Eric Deutsch

Eric Deutsch

Talk title: Enabling the Dissemination and Reuse of Proteomics Data: Status and New Projects of the HUPO Proteomics Standards Initiative


Dr. Eric Deutsch is a senior research scientist at the Institute for Systems Biology, specializing in bioinformatics and integration of data for systems biology research, with a focus on proteomics. He contributes to the development of minimum information and data format standards as co-chair of the HUPO Proteomics Standards Initiative (PSI). He participates in several key roles in the Human Proteome Project, including chair of the Knowledge Base Pillar Committee. Dr. Deutsch leads the PeptideAtlas Project, which aims to collect proteomic mass spectrometry data from labs around the world to synthesize a master list of observed peptides and proteins and disseminate the results back to the community. He also leads the team that develops the Trans-Proteomic Pipeline (TPP), a widely used free and open source suite of tools for the complete analysis of shotgun proteomics data.


The HUPO Proteomics Standards Initiative (PSI) defines community standards for data representation in proteomics to facilitate data comparison, exchange, and verification. Through yearly workshops and ongoing efforts, we are currently working on updating and releasing new versions of the existing standards mzML, mzTab, mzIdentML, and PSI-MI XML. We have also released new proteogenomics formats proBAM and proBED. Four new standards are under active development. The PSI Enhanced FASTA Format (PEFF) will encode protein sequences along with extensive PTM and variant annotations for the next generation of sequence search engines. A new PSI Spectral Library Format will encode consensus spectra with more metadata that currently possible. A Universal Spectrum Identifier will enable referencing and access to all spectra deposited to any repository. The PROXI API will allow programmatic querying and access to proteomics data across repositories. These past successes and future directions of the PSI will be presented.