SysteMHC v.180409
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About

The SysteMHC Atlas project is part of the Human Immuno-Peptidome Project (HIPP). HIPP was launched in 2015 as a new initiative of the Human Proteome Organization (HUPO). The long-term goal of the HIPP is to map the entire repertoire of peptides presented by MHC molecules using mass spectrometry technologies and make its robust analysis accessible to any immunologist. Toward this end, HIPP plans to embrace partnerships, prioritize technology development and maximize data sharing. The SysteMHC Atlas project supports this latter goal.

Overview of the build process of SysteMHC Atlas.

Overview of the SysteMHC build process:

Raw mass spectrometry files were converted into the mzXML format by msConvert. The mzXML files were then individually searched by Comet and X!Tandem using a decoy sequence database approach. We used default search settings for both engines with the following key parameters:

ParameterValue
Precursor tolerance15ppm
High accuracty fragment ion tolerance (Orbi/TOF)0.05Da
Low accuracty fragment ion tolerance0.5Da
Digestion specificityunconstrained
Variable modificationsmethionie oxidation

The search results were then processed by Trans-proteomic Pipeline version 4.8.0 -- PeptideProphet was first applied with the accurate mass model enabled. Finally iProphet was used to combine the outputs of PeptideProphet from two search engines.

NetMHCcons was used to predict the binding affinities of Class I peptides with the default settings. Based on the prediction, the peptides were then annotated for the allele using the strategy described in Caron et al. eLife 2015.

Spectral libraries were generated by SpectraST with default consensus library building parameters. And iProphet estimated cut-off of 1% FDR was used. For each sample, a sample-specific consensus spectral library was generated. For each allele, an allele-specific spectral library was generated on the atlas level that contains consensus spectra of peptides from different samples. In the allele-specific spectral library, the same peptide ions generated under various fragmentation methods were specified and kept separated as different library entries.

For more details about the tools and methodology also see the SysteMHC GitHub repository.

The current build version is 180409.

Current and past builds can be downloaded here

How to cite SysteMHC Atlas

Please acknowledge the SysteMHC Atlas in your publications by citing the following manuscript:

Shao, W.; Pedrioli, P.G.A. et al. The SysteMHC Atlas project. Nucleic Acids Res doi:10.1093/nar/gkx664

The team behind SysteMHC Atlas:

Licenses

SysteMHC Atlas is made available under the Open Database License: http://opendatacommons.org/licenses/odbl/1.0/.

Any rights in individual contents of the database are licensed under the Database Contents License: http://opendatacommons.org/licenses/odbl/1.0/.

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