Z
Zhi Sun
Researcher at Institute for Systems Biology
Publications - 54
Citations - 5250
Zhi Sun is an academic researcher from Institute for Systems Biology. The author has contributed to research in topics: PeptideAtlas & Proteome. The author has an hindex of 22, co-authored 43 publications receiving 4149 citations.
Papers
More filters
Journal ArticleDOI
A guided tour of the Trans‐Proteomic Pipeline
Eric W. Deutsch,Luis Mendoza,David Shteynberg,Terry Farrah,Henry H N Lam,Natalie Tasman,Zhi Sun,Erik Nilsson,Brian S. Pratt,Bryan J. Prazen,Jimmy K. Eng,Daniel Martin,Alexey I. Nesvizhskii,Ruedi Aebersold +13 more
TL;DR: The full workflow of the TPP is described, along with an example on a sample data set, demonstrating that the setup and use of the tools are straightforward and well supported and do not require specialized informatic resources or knowledge.
Journal ArticleDOI
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 Perez-Riverol,Tobias Ternent,David S. Campbell,Manuel Bernal-Llinares,Shujiro Okuda,Shin Kawano,Robert L. Moritz,Jeremy Carver,Mingxun Wang,Mingxun Wang,Yasushi Ishihama,Nuno Bandeira,Nuno Bandeira,Henning Hermjakob,Henning Hermjakob,Juan Antonio Vizcaíno +19 more
TL;DR: The ProteomeXchange Consortium of proteomics resources was formally started in 2011 to standardize data submission and dissemination of mass spectrometry proteomics data worldwide and is supporting a change in culture of the proteomics field.
Journal ArticleDOI
iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates
David Shteynberg,Eric W. Deutsch,Henry H N Lam,Jimmy K. Eng,Zhi Sun,Natalie Tasman,Luis Mendoza,Robert L. Moritz,Ruedi Aebersold,Ruedi Aebersold,Alexey I. Nesvizhskii +10 more
TL;DR: The use of iProphet in the Trans-Proteomics Pipeline increases the number of correctly identified peptides at a constant false discovery rate as compared with both PeptideProphet and another state-of-the-art tool Percolator.
Journal ArticleDOI
The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics.
Eric W. Deutsch,Nuno Bandeira,Nuno Bandeira,Vagisha Sharma,Yasset Perez-Riverol,Jeremy Carver,Jeremy Carver,Deepti J. Kundu,David García-Seisdedos,Andrew F. Jarnuczak,Suresh Hewapathirana,Benjamin Pullman,Benjamin Pullman,Julie Wertz,Julie Wertz,Zhi Sun,Shin Kawano,Shujiro Okuda,Yu Watanabe,Henning Hermjakob,Henning Hermjakob,Brendan MacLean,Michael J. MacCoss,Yunping Zhu,Yasushi Ishihama,Juan Antonio Vizcaíno +25 more
TL;DR: The updated submission guidelines are described and it is demonstrated that the proteomics field is now actively embracing public open data policies and an unprecedented increase of data re-use activities in the field is enabling novel research and new data resources.
Journal ArticleDOI
A High-Confidence Human Plasma Proteome Reference Set with Estimated Concentrations in PeptideAtlas
Terry Farrah,Eric W. Deutsch,Gilbert S. Omenn,Gilbert S. Omenn,David S. Campbell,Zhi Sun,Julie A. Bletz,Parag Mallick,Jonathan E. Katz,Johan Malmström,Reto Ossola,Julian D. Watts,Biaoyang Lin,Hui Zhang,Robert L. Moritz,Ruedi Aebersold +15 more
TL;DR: This work has identified 20,433 distinct peptides, from which it inferred a highly nonredundant set of 1929 protein sequences at a false discovery rate of 1%, and compiled a high-confidence human plasma proteome reference set with well over twice the identified proteins of previous high- confidence sets.