SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. - Bruz Marzolf; Eric W. Deutsch; Patrick Moss; David S. Campbell; Michael H. Johnson; Timothy Galitski (BMC Bioinform., 2006)

The PeptideAtlas project. - Frank Desiere; Eric W. Deutsch; Nichole L. King; Alexey I. Nesvizhskii; Parag Mallick; Jimmy K. Eng; Sharon Chen; James Eddes; Sandra N. Loevenich; Ruedi Aebersold (Nucleic Acids Res., 2006)

The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation. - Sandra N. Loevenich; Erich Brunner; Nichole L. King; Eric W. Deutsch; Stephen E. Stein; Ruedi Aebersold; Ernst Hafen (BMC Bioinform., 2009)

The PeptideAtlas Project. - Eric W. Deutsch (Proteome Bioinformatics, 2010)

Mass Spectrometer Output File Format mzML. - Eric W. Deutsch (Proteome Bioinformatics, 2010)

ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry. - Mi-Youn K. Brusniak; Sung-Tat Kwok; Mark Christiansen; David S. Campbell; Lukas Reiter; Paola Picotti; Ulrike Kusebauch; Hector Ramos; Eric W. Deutsch; Jingchun Chen; Robert L. Moritz; Ruedi Aebersold (BMC Bioinform., 2011)

Interfaces to PeptideAtlas: a case study of standard data access systems. - Sarah A. Killcoyne; Jeremy Handcock; Thomas Robinson; Eric W. Deutsch; John Boyle (Briefings Bioinform., 2012)

Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework. - Steven Lewis; Attila Csordas; Sarah A. Killcoyne; Henning Hermjakob; Michael R. Hoopmann; Robert L. Moritz; Eric W. Deutsch; John Boyle (BMC Bioinform., 2012)

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. - Gerhard Mayer; Luisa Montecchi-Palazzi; David Ovelleiro; Andrew R. Jones; Pierre-Alain Binz; Eric W. Deutsch; Matthew Chambers; Marius Kallhardt; Fredrik Levander; James Shofstahl; Sandra E. Orchard; Juan Antonio Vizcaíno; et al. (Database J. Biol. Databases Curation, 2013)

Development of data representation standards by the human proteome organization proteomics standards initiative. - Eric W. Deutsch; Juan P. Albar; Pierre-Alain Binz; Martin Eisenacher; Andrew R. Jones; Gerhard Mayer; Gilbert S. Omenn; Sandra E. Orchard; Juan Antonio Vizcaíno; Henning Hermjakob (J. Am. Medical Informatics Assoc., 2015)

Big biomedical data as the key resource for discovery science. - Arthur W. Toga; Ian T. Foster; Carl Kesselman; Ravi K. Madduri; Kyle Chard; Eric W. Deutsch; Nathan D. Price 001; Gustavo Glusman; Benjamin D. Heavner; Ivo D. Dinov; Joseph Ames; John D. Van Horn; et al. (J. Am. Medical Informatics Assoc., 2015)

Chapter 11. Data Formats of the Proteomics Standards Initiative. - Juan Antonio Vizcaíno; Simon Perkins; Andrew R. Jones; Eric W. Deutsch (Proteome Informatics, 2016)

I'll take that to go: Big data bags and minimal identifiers for exchange of large, complex datasets. - Kyle Chard; Mike D'Arcy; Benjamin D. Heavner; Ian T. Foster; Carl Kesselman; Ravi K. Madduri; Alexis A. Rodriguez; Stian Soiland-Reyes; Carole A. Goble; Kristi Clark; Eric W. Deutsch; Ivo D. Dinov; et al. (IEEE BigData, 2016)

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition. - Eric W. Deutsch; Attila Csordas; Zhi Sun; Andrew F. Jarnuczak; Yasset Pérez-Riverol; Tobias Ternent; David S. Campbell; Manuel Bernal Llinares; Shujiro Okuda; Shin Kawano; Robert L. Moritz; Jeremy Carver; et al. (Nucleic Acids Res., 2017)

The SysteMHC Atlas project. - Wenguang Shao; Patrick G. A. Pedrioli; Witold Wolski; Christian Scurtescu; Emanuel Schmid; Juan Antonio Vizcaíno; Mathieu Courcelles; Heiko Schuster; Daniel Kowalewski; Fabio Marino; Cecilia S. Lindestam Arlehamn; Kerrie Vaughan; et al. (Nucleic Acids Res., 2018)

BioHackathon 2015: Semantics of data for life sciences and reproducible research. - Rutger A. Vos; Toshiaki Katayama; Hiroyuki Mishima; Shin Kawano; Shuichi Kawashima; Jin-Dong Kim; Yuki Moriya; Toshiaki Tokimatsu; Atsuko Yamaguchi; Yasunori Yamamoto; Hongyan Wu; Peter Amstutz; et al. (F1000Research, 2020)

The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics. - Eric W. Deutsch; Nuno Bandeira; Vagisha Sharma; Yasset Pérez-Riverol; Jeremy Carver; Deepti Jaiswal Kundu; David García-Seisdedos; Andrew F. Jarnuczak; Suresh Hewapathirana; Benjamin S. Pullman; Julie Wertz; Zhi Sun; et al. (Nucleic Acids Res., 2020)

RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine. - E. C. Wood; Amy Glen; Lindsey G. Kvarfordt; Finn Womack; Liliana Acevedo; Timothy S. Yoon; Chunyu Ma; Veronica Flores; Meghamala Sinha; Yodsawalai Chodpathumwan; Arash Termehchy; Jared C. Roach; et al. (BMC Bioinform., 2022)

The ProteomeXchange consortium at 10 years: 2023 update. - Eric W. Deutsch; Nuno Bandeira; Yasset Pérez-Riverol; Vagisha Sharma; Jeremy Carver; Luis Mendoza; Deepti Jaiswal Kundu; Shengbo Wang; Chakradhar Bandla; Selvakumar Kamatchinathan; Suresh Hewapathirana; Benjamin S. Pullman; et al. (Nucleic Acids Res., 2023)

ARAX: a graph-based modular reasoning tool for translational biomedicine. - Amy Glen; Chunyu Ma; Luis Mendoza; Finn Womack; E. C. Wood; Meghamala Sinha; Liliana Acevedo; Lindsey G. Kvarfordt; Ross C. Peene; Shaopeng Liu; Andrew S. Hoffman; Jared C. Roach; et al. (Bioinform., 2023)

Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence. - Yingying Sun; Jun A; Zhiwei Liu; Rui Sun; Liujia Qian; Samuel H. Payne; Wout Bittremieux; Markus Ralser; Chen Li 021; Yi Chen; Zhen Dong; Yasset Pérez-Riverol; et al. (CoRR, 2025)