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Welcome to the systeMHC wiki!

Brief Description of workflow:

• input are mzXML files from Pride which where analyzed 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 an R/Bioconductor package and an open source graphical user interface
• Validation using a new HLA peptidomics dataset (Buffy samples acquired in Tübingen; data stored in OpenBis)
• Build the database, design website and implementation (www.systemhcatlas.org)
• Publication

The workflow is implemented using the applicake plumbing toolkiet

Open questions:

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

Sample input and output

• sample input metadata
• sample output

install required python packages

pip install Uniprot
pip install lxml
pip install ruffus
pip install pandas

getting all the required code

sudo apt-get install git

Directory structure

Create a folder systemhc in your home direktory. Change into it and checkout package.

Documentation

git clone https://github.com/systemhc/systemhc

Python packages

git clone https://github.com/systemhc/systemhccake
git clone https://github.com/applicake-tools/applicake2
git clone https://github.com/applicake-tools/searchcake

data and binary packages packages

git clone https://github.com/SysteMHC/SysteMHC_Binaries
git clone https://github.com/SysteMHC/SysteMHC_Data
git clone https://github.com/applicake-tools/searchcake_binaries

You can install those packages in develper mode by changing into the respective project directory and running

pip install -e .

To run the application first, change into the installation directory. On the systemhc server, it is ~/prog change into

~prog/systemhc
source setup.sh

This sets two variables:

export SYSTEMHC=$HOME/prog
export LC_ALL=C

To run the workflow go to:

/mnt/Systemhc/Data/version3
python ~/prog/searchcake2/samples/pepidentWFapp.py

Related projects:

applicake

Related projects

immuneepitope

iedb