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Witold Wolski edited this page Dec 22, 2015 · 36 revisions

Welcome to the systeMHC wiki!

Brief description of workflow:

  • input are mzXML files from Pride which where analysed as part of the eLife paper. Priority = MHC class I peptides (not class II from Mtb mzXML files).
  • 2-3 search engines: comet, myrimatch, (msgf+) for identification of MHC peptides from centroided MS/MS data.
  • TPP - peptide prophet and iprophet for rescoring and fdr estimation
  • NetMHCcons 1.1 for filtering/verification and annotation of identified peptides
  • recomputation of the fdr for verified peptides
  • spectrast for swath library creation
  • Data visualization (heat map (see figure 2 in eLife) and distribution of predicted HLA binding affinities (see Figure 2—figure supplement 4 and Figure 2—figure supplement 5; other visualization tools are optional)
  • Create a R/Bioconductor package for publication as an Application Note in Bioinformatics

The workflow is implemented using the applicake plumbing toolkiet

Open questions :

  • how does the output of the workflow looks like:
    • meta information about sample
    • annotation of the identified peptides

getting all the required code

sudo apt-get install git

git clone https://github.com/systemhc/systemhc
git clone https://github.com/SysteMHC/SysteMHC_Binaries
git clone https://github.com/SysteMHC/RnetMHC
git clone https://github.com/SysteMHC/SysteMHC_Data
git clone https://github.com/applicake-tools/applicake
git clone https://github.com/applicake-tools/toolscake

at a later stage we might use git submodules

Related projects:

applicake

aboutSystemMHC

Related projects

immuneepitope

iedb

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