lcms-v0.yaml

files:
  -
    example: 'raw_data/20200707_rmi049_75umPLRPS_Kidney_GF10pc_VAN0003LK32_biorep05_techrep02.raw'
    pattern: 'raw_data/[^/]+\.(raw|mzML|d)'
    description: '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.'
    required: True
  -
    pattern: 'ID_search_results/[^/]+\.(txt|csv)'
    description: 'Identification results. Annotated data describing (qualitative or quantitative) the proteins, metabolites, lipids, peptides, phosphopeptides, or glycans identified from the corresponding raw data.'
    required: True
  -
    pattern: 'ID_metadata/[^/]+\.(csv|tsv|txt|xml)'
    description: 'Identification search parameters/metadata. Software settings used during the analyte identification process (e.g., from MaxQuant or Proteome Discoverer).'
    required: True
  -
    pattern: 'QC_results/[^/]+\.(xml|txt|html|pdf|log|yaml)'
    description: 'Output file resulting from QC analysis. A list of metrics with the score of the current dataset that shows the quality of data collection.'
    required: False
  -
    pattern: extras\/.*
    required: False
    description: Folder for general lab-specific files related to the dataset. [Exists in all assays]