my_custom_field present in your Index Pattern? Go to Management -> Index Patterns and select your Index Pattern. Use the "Filter" to locate your field.
If your field is not present, then click the
Refresh field list button to update the Index Pattern from the latest mappings from Elasticsearch.
If your field is present, then where are you using the
Add filter dialog? This filter is populated with the index patterns used in the application or the Default Index Pattern. For example, on Dashboard, it will only contain Index Patterns used by Visualizations loaded in the Dashboard. Try adding an Visualization that contains the Index Pattern with the target field