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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).
• Annotation of mzXML files including IEDB metadata
• 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
• Validation of R/Bioconductor package using a new HLA peptidomics dataset (Buffy samples acquired in Tübingen; data stored in OpenBis)
• Publication

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

Related projects

immuneepitope

iedb