Special expertise

1.1. Chromosome 1

1.2. Chromosome 2

1.3. Chromosome 3

1.4. Chromosome 4

1.5. Chromosome 5

  • Henry Lam dispose of special expertise in creating spectral libraries and using them for MS/MS peptide identification.
  • Manfred Wuhrer group disposes glycopeptide measurement method to determine exact sequence compositions of N-glycopeptides.

1.6. Chromosome 6

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

1.7. Chromosome 7

1.8. Chromosome 8

1.9. Chromosome 9

1.10. Chromosome 10

1.11. Chromosome 11

1.12. Chromosome 12

1.13. Chromosome 13

  1. Construction of database
  2. Bioinformatic tool development
  3. Cancer proteomics
  4. Developmental biology
  5. Functional study on the model organism (C. elegans, Cell lines)

1.14. Chromosome 14

Absolute quantification (PSAQ technology); contact: virginie.brun at cea.fr

1.15. Chromosome 15

1.16. Chromosome 16

1.17. Chromosome 17

RNA-Seq data sets, contac person Hogune Im
Strand-specific RNA-Seq libraries were prepared and sequenced on a lane of the Illumina HiSeq 2000 instrument per sample to obtain transcript data15. All RNAseq data are available at Short Read Archive (SRS366582, SRS366583, SRS366584, SRS366609, SRS366610, SRS366611).

1.18. Chromosome 18

  • Comparative ranking of chromosomes based on post-genomic data shows that all chromosomes are not much different from each other except ChrY and ChrMt due to their shortest length. Chr18 for the Russian portion of the HPP was selected based on the combination of proposed criteria. (Ponomarenko et al., 2012)
  • meta-analysis of proteomics data from publication and databases for Chr18 shows that only 37%, 43% and 7% of total number of master proteins coding on chromosome detected in blood plasma, liver tissue and HepG2 cells, respectively, and the very few of them measured.
  • detection of ultra-low abundant protein specified in concentrations as low as 10-18 M (e.g. 1 molecula per 1 μL of plasma). These low-copied proteins are enriched from the excessive sample volume by the irreversible binding to the beads. See Kopylov et al., 2013 for details.
  • quantitative correlations of transcriptome-to-proteome data to evaluate the quality of measurements obtained by RNAseq, survey and targeted proteomics. See Ponomarenko et al., 2014.
  • development of technology for direct molecular fishing on paramagnetic particles for protein interactomics (Ivanov et al., 2014)
  • cataloguing the non-canonical protein species (proteoforms) by in-depth analysis of trasncriptome data (Shargunov et al., 2013) and prediction of post-translational modifications (Lisitsa et. al., 2014).

1.19. Chromosome 19

1.20. Chromosome 20

1.21. Chromosome 21

1.22. Chromosome 22

1.23. Chromosome X

1.24. Chromosome Y

1.25. Mitochondrial Chromosome