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Chromosome 16

1.1. Group composition


Participating country(ies): Spain
Head: Fernando J Corrales
Members:

  • Concha Gil
  • Francisco J. Blanco

1.2. Missing proteins


Protein evidence according to NeXtProt for Chromosome 16:
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

  • PXD000039 MCF7 breast cancer human epithelial cells, CCD18 human colon fibroblasts, and Jurkat human T lymphocytes.
  • PXD000442 MCF7 epithelial cells, CCD18 colon fibroblasts, Ramos and Jurkat B and T lymphocytes respectively. In particular, this subset includes all the data regarding the MCF7 cell line. 6 laboratories contributed to compile all the reported data.
  • PXD000443 MCF7 epithelial cells, CCD18 colon fibroblasts, Ramos and Jurkat B and T lymphocytes respectively. In particular, this subset includes all the data regarding the Jurkat cell line. 2 laboratories contributed to compile all the reported data.
  • PXD000447 MCF7 epithelial cells, CCD18 colon fibroblasts, Ramos and Jurkat B and T lymphocytes respectively. In particular, this subset includes all the data regarding the Ramos cell line. 3 laboratories contributed to compile all the reported data.
  • PXD000449 MCF7 epithelial cells, CCD18 colon fibroblasts, Ramos and Jurkat B and T lymphocytes respectively. In particular, this subset includes all the data regarding the CCD18 cell line. 6 laboratories contributed to compile all the reported data.
  • PASS00925 SRM DNAH3 in spermatozoa and ATAD3C in HEK293 cells

1.8. Special expertise


1.9. Major achievements


Publications:

Posters presented in the HUPO 2013 (Yokohama, Japan) Meeeting:
Bioinformatic workflow for Chr16 characterization using proteomic shotgun and transcriptomic RNA-seq experiments
Development of SRM methods for the detection and quantification of chromosome 16 proteins
Dissecting subcellular compartments for deep proteome coverage of chromosome 16 in t cells
Improving Chr-16 proteins coverage with high confidence and MIAPE compliant MS data
Missing proteins in Chromosome 16 - Spanish HPP

Presentations:
Identification of proteins driving the progression of liver injury and potential biomarkers
How to submit MIAPE compliant data to ProteomeXchange Repository in the context of the human proteome project
Chromosome 16 Update: Surfing transcriptomics landscapes. A step beyond the annota=on of Chr-­‐16 proteome
European initiatives in the field of Proteomics Standarization

Other files:
SpanishContributiontoPX_Jan16.xlsx

1.10. The neXt-MP50 challenge


Step by step milestone plan to find, identify and validate MPs:

• Prioritization of the 50 chr16 MPs to be targeted. Annotation with Missing Proteinpedia, HPA, Human MRM Atlas and Chr16 already generated information. February 2017.
• List of chr16 MPs that would require non standard procedures (non-trypsin digestion sites, lack of unique peptides...). March 2017.
• Preparation of SRM methods and identification of the biological sources with highest probability of finding the selected chr16 MPs. June 2017
• SRM analysis, 10 MPS/lab. Starting on June-July 2017).
• IVTT initiative (5 chromosomes participating). 5-10 proteins/year. (2 MPs already identified by SRM and 2 aditional are pending on validation)