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:

General Publications

General purpose citation: Desiere et al., "The PeptideAtlas Project", Nucleic Acids Research, 2006, 34, D655-D658 - [PDF]

Latest publication: Detection of the Arabidopsis Proteome and Its Post-translational Modifications and the Nature of the Unobserved (Dark) Proteome in PeptideAtlas; van Wijk KJ, Leppert T, Sun Z, Kearly A, Li M, Mendoza L, Guzchenko I, Debley E, Sauermann G, Routray P, Malhotra S, Nelson A, Sun Q, Deutsch EW.J Proteome Res. 2024 Jan 5;23(1):185-214. doi: 10.1021/acs.jproteome.3c00536. Epub 2023 Nov 21.PMID: 38104260

Tutorial: Farrah et al., Using the Human Plasma PeptideAtlas to Study Human Plasma Proteins , Serum/Plasma Proteomics, Methods in Molecular Biology, 2011 - [pre-publication PDF]

Human Proteome

Latest publication: Omenn GS, Lane L, Overall CM, Pineau C, Packer NH, Cristea IM, Lindskog C, Weintraub ST, Orchard S, Roehrl MHA, Nice E, Liu S, Bandeira N, Chen YJ, Guo T, Aebersold R, Moritz RL, Deutsch EW. The 2022 Report on the Human Proteome from the HUPO Human Proteome Project; J Proteome Res. 2022 Nov 1. doi: 10.1021/acs.jproteome.2c00498. PMID: 36318223,

Deutsch EW, Omenn GS, Sun Z, Maes M, Pernemalm M, Palaniappan KK, Letunica N, Vandenbrouck Y, Brun V, Tao SC, Yu X, Geyer PE, Ignjatovic V, Moritz RL, Schwenk JM, Advances and Utility of the Human Plasma Proteome, J Proteome Res. 2021 Dec 3;20(12):5241-5263

Schwenk et al., The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays, Journal of Proteome Research (2017)

Deutsch et al., State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet., Journal of Proteome Research (2015)

Farrah, et al., State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project, Journal of Proteome Research (2014)

Farrah, et al., The State of the Human Proteome in 2012 as Viewed through PeptideAtlas, Journal of Proteome Research, 2013, 12 (1), pp162-171 - [PDF]

Initial publication: Desiere et al., "Integration of Peptide Sequences Obtained by High-Throughput Mass Spectrometry with the Human Genome", Genome Biology 2004, 6:R9 - [PDF]

Human Plasma

Latest publication: Deutsch EW, Omenn GS, Sun Z, Maes M, Pernemalm M, Palaniappan KK, Letunica N, Vandenbrouck Y, Brun V, Tao SC, Yu X, Geyer PE, Ignjatovic V, Moritz RL, Schwenk JM, Advances and Utility of the Human Plasma Proteome, J Proteome Res. 2021 Dec 3;20(12):5241-5263

Previous publication: Schwenk et al., The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays, Journal of Proteome Research (2017)

Original publication: Deutsch, et al., "Human Plasma PeptideAtlas", Proteomics. 2005 Aug;5(13):3497-500 - [PDF]

Protein concentation estimation: Farrah, et al., A High-Confidence Human Plasma Proteome Reference Set with Estimated Concentrations in PeptideAtlas, Mol Cell Proteomics (2011) - [PDF]

Specific Species and Sub-proteomes

Arabidopsis Latest: Detection of the Arabidopsis Proteome and Its Post-translational Modifications and the Nature of the Unobserved (Dark) Proteome in PeptideAtlas; van Wijk KJ, Leppert T, Sun Z, Kearly A, Li M, Mendoza L, Guzchenko I, Debley E, Sauermann G, Routray P, Malhotra S, Nelson A, Sun Q, Deutsch EW.J Proteome Res. 2024 Jan 5;23(1):185-214. doi: 10.1021/acs.jproteome.3c00536. Epub 2023 Nov 21.PMID: 38104260
Previous: van Wijk et al, The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource, The Plant Cell (2021 Aug 19) -- [ Pubmed -- bioRxiv ]

Chicken: McCord et al., The PeptideAtlas of the Domestic Laying Hen, Journal of Proteome Research (2017)

Pig: Hesselager et al., The Pig PeptideAtlas: A resource for systems biology in animal production and biomedicine, Proteomics (2016)

Candida Albicans: Vialas et al., A comprehensive Candida albicans PeptideAtlas build enables deep proteome coverage, Journal of Proteomics (2016)

Horse: Bundgaard et al., The Equine PeptideAtlas: a resource for developing proteomics-based veterinary research, Proteomics (2014)

Candida Albicans: Vialas et al., A Candida albicans PeptideAtlas, Journal of Proteomics (2014)

Cow: Bislev, et al., A Bovine PeptideAtlas of milk and mammary gland proteomes, Proteomics 2012, 12:18 - [PDF]

Honeybee: Queenie, et al., A honey bee (Apis mellifera L.) PeptideAtlas crossing castes and tissues, BMC Genomics 2011, 12:290 - [PDF]

Halobacterium: Van, et al., Halobacterium salinarum NRC-1 PeptideAtlas: Toward Strategies for Targeted Proteomics and Improved Proteome Coverage, J. Proteome Res.; 2008; ASAP Article; DOI: 10.1021/pr800031f

Mouse Plasma: Zhang, et al., A Mouse Plasma Peptide Atlas as a Resource for Disease Proteomics , Genome Biology, 9, 6, R93 (2008) - [PDF]

Yeast (S. cerevisiae): King, et al., "Analysis of the S. cerevisiae proteome with PeptideAtlas.", Genome Biol. 2006 Nov 13;7(11)

SRM

SRMAtlas (whole proteome synthetic peptide SRM library)

Initial publication (yeast): Picotti, et al., High-throughput generation of selected reaction-monitoring assays for proteins and proteomes , Nat. Methods 7, 43-46 (2010) - [PDF]

Yeast whole proteome: Picotti, et al., A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis, Nature 494 (7436):266-70 (2013) - [PDF]

Human whole proteome: Kusebauch U, Campbell DS, Deutsch EW, Chu CS, Spicer DA, Brusniak MY, Slagel J, Sun Z, Stevens J, Grimes B, Shteynberg D, Hoopmann MR, Blattmann P, Ratushny AV, Rinner O, Picotti P, Carapito C, Huang CY, Kapousouz M, Lam H, Tran T, Demir E, Aitchison JD, Sander C, Hood L, Aebersold R, Moritz RL. Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome, 2016, Cell, 166(3):766-78, PMCID: PMC5245710

SRM design (pre-SRMAtlas): Deutsch, et al., PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows , EMBO reports 9, 5, 429–434 (2008) - [PDF]

PASSEL: Farrah, et al., PASSEL: the PeptideAtlas experiment library , Proteomics. 2012 Feb 9 (Epub ahead of print) - [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.