Proteomics QC

A web-server to setup processing pipelines proteomics .RAW files.

  1. Create a project
  2. Create a pipeline by providing a fasta file and a MaxQuant parameter template (mqpar.xml)
  3. Submit .RAW files to the pipeline
  4. Download results
  5. Explore data with the integrated dashboard

The server organizes files into projects. Therefore, at least one project hast to be created. Then a pipeline can be created. Herefore, a MaxQuant parameter file (mqpar.xml) and a fasta file have to be provided.

MaxQuant Parameter file (mqpar.xml)

The mqpar.xml has to be created as a blueprint for the pipeline jobs for example using the MaxQuant GUI. The pipeline is currently restricted to process a single .RAW per job, therefore the mqpar.xml file has to be created with a single .RAW file. The MaxQuant version supported is MaxQuant 1.6.10 due to limited compatability between .NET versions used by MaxQuant and current mono versions. mono is a reimplementation for .NET that runs on Linux platforms.ll