First, check if there is an existing naming convention of your research community, for example “The Open Biological and Biomedical Ontology (OBO)“.
If there is no such ontology/naming convention you can adopt, you need to define a new one.
Naming conventions should be:
- Descriptive; consider including
- Unique identifier (e.g. project name)
- Conditions (e.g. lab instrument, solvent, temperature etc.)
- Run of experiment (e.g. sequential)
- Date (e.g. in file properties, too)
- Version number (e.g. v1, v1a, v2c)
- Date: stick to one date-format, preferably YYYY-MM-DD (e.g. 2020-01-31)
- Numbers: use the same length for number and if necessary fill up with zeros (e.g. 00123, 03948)
For some best practices see the handout of the MIT Libraries Data Management Services.
Regarding the lab instruments, check if your instrument, software, or other equipment that outputs your data files can be set with a file naming system.
The last step is to document your data organizing structure and your naming convention.
This is typically and ideally done with a data management plan.