SWATH-MS Data Analysis

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Tasks and extent that StABU can help.

Background notes

  • The species-wide terminology is MHC: Major Histocompatibility Complex
  • In humans MHC is (mostly) represented by HLA Human Leukocyte Antigens
  • T-cells


Heavy use of on-line proteins databases

"Peptides were identified using multiple open-source database search engines. The search identifications were combined and statistically scored using PeptideProphet and iProphet within the Trans-Proteomic Pipeline (TPP) as shown previously"

  • iProphet combines results of three open-source database search engines in immunopeptidomics.
  • Search identifications combined and statistically scored using PeptideProphet (Keller et al., 2002) and iProphet (Shteynberg et al., 2011
  • PyProphet for statistics of HLA peptidomic data.


  • The HLA peptidome of JYEBV+ cells analyzed using OpenSWATH (Röst et al., 2014) software.

Scripting procedure

Although the entire pipeline includes many steps accomplished by third party software, as is common there will always be some custom scripting that is necessary. These are dlletailed in Caron et al.


  • Main paper, "An open-source computational and data resource to analyze digital maps of immunopeptidomes", Etienne Caron et al.
  • Pyprophet