Parameter file format

mqrun parameter files can be json or yaml formatted. To keep this tutorial easy to read we will only use yaml files. Just replace all yaml file endings by .json and use the standard library json module to load the data if you want to use json instead.

mqrun parameter files must contain the sections rawFiles, fastaFiles and globalParams. The sections topLevelParams (will probably move to globalParams soon) and MSMSParams are optional.

The sections globalParams, topLevelParams, MSMSParams and the params subsection of rawFiles must contain a defaults value. This will set default values for all other parameters in this section. The output of mqrun includes a file with all parameters explicitly set so you can see what values have been used.

Global parameters

This section corresponds to the global tab in the MaxQuant GUI and includes parameters that are not specific to a particular input file. For example

globalParams:
  defaults: default
  equalIl: true
  matchBetweenRuns: true
  fixedModifications:
    - "Carbamidomethyl (C)"

Raw file section

The parameter files do not include paths to raw data, instead each input file is specified by a name and corresponding parameters. When mqrun is called, it expects a mapping from input file names to actual file paths. This way the same configuration can be used for different data sets and on different computers without changing the parameter file.

In theory each input file could use a different set of file specific parameters, but usually a large number of input files share their configuration. Theses groups of input files correspond to the parameter groups in the MaxQuant GUI. The section rawFiles is a list of these groups.

Each group has two sections of its own: files, a list of names, fractions and experiments, and a parameter section params.

A configuration with two parameter groups could look like this:

rawFiles:
- files:
    - name: 20090812_SvNa_SA_phospho_2_p1
      fraction: 1
    - name: 20090812_SvNa_SA_phospho_2_p2
      fraction: 2
    - name: 20090812_SvNa_SA_phospho_2_p7
      fraction: 3
    - name: 20090812_SvNa_SA_phospho_2_p8
      fraction: 4
  params:
    defaults: default
    intensityDependentCalibration: true
    isotopeTimeCorrelation: 0.8
    centroidMatchTol: 10
    isotopeMatchTol: 3
    mainSearchTol: 7.5
    variableModifications:
      - "Acetyl (Protein N-term)"
      - "Oxidation (M)"
      - "Phospho (STY)"
    useMs1Centroids: true
    matchType: "NoMatching"
    multiplicity: 2
    maxLabeledAa: 3
    labelMods:
      - ["Arg6", "Lys8"]
      - ["Arg10", "Lys8"]
- files:
    - name: 20090812_SvNa_SA_phospho_2_FT1
      fraction: 5
    - name: 20090812_SvNa_SA_phospho_2_FT2
      fraction: 6
    - name: 20090812_SvNa_SA_phospho_2_FT3
      fraction: 7
    - name: 20090812_SvNa_SA_phospho_2_7
      fraction: 8
    - name: 20090812_SvNa_SA_phospho_2_8
      fraction: 9
    - name: 20090812_SvNa_SA_phospho_2_9
      fraction: 10
    - name: 20090812_StPe_SA_phospho_2_10
      fraction: 11
  params:
    defaults: default
    intensityDependentCalibration: true
    isotopeTimeCorrelation: 0.8
    centroidMatchTol: 10
    isotopeMatchTol: 3
    mainSearchTol: 7.5
    variableModifications:
      - "Acetyl (Protein N-term)"
      - "Oxidation (M)"
      - "Phospho (STY)"
    useMs1Centroids: true
    matchType: "NoMatching"
    multiplicity: 2
    maxLabeledAa: 3
    labelMods:
      - ["Arg6", "Lys8"]
      - ["Arg10", "Lys8"]

Fasta files

The fasta files are specified in the fastaFiles section. It must include two subsections, fileNames and firstSearch. The as with the raw files the actual file paths are set when mqrun is executed.

An example:

fileNames:
  - uniprot_sprot
firstSearch: []