Galaxy |

MaxQuant (using mqpar.xml) (version 2.0.3.0+galaxy0)

choose the type of your input files:

RAW Files:

Specify one or more Thermo RAW files

FASTA files:

Specify one or more FASTA databases.

identifier parse rule:

description parse rule:

Modify parse rules if needed

mqpar.xml file with your search parameters. RAW file names must match the names displayed in galaxy. Their paths from the local machine are ignored. E.g. a file named 'test01.raw' in galaxy can either be named 'test01.raw' or 'D:\path\to\test01.raw' in the mqpar.xml.:

Generate PTXQC (proteomics quality control pipeline) report? (experimental setting):

Select the desired outputs.:

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. It gets its search parameters from a previously created parameter file (mqpar.xml). A similiar tool that allows the specification of search parameters directly through galaxy is available as well and should be preferred, if possible.

Input files

Thermo raw file or mzXML file
- The datatype has to be 'thermo.raw' or 'mzxml'. Make sure to specify the correct datatype either during upload to Galaxy or afterwards (edit attributes --> datatypes)
mqpar.xml:
- MaxQuant parameters will be taken from the provided mqpar.xml file. This parameter file MUST be created using the same version of MaxQuant as is used by this tool. The correct version of MaxQuant can be obtained via the bioconda channel for the conda package manager.

Output files

Different output file options are available, most of them are part of the MaxQuant txt folder. An additional mztab output option is implemented.