Action Items for Chromosome 19 Team Meeting, Salamanca, Spain

October 2-3-4 2014

Thursday , October 2nd

20.00 Meeting at “Colegio Arzobispo Fonseca”
Hotel Lobby meeting point

20.30 “Tapas Tour”
Enjoy traditional and new cusine tapas

Friday , October 3rd

  • 9:30 Meeting at Cancer Research Center. University of Salamanca


  1. Summary of Uppsala meeting in August / Gyorgy Marko-Varga
  2. Overview of Glioma Study / Carol Nilsson
  3. Protein Array Platform dev/ Joshua LaBaer
  4. C-HPP database updates - Chrom 19 / Peter Horvatovich. This presentation in pdf is available here.
  5. Chromosome 19 strategy for identifying the missing Proteins / Manuel Fuentes & Carol Nilsson & Tom Fehniger
  6. Plan for complementing each other experimentally / ALL
  7. AOB

* coffee break at CIC

  • 14:00 Lunch served at Fonseca Restaurant
  • 16:00 Visit Facilities
  • 20.30 Dinner ( Restaurant TBA)

Saturday , October 4th

  • 10.00- City Tourist Tour
  • 13.00 Lunch on your own expense.

Departure to Madrid HUPO 2014 at your convenience.


Javier Rodriguez Bioinformatics
Josh LaBaer
Johan Malm
Frode Berven
Elisabet Carlsohn
Peter Horvatovich
Thomas Fehniger
Akos Vegvari
Sven Kjellstrom
Gyorgy Marko-Varga
Carol Nilsson
Manuel Fuentes
Nieves Evarola


  1. Introduction and presentation of the team members and invites scientists
  2. Peter Horvatovich gave a presentation on the status of the missing proiteins in Chromosome 19. Current number of missing protein is defined to be 374 proteins.
  3. Missing proteins that has been identified by Peter H and Akos, can be acted on by Manuel, supported by Josh. Manuel already started with a sub set of 25 missing proteins. These 25 already shows successful data where the proteins cloned and expressed followed by MRM assays. This has been successfully perused. All of these proteins in the pilot transcribed. The cost is approx.., 150 Euro/protein
  4. Josh presented the developments in Arizona applied to Chromosome 10 genes. cDNA clone collections being used at Arizona state. cDNA plasmids (210.000 unique plasmids, “DNASU”) are used to express the proteins, about 1 microgram, identifying by both Orbitrap and triple quad. Completing the human ORFeome, there is now 10.648 and 14.951 within a year., getting to 18.974 and then 4.000 are missing, and that will be handled separately.
  5. We agreed on that we need a road map and work plan to move forward work plan. We start with synchronizing the gene list from Josh with the list of missing 374 proteins.
  6. We agreed to action the activities by writing a paper and Peter H will have the lead to put a draft together with the background informatics work. Josh will add the protein expression part with Manuel and Carol and Gyorgy will support with Tom to get the completion of the paper.
    1. Produce Test Protein (Manuel, Josh)
    2. Identify target peptides (Niewes, Frode*, Elisabet, Carol, Peter)
    3. Identify Tissue/Cell Sources 10to the9 cells (Javier, Peter)
      1. MS experiments to identify target peptides in expressed proteins (Manuel, Johan) core facilities at NIH)
      2. Investigate Broad database on RNA seq.
      3. GEO
      4. TCGA
      5. Find 4-6 cell lines – 80% of our missing proteins. (Niewes, Frode*, Elisabet, Carol, Peter, Akos)
      6. How much 10tothe9
      7. Do we need a fermentor
      8. Su cellular fractionation
      9. Block selection
      10. Block Proteosome
      11. Membrane proteins
    4. Findpeptide evidence of missing proteins
    5. What is peptide evidence ? Unique ?
    6. Survey of dominant peptides
    7. Test samples predicted
    8. based on RNA seq
    9. based in predicted sample type
    10. Find protein – what is next? Functional studies/ Diseases-Biobanks
    • Salvage pathway – what do we do if we don’t find it ? (Tom&Josh)


Photos are available here:

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