templates.rst

SDRF-Proteomics Templates

The sample metadata Templates are a set of guidelines to annotate the different types of proteomics experiments (use cases) to ensure that Minimum Metadata and characteristics are provided to understand the dataset. These templates respond to the distribution and frequency of experiment types in public databases like PRIDE and ProteomeXchange. The Python/Java validators will check the columns checklists depending on the template.

NOTE: It is planned that, unlike in other PSI formats, regular updates will need to be done to be able to explain how new use cases for the format can be accommodated.

• Default proteomics experiment: Minimum information for any proteomics experiment - Default template
• Human experiment: All experiments that use Human samples
• Vertebrates experiment: Vertebrate experiment - Vertebrate template
• Non-vertebrates experiment: Non-vertebrate experiment - Non-vertebrate template
• Plants experiment: Plant experiment - Plant template
• Cell lines experiment: Experiments using cell-lines - Cell lines template

Note

Each of the template is a tsv file with the minimum columns to describe the experiment. The community can create they are own templates for example for meta-proteomics experiments, imaging proteomics or top-down. If the community would like to add a new template, the following table should be modified and the corresponding tsv should be created in this folder.

Sample attributes: Minimum sample attributes for primary cells from different species and cell lines

SDRF-Proteomics templates sample attributes

	Default	Human	Vertebrates	Non-vertebrates	Plants	Cell lines
source name	required	required	required	required	required	required
characteristics[organism]	required	required	required	required	required	required
characteristics[strain/breed]				required
characteristics[ecotype/cultivar]					required
characteristics[ancestry category]		required
characteristics[age]		required	required		required
characteristics[developmental stage]		required	required		required
characteristics[sex]		required	required		required
characteristics[organism part]	required	required	required	required	required	required
characteristics[cell type]	required	required	required	required	required	required
technology type	required	required	required	required	required	required
characteristics[disease]	required	required	required	required	required	required
characteristics[individual]		required
characteristics[biological replicate]	required	required	required	required	required	required
characteristics[cell line]						required
assay name	required	required	required	required	required	required
comment[data file]	required	required	required	required	required	required
comment[technical replicate]	required	required	required	required	required	required
comment[fraction identifier]	required	required	required	required	required	required
comment[label]	required	required	required	required	required	required
comment[instrument]	required	required	required	required	required	required