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==Methods== | ==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 publications will be considered in the curation process, but they will be considered as secondary sources if the raw mass spectrometry data they are based on has not been made publicly available. | + | 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 raw mass spectrometry data they are based on has not been made publicly available. |
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| + | 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. | ||
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| + | ==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. | ||
| + | #Biomedical Research Centre, University of British Columbia; | ||
| + | #Biomolecular Resource Center Mass Spectrometry Facility, UCSF; | ||
| + | #Manitoba Centre for Proteomics and Systems Biology, University of Manitoba; | ||
| + | #Buck Institute for Aging; | ||
| + | #Proteomics Research Resource for Integrative Biology, Pacific Northwest National Laboratories; | ||
| + | #Novartis - GeneProt collaboration (PeptideAtlas); | ||
| + | #Goodlett Proteomics Laboratory, University of Washington (PeptideAtlas); | ||
| + | #Western Mouse Models Consortium, Fred Hutchinson Cancer Research Center (Tranche); | ||
| + | #Institute for Systems Biology (through PeptideAtlas); | ||
| + | #HUPO Plasma Proteome Project; | ||
| + | #Proteomics Shared Resource, Oregon Health Sciences University (PeptideAtlas); | ||
| + | #Barnett Institute, Northeastern University (Human ProteinPedia); | ||
| + | #Research Centre for Molecular Medicine of the Austrian Academy of Science (Human Proteinpedia); | ||
| + | #Conway Institute, University College Dublin (Human Proteinpedia); | ||
| + | #Skirball Institute for Biomolecular Medicine, New York University Medical Center (Human Proteinpedia); and | ||
| + | #Pandey Lab, Johns Hopkins University (Human Proteinpedia). | ||
==Clinical human tissues currently under curation== | ==Clinical human tissues currently under curation== | ||
The Normal Clinical Tissue Alliance was created to provide clinical proteomics information about normal 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.
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The NCTA was created to develop and maintain list of proteins that can be detected by current, mass spectrometry-based proteomics experiments, on a tissue-by-tissue basis.
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 raw 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.
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.
The following links are to Excel spreadsheets that contain the lists of proteins for the corresponding normal tissue.
The following spreadsheets contain the lists of proteins with the plasma proteome removed.