MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets.

This tool is a wrapper for MaxQuant v2.0.3.0. The current version of the wrapper only supports a reduced set of parameters, but another version of the tool that gets its parameters directly from a mqpar.xml file is available, too.

Input files

• Thermo raw, mzML, or mzXML files (in parameter group section)

  • The datatype of all files has to be either 'thermo.raw', 'mzml' or 'mzxml'. Make sure to specify the correct datatype either during upload to Galaxy or afterwards (edit attributes --> datatypes)

• Fasta file: specify parse rules according to your fasta file (header). Some examples for different fasta headers:

                          identifier parse rule     description parse rule
  
  Uniprot identifier          >.*\|(.*)\|           >.*\|.*\|[^ ]+ (.*) OS
  
  NCBI accession              >(gi\|[0-9]*)
  
  IPI accession               >IPI:([^\| .]*)
  
  Everything after '>'        >(.*)
  
  Up to first space           >([^ ]*)
  
  Up to first tab character   >([^\t]*)
  

• Optional files:

  • Tabular file with experimental design template:

    • Currently four columns are needed: Name, Fraction, Experiment and PTM. The headers must have this exact naming. Name and Experiment are abitrary strings, Fraction is an integer or emtpy, PTM is either 'True', 'False' or empty. Consider you uploaded files named File1.mzxml, ..., File5.mzxml. Thermo RAW files are handled differently (see table below). This is a (syntactically) correct experimental design template:

      Name     Fraction    Experiment   PTM
      File1        1          E1       False
      File2        2          E1       False
      ghost       234        none
      File3        3          E1       False
      File4                   E2       True
      File5                   E1
      

    • This is the counter-example with one error per line:

      Name     Fraction    Experiment   PTM
      File1       1           E1        no  (wrong PTM value)
      File2.mzxml 1           E2            (filename with extension)
      File3       f3          E1            (fraction not an integer)
      File4       1                         (missing experiment)
                                            (File5 missing)
      

    • However, “.raw” (Thermo) is considered a part of the filename:

      Name         Fraction    Experiment   PTM
      File1.raw        1          E1       False
      File2.raw        2          E1       False
      File3.raw        3          E1       False
      File4.raw        1          E2       False
      File5.raw        2          E2       False
      File6.raw        3          E2       False
      

Parameter Options

• Quantitation methods (in section parameter groups)

  • label free (LFQ): Protein intensity will be reported as 'LFQ intensity' columns in the proteinGroups table

  • label based: quantifies MS1 labelled samples ('SILAC', 'Dimethyl', 'ICAT', 'ICPL', 'mTRAQ', '18 O')

    • for two channels: choose options from light and heavy sections
    • for three channels: choose options from light, medium and heavy sections

  • reporter ion ms2/ms3: quantifies conventional isobaric labelling samples. Either use the pre-defined labellings with correction factors set to 0 or specify a custom labelling

• PTXQC quality control: quality control software creates an automatic quality control pdf report

Output files

Different output file options are available, most of them are part of the MaxQuant txt directory.