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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 and/or an open source graphical user interface
Validation using a new HLA peptidomics dataset (Buffy samples acquired in Tübingen; data stored in OpenBis)
Publication
Design and build the SysteMHC Atlas project (www.systemhcatlas.org)

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

Sample input and output

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