Home

Welcome to the systeMHC wiki!

Brief description of workflow:

• input are mzXML files from Pride which where analysed as part of the eLife paper.
• 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 for verification and annotation of identified peptides
• recomputation of the fdr for verified peptides
• spectrast for swath library creation

The workflow is implemented using the applicake plumbing toolkiet

Open questions :

• is visualization of results as described in the eLife paper essential?
• how does the output of the workflow looks like:
  • meta information about sample
  • annotation of the identified pepites

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