PeptideAtlas Publications

If you make use of any data or results from the PeptideAtlas project in a publication, please cite one or more of our PeptideAtlas papers:

Initial PeptideAtlas Publication

Frank Desiere, Eric W. Deutsch, Alexey I. Nesvizhskii, Parag Mallick, Nichole King, Jimmy K. Eng, Alan Aderem, Rose Boyle, Erich Brunner, Samuel Donohoe, Nelson Fausto, Ernst Hafen, Lee Hood, Michael G. Katze, Kathleen Kennedy, Floyd Kregenow, Hookeun Lee, Biaoyang Lin, Dan Martin, Jeff Ranish, David J. Rawlings, Lawrence E. Samelson, Yuzuru Shiio, Julian Watts, Bernd Wollscheid, Michael E. Wright, Wei Yan, Lihong Yang, Eugene Yi, Hui Zhang and Ruedi Aebersold: "Integration of Peptide Sequences Obtained by High-Throughput Mass Spectrometry with the Human Genome", Genome Biology 2004, 6:R9 - [PDF]

Human Plasma PeptideAtlas

Eric W. Deutsch, Jimmy K. Eng, Hui Zhang, Nichole L. King, Alexey I. Nesvizhskii, Biaoyang Lin, Hookeun Lee, Eugene C. Yi, Reto Ossola, and Ruedi Aebersold: "Human Plasma PeptideAtlas", Proteomics. 2005 Aug;5(13):3497-500 - [PDF]

Yeast (S. cerevisiae) PeptideAtlas

Nichole L. King, Deutsch EW, Ranish JA, Nesvizhskii AI, Eddes JS, Mallick P, Eng J, Desiere F, Flory M, Martin DB, Kim B, Lee H, Raught B, Aebersold R. "Analysis of the S. cerevisiae proteome with PeptideAtlas.", Genome Biol. 2006 Nov 13;7(11)

PeptideAtlas MRM

Eric W Deutsch, Henry Lam & Ruedi Aebersold: PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows , EMBO reports 9, 5, 429–434 (2008)

Halobacterium PeptideAtlas

Phu T. Van, Amy K. Schmid, Nichole L. King, Amardeep Kaur, Min Pan, Kenia Whitehead, Tie Koide, Marc T. Facciotti, Young Ah Goo, Eric W. Deutsch, David J. Reiss, Parag Mallick, Nitin S. Baliga: Halobacterium salinarum NRC-1 PeptideAtlas: Toward Strategies for Targeted Proteomics and Improved Proteome Coverage , J Proteome Research (in press)

Latest Update

Frank Desiere, Eric W. Deutsch, Nichole L. King, Alexey I. Nesvizhskii, Parag Mallick, Jimmy Eng, Sharon Chen, James Eddes, Sandra N. Loevenich, and Ruedi Aebersold: "The PeptideAtlas Project", Nucleic Acids Research, 2006, 34, D655-D658 - [PDF]

DATA PUBLICATIONS

The publications further describing datasets used in the PeptideAtlas builds can be found on the Raw Data Repository page and on the Data Contributors page.