lcms-v2.yaml

files:
  -
    pattern: extras\/.*
    required: True
    description: Folder for general lab-specific files related to the dataset.
  -
    pattern: extras\/mass-spec_environment\.(?:json|tsv)
    required: False
    description: 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.
  -
    pattern: raw\/.*
    required: True
    description: Raw data files for the experiment.
  -
    pattern: raw\/[^\/]+\.raw
    required: True
    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.
    example: raw/20200707_rmi049_75umPLRPS_Kidney_GF10pc_VAN0003LK32_biorep05_techrep02.raw
  -
    pattern: raw\/[^\/]+\.(?:mzML|d)
    required: True
    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.
  -
    pattern: lab_processed\/.*
    required: True
    description: Lab processed files
  -
    pattern: lab_processed\/ID_search_results\/.*
    required: True
    description: Identification results.
  -
    pattern: lab_processed\/ID_search_results\/[^\/]+\.csv
    required: True
    description: 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.
  -
    pattern: lab_processed\/ID_metadata\/.*
    required: True
    description: Identification search parameters/metadata.
  -
    pattern: lab_processed\/ID_metadata\/[^\/]+\.csv
    required: True
    description: Software settings used during the analyte identification process (e.g., from MaxQuant or Proteome Discoverer).
  -
    pattern: lab_processed\/QC_results\/.*
    required: False
    description: Output file resulting from QC analysis.
  -
    pattern: lab_processed\/QC_results\/[^\/]+\.txt
    required: False
    description: A list of metrics with the score of the current dataset that shows the quality of data collection.
  -
    pattern: raw\/RNA\/.*
    required: True
    description: Directory containing fastq files pertaining to RNAseq sequencing.
  -
    pattern: raw\/RNA\/[^\/]+_R\.fastq\.gz
    required: True
    description: This is a GZip'd version of the forward and reverse fastq files from RNAseq sequencing (R1 and R2).