Assembling the Community-Scale Discoverable Human Proteome.
The increasing throughput and sharing of proteomics mass spectrometry data have now yielded over one-third of a million public mass spectrometry runs. However, these discoveries are not continuously aggregated in an open and error-controlled manner, which limits their utility. To facilitate the reusability of these data, we built the MassIVE Knowledge Base (MassIVE-KB), a community-wide, continuously updating knowledge base that aggregates proteomics mass spectrometry discoveries into an open reusable format with full provenance information for community scrutiny. Reusing >31 TB of public human data stored in a mass spectrometry interactive virtual environment (MassIVE), the MassIVE-KB contains >2.1 million precursors from 19,610 proteins (48% larger than before; 97% of the total) and doubles proteome coverage to 6 million amino acids (54% of the proteome) with strict library-scale false discovery controls, thereby providing evidence for 430 proteins for which sufficient protein-level evidence was previously missing. Furthermore, MassIVE-KB can inform experimental design, helps identify and quantify new data, and provides tools for community construction of specialized spectral libraries.
['Wang|Mingxun|M|', 'Wang|Jian|J|', 'Carver|Jeremy|J|', 'Pullman|Benjamin S|BS|', 'Cha|Seong Won|SW|', 'Bandeira|Nuno|N|']
D000465:Algorithms D000073537:Biological Variation, Population D030562:Databases, Protein D006801:Humans D013058:Mass Spectrometry D020543:Proteome D040901:Proteomics
proteomics knowledge base spectral libraries algorithms big data repositories tandem mass spectrometry