Normal Clinical Tissue Alliance

Revision as of 19:13, 10 February 2008

Mission

The Normal Clinical Tissue Alliance was created to provide clinical proteomics information about normal human tissues. It was initially conceived as a collaboration between the UCSF Medical School, Lawrence Berkeley Laboratories, the Buck Institute for Aging and the University of British Columbia as part of the Clinical Proteomic Technology Assessment for Cancer program. The NCTA will develop and maintain list of proteins that can be detected by current, mass spectrometry-based proteomics experiments, on a tissue-by-tissue basis. These lists are meant to be practical guides to what proteins are commonly observed, rather than exhaustive catalogues of every protein that has ever been attributed to a particular tissue.

Methods

These protein lists (proteomes) will be generated directly from mass spectra and the curated to generate the lists given below. The selection of which tissues will be annotated is dependent on the public availability of data and tissue provenance of the data. Lists of proteins in literature publications will be considered in the curation process, but they will be considered as secondary sources if the supporting mass spectrometry data they are based on has not been made publicly available.

The BRENDA tissue ontology will be used to identify tissues, with the CELL ontology being used when BRENDA does not contain an entry for a particular type of cell that may be considered a tissue for practical purposes, such as erythrocytes.

Data contributors

The following laboratories have contributed the raw data that was used to generate the current release. This contribution has either been through direct submission of data through the GPM interface, posting data to public repository sites such as Tranche, PeptideAtlas or Human Proteinpedia, or through collaboration with Alliance members.

1. Biomedical Research Centre, University of British Columbia;
2. Biomolecular Resource Center Mass Spectrometry Facility, UCSF;
3. Manitoba Centre for Proteomics and Systems Biology, University of Manitoba;
4. Buck Institute for Aging;
5. Proteomics Research Resource for Integrative Biology, Pacific Northwest National Laboratories;
6. Novartis - GeneProt collaboration (PeptideAtlas);
7. Goodlett Proteomics Laboratory, University of Washington (PeptideAtlas);
8. Western Mouse Models Consortium, Fred Hutchinson Cancer Research Center (Tranche);
9. Institute for Systems Biology (through PeptideAtlas);
10. HUPO Plasma Proteome Project;
11. Proteomics Shared Resource, Oregon Health Sciences University (PeptideAtlas);
12. Barnett Institute, Northeastern University (Human ProteinPedia);
13. Research Centre for Molecular Medicine of the Austrian Academy of Science (Human Proteinpedia);
14. Conway Institute, University College Dublin (Human Proteinpedia);
15. Skirball Institute for Biomolecular Medicine, New York University Medical Center (Human Proteinpedia); and
16. Pandey Lab, Johns Hopkins University (Human Proteinpedia).

Clinical tissues

The following links are to spreadsheets that contain the proteomes for the corresponding normal tissue.

1. Blood plasma, BTO:0000131, excel, html;
2. Blood platelets (BTO:0000132), excel, html;
3. Blood serum (BTO:0000133) excel, html;
4. Bone (BTO:0000140), excel, html;
5. Brain (BTO:0000142), excel, html;
6. Bronchoalveolar lavage (BTO:0000155), excel, html;
7. Cerebrospinal fluid (BTO:0000237), excel, html;
8. Erythrocytes (CL:0000232), excel, html;
9. Gastric fundus (BTO:0000502), excel, html;
10. Hair (BTO:0001501), excel, html;
11. Lens (BTO:0000723), excel, html;
12. Saliva (BTO:0001202), excel, html; and
13. Urine (BTO:0001419), excel, html.

The following spreadsheets contain the same proteomes, with the plasma proteome removed.

1. Blood platelets (BTO:0000132), excel, html;
2. Blood serum (BTO:0000133) excel, html;
3. Bone (BTO:0000140), excel, html;
4. Brain (BTO:0000142), excel, html;
5. Bronchoalveolar lavage (BTO:0000155), excel, html;
6. Cerebrospinal fluid (BTO:0000237), excel, html;
7. Erythrocytes (CL:0000232), excel, html;
8. Gastric fundus (BTO:0000502), excel, html;
9. Hair (BTO:0001501), excel, html;
10. Lens (BTO:0000723), excel, html;
11. Saliva (BTO:0001202), excel, html; and
12. Urine (BTO:0001419), excel, html.

Data

All of the tandem mass spectra that have been used to generate these proteomes are available for reanalysis, on an ftp site. The files are organized by tissue type. They are in the standard compression format used by GPMDB, COMMON 1.0. These files can be converted into the Mascot-standard format MGF using a utility program available here.

Members

• Ronald Beavis, Canada Research Chair in Experimental Bioinformatics, University of British Columbia;
• David Fenyo, Rockefeller University;
• Susan Fisher, Professor of Cell and Tissue Biology, University of California, San Francisco; and
• Brad Gibson, Professor, The Buck Institute for Aging

Other sources

1. PeptideAtlas Plasma Proteome
2. HUPO Plasma Proteome
3. HUPO Liver Proteome
4. HUPO Brain Proteome
5. Human Proteinpedia
6. Tranche
7. PRIDE