Chromosome 6

1.1. Group composition

Participating country(ies): USA\Canada\Qatar
Head: Robert Moritz - Institute for Systems Biology, USA
Co-Lead:Christopher Overall - U. British Columbia, Canada
Member:Frank Schmidt - Weill-Cornell, Qatar
Member:John Wilson - Protifi, USA
Member:Eric Deutsch - Institute for Systems Biology, USA

1.2. Missing proteins

Protein evidence according to NeXtProt for Chromosome 6:
Protein evidence status in text format is available here.

1.3. Bioinformatics protocols

1.4. Analytical protocols

1.5. Biological projects

1.6. Biomaterials

1.7. Data sets

1.8. Special expertise

The exact position and N-terminal chemistry of a protein chain often define the biological activity of a protein. The Chris Overall group, UBC has unique expertise in defining the N (and C-termini) of proteins by proteomics. By analysis of common and rare human tissues the Overall Lab is annotating the N-termini of proteins of Chromosome 6 and other chromosomes for the HPP. Thus we are identifying:

  • Co-translational derived mature original N-terminus
  • Post-translational cleavage derived stable cleavage chains
  • Annotation of +/- Met, site of signal peptide removal, zymogen activation
  • +/- Acetylation, other modifications
  • Alternate start sites
  • Archetypical N-terminal peptides
  • SRMs to quantify amounts of cleaved vs. uncleaved
  • Neo-epitope antibodies to biologically important protein chains directed to the N or C termini after cleavage

For harsh sample solubilization, we are employing methods with high detergent concentration (e.g., SDS) and a processing method that will clear the protein lysate of detergents and digest the proteins in situ (STraps). Our unique expertise (Protifi) in sample treatment is being developed to tackle heavily membrane bound proteins that are frequently missing from proteome analysis results.

For rare sample and targeted human tissue access, our Qatar based group headed by Frank Schmidt has a repository of human tissue that is being used to extensively mine with the methods developed within the Ch6 team

1.9. Major achievements

A review of the chromosome 6 project has been published, link
Borchers et al., 'The Human Proteome Organization Chromosome 6 Consortium: Integrating chromosome-centric and biology/disease driven strategies', Journal of Proteomics 100 (2014), 60-67.

Rare tissue analysis:

Database search tool

Other papers:

Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome.
Kusebauch U, Campbell DS, Deutsch EW, Chu CS, Spicer DA, Brusniak MY, Slagel J, Sun Z, Stevens J, Grimes B, Shteynberg D, Hoopmann MR, Blattmann P, Ratushny AV, Rinner O, Picotti P, Carapito C, Huang CY, Kapousouz M, Lam H, Tran T, Demir E, Aitchison JD, Sander C, Hood L, Aebersold R, Moritz RL. Cell. 2016 Jul 28;166(3):766-778. doi: 10.1016/j.cell.2016.06.041. Epub 2016 Jul 21. PMID: 27453469

1.10. The neXt-MP50 challenge