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Production of Tissue Microarrays, Immunohistochemistry Staining and Digitalization Within the Human Protein Atlas
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The SysteMHC Atlas project.

Wenguang Shao1, Patrick G A Pedrioli1, Witold Wolski2

  • 1Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland.

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|October 7, 2017
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Summary
This summary is machine-generated.

SysteMHC Atlas is a new public database for organizing and sharing mass spectrometry-based immunopeptidomic data. This resource standardizes and visualizes major histocompatibility complex-associated peptides to advance precision medicine research.

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Area of Science:

  • Immunology and Proteomics
  • Computational Biology and Bioinformatics

Background:

  • Mass spectrometry (MS)-based immunopeptidomics analyzes peptides presented by major histocompatibility complex (MHC) molecules.
  • MHC-associated peptides are crucial for precision medicine, driving the need for large-scale immunopeptidomic datasets.
  • Standardization and data sharing are essential for collaboration and quality control in immunopeptidomics.

Purpose of the Study:

  • To establish SysteMHC Atlas, a public database for collecting, organizing, sharing, visualizing, and exploring MS-based immunopeptidomic data.
  • To provide a centralized resource for researchers studying MHC-associated peptides.
  • To facilitate the advancement of immunopeptidomics through standardized data and improved collaboration.

Main Methods:

  • Collected raw mass spectrometer output files from global laboratories.
  • Curated context-specific datasets of MHC class I and class II peptides.
  • Developed standardized MHC allele-specific peptide spectral libraries using consensus spectra.
  • Implemented a uniform and open computational pipeline for quality control of peptide identifications and annotations.

Main Results:

  • Established SysteMHC Atlas (https://systemhcatlas.org) as a public repository for immunopeptidomic data.
  • Integrated raw data, curated datasets, and standardized spectral libraries.
  • Ensured quality control of peptide identifications and annotations through a uniform computational pipeline.
  • Provided links to relevant proteomics and immunology databases.

Conclusions:

  • SysteMHC Atlas disseminates quality-controlled immunopeptidomic information.
  • The database serves as a community resource for mapping the human immunopeptidome.
  • It supports consistent measurement of immunopeptidomic sample cohorts and advances precision medicine.