Mass Spectrometry
LC-MS
Prepare your metadata based on the latest metadata schema using one of the template files below. See the instructions in the Metadata Validation Workflow document for more information on preparing and validating your metadata.tsv file prior to submission.
Related files:
- 📝 Excel template: For metadata entry.
- 📝 TSV template: Alternative for metadata entry.
Metadata schema
Directory schemas
| pattern | required? | description |
|---|---|---|
extras\/.* |
✓ | Folder for general lab-specific files related to the dataset. |
extras\/mass-spec_environment\.(?:json|tsv) |
JSON or TSV file containing the machine parameters/settings. This is akin to the microscope_environment.json file that’s used to describe the imaging equipment. | |
raw\/.* |
✓ | Raw data files for the experiment. |
raw\/[^\/]+\.raw (example: raw/20200707_rmi049_75umPLRPS_Kidney_GF10pc_VAN0003LK32_biorep05_techrep02.raw) |
✓ | Raw mass spectrometry data from an assay of LC-MS, MS, LC-MS Bottom-Up, MS Bottom-Up, LC-MS Top-Down, or MS Top-Down that describes an analyte class of protein, metabolites, lipids, peptides, phosphopeptides, or glycans. |
raw\/[^\/]+\.(?:mzML|d) |
✓ | Raw mass spectrometry data from an assay of LC-MS, MS, LC-MS Bottom-Up, MS Bottom-Up, LC-MS Top-Down, or MS Top-Down that describes an analyte class of protein, metabolites, lipids, peptides, phosphopeptides, or glycans. |
lab_processed\/.* |
✓ | Lab processed files |
lab_processed\/ID_search_results\/.* |
✓ | Identification results. |
lab_processed\/ID_search_results\/[^\/]+\.csv |
✓ | Annotated data describing (qualitative or quantitative) the proteins, metabolites, lipids, peptides, phosphopeptides, or glycans identified from the corresponding raw data. In the case of MS1 this file should include a list of features. |
lab_processed\/ID_metadata\/.* |
✓ | Identification search parameters/metadata. |
lab_processed\/ID_metadata\/[^\/]+\.csv |
✓ | Software settings used during the analyte identification process (e.g., from MaxQuant or Proteome Discoverer). |
lab_processed\/QC_results\/.* |
Output file resulting from QC analysis. | |
lab_processed\/QC_results\/[^\/]+\.txt |
A list of metrics with the score of the current dataset that shows the quality of data collection. |