Assembling the Community-Scale Discoverable Human Proteome.

Mingxun Wang, Jian Wang, Jeremy Carver, Benjamin S Pullman, Seong Won Cha, Nuno Bandeira

Journal: Cell systems 2019;7(4):412-421.e5

PMID: 30172843

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Abstract

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.

Address: Center for Computational Mass Spectrometry and Department of Computer Science and Engineering, University of California, San Diego, La Jolla, San Diego, CA 92093, USA.; Electrical and Computer Engineering, University of California, San Diego, La Jolla, San Diego, CA 92093, USA.; Center for Computational Mass Spectrometry and Department of Computer Science and Engineering, University of California, San Diego, La Jolla, San Diego, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: [email protected].

DOI: 10.1016/j.cels.2018.08.004

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MeSH Terms: Algorithms, Biological Variation, Population, Databases, Protein, Humans, Mass Spectrometry, Proteome, Proteomics