the graph and click Add Data add it to the Data List. After all data is entered, click Submit Metabolite Selections to generate the graph.
Select a condition you would like to normalize data to.
Select desired color scheme. Change any scheme by clicking and choosing desired color or entering in a HEX code. Define a new scheme or add new colors to an existing scheme by clicking the adjacent +. Click Submit after you have chosen your color scheme.
Import Escher-Trace Workspace settings from a previously saved workspace JSON by uploading the file below. Select settings to import from the table. Import settings by clicking Submit Form.