Normal Clinical Tissue Alliance

Latest revision as of 13:37, 6 June 2014

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 evolving lists of proteins (proteomes) that can be detected by current mass spectrometry-based proteomics experiments. These proteomes are organized on a tissue-by-tissue basis, with emphasis on those tissues that important for clinical diagnosis. 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

The tissue-specific proteomes will be generated directly from mass spectra and then 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. Juergen Kast, Biomedical Research Centre, University of British Columbia;
2. Susan Fisher, Biomolecular Resource Center Mass Spectrometry Facility, UCSF;
3. John Wilkins, Manitoba Centre for Proteomics and Systems Biology, University of Manitoba;
4. Brad Gibson, Buck Institute for Aging;
5. Richard Smith and Weijun Qian, Pacific Northwest National Laboratories;
6. Novartis - GeneProt collaboration (PeptideAtlas);
7. Dave Goodlett, Goodlett Proteomics Laboratory, University of Washington (PeptideAtlas);
8. Martin McIntosh and Amanda Paulavitch, Western Mouse Models Consortium, Fred Hutchinson Cancer Research Center (Tranche);
9. Phillip Wilmarth, Institute for Systems Biology (PeptideAtlas);
10. HUPO Plasma Proteome Project;
11. Proteomics Shared Resource, Oregon Health Sciences University (PeptideAtlas);
12. William Hancock, 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. Tom Neubert, Skirball Institute for Biomolecular Medicine, New York University Medical Center (Human Proteinpedia);
16. Akhilesh Pandey, Pandey Lab, Johns Hopkins University (Human Proteinpedia); and
17. Fuchu He, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, China (PRIDE).
18. Albert Heck, Netherlands Proteomics Centre, University of Utrecht, Holland (Tranche).
19. Dan Liebler, Mass Spectrometry Research Center, Vanderbilt University Medical Center, USA (Tranche).

Clinical tissues

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

1. BTO:0000131: Blood plasma | excel | html |
2. BTO:0000132: Blood platelets | excel | html |
3. BTO:0000133: Blood serum | excel | html |
4. BTO:0000140: Bone | excel | html |
5. BTO:0000142: Brain | excel | html |
6. BTO:0000155: Bronchoalveolar lavage | excel | html |
7. BTO:0000237: Cerebrospinal fluid | excel | html |
8. BTO:0001086: Embryonic Stem Cell | excel | html |
9. CL:0000232: Erythrocytes] | excel | html |
10. BTO:0000502: Gastric fundus] | excel | html |
11. BTO:0001501: Hair] | excel | html |
12. BTO:0000723: Lens | excel | html |
13. BTO:0000759: Liver | excel | html |
14. BTO:0001202: Saliva | excel | html |
15. BTO:0001419: Urine | excel | html |

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

1. BTO:0000132: Blood platelets | excel | html |
2. BTO:0000133: Blood serum | excel | html |
3. BTO:0000140: Bone | excel | html |
4. BTO:0000142: Brain | excel | html |
5. BTO:0000155: Bronchoalveolar lavage | excel | html |
6. BTO:0000237: Cerebrospinal fluid | excel | html |
7. BTO:0001086: Embryonic Stem Cell | excel | html |
8. CL:0000232: Erythrocytes] | excel | html |
9. BTO:0000502: Gastric fundus] | excel | html |
10. BTO:0001501: Hair] | excel | html |
11. BTO:0000723: Lens | excel | html |
12. BTO:0000759: Liver | excel | html |
13. BTO:0001202: Saliva | excel | html |
14. BTO:0001419: Urine | 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. Each data set used for that tissue type is represented by two files that contain the information used to generate the protein list for that data set.

1. Files that end with .xml contain the search parameters used to generated the identifications.
2. Files that end with .xml.cmn are the associated tandem mass spectra 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;
• Brad Gibson, Professor, The Buck Institute for Aging; and
• John Wilkins, Director, Manitoba Centre for Proteomics and Systems Biology.

Releases

1. 2008.02.01 - first release
2. 2008.04.01 - maintenance release, improved curation process
3. 2008.10.01 - added new HUPO Plasma and Liver Proteome data and added Liver as a curated tissue
4. 2009.04.01 - added Embryonic Stem Cell as a curated tissue
5. 2010.08.01 - added Lung as a curated tissue

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