gfellerlab/mhcpext

Identification of N- and C-terminal extensions in HLA-I ligands

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Written by David Gfeller

The script requires MixMHCp to be installed in your path (see https://github.com/GfellerLab/MixMHCp)

For any question, please contact [email protected]

MHCpExt1.0 can be used freely by academic groups for non-commercial purposes (see license). The product is provided free of charge, and, therefore, on an "as is" basis, without warranty of any kind.

FOR-PROFIT USERS If you plan to use MHCpExt in any for-profit application, you are required to obtain a separate license. To do so, please contact [email protected] or [email protected] at the Ludwig Institute for Cancer Research Ltd.

If you use MHCpExt in a publication, please cite: Guillaume et al. The C-terminal extension landscape of naturally presented HLA-I ligands, PNAS (2018).

Copyright (2017) David Gfeller

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Explanations

This scripts allows you to find cases of C- or N-terminal extensions in large datasets of peptide ligands, assuming that the canonical peptides have length 9. It is therefore especially designed to analyse HLA peptidomics datasets

As input, you should give a file containing a list of all peptides (any length). Typically, this could be the results of an HLA peptidomics screen on a cell line and tissue sample.

The script will first run MixMHCp on the 9-mers, providing an unsupervised view of the different motifs. It will then identify longer peptides (10-, 11-, 12-mers) that cannot be explained by the bulge model derived from the 9-mers, but fit a N- or C-terminal extension model, and assign statisical significance (Z-score) to these cases.

To know which allele corresponds to which cluster, and to optimize the number of motifs, it is best to have a look at the logos found by MixMHCp and compare them with known logos. Alternatively, you can run MixMHCp on the 9-mers and see in KLD/best_ncl.txt file the "optimal" number of motifs (this is the default value if the number of cluster is not specificied in MHCpExt).

Installation

In MHCpExt, manually put the path to the MHCpExt/lib folder at "YOUR PATH TO MHCpExt/lib FOLDER".

Make sure awk and perl are installed on your computer and MixMHCp is installed and in your $PATH (see https://github.com/GfellerLab/MixMHCp).

The script should work on Mac and Linux. Depending on the size of the dataset, it can take several minutes to run.

Running

Usage: MHCpExt -i INPUT_FILE -o OUTPUT_DIR

Mandatory parameters:

-i, --input Absolute or relative path to the input file (list of peptides) -o, --output Name of the output directopry

Optional parameters:

-n, --ncl Number of clusters to be used in MixMHCp - if not provided, the algorithm chooses it between 1 and 6 -nm, --name Name of the different clusters (separated by commas, e.g., A0101,A0201,B0702,B0801). Only valid if the number of clusters(-n) is given in input.

Testing

To test your installation, from the MHCpExt/ directory, run:

MHCpExt -i test/A0301.txt -o test/out -n 1

This should take between one and two minutes on a standard computer. Apart from path names, the output should be the same as in test/out_compare. This file corresponds to peptides identified in HLA peptidomics study of a mono-allelic HLA-A03:01 positive cell line [Abelin et al Immunity 2017].