PeptideAtlas Home
 Seattle Proteome

  Data Contributors
  Database Schema

Atlas Data:
  Data Repository
  Human Plasma
(Farrah, et al.)

  HPPP Data Central
  PeptideAtlas Builds
  Search Database

  Contribute Data
  Genome Browser


Spectral Libs:
  Libraries + Info
  SpectraST Search

  Atlas nomenclature
  SGD nomenclature
  Protein ID terms


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: 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]

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

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]

Publications regarding 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, et al. and Deutsch, et al. publications in preparation as of May 2013.

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].

Publications for specific species and sub-proteomes

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

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

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

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.

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


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.

© 2004-2015, Institute for Systems Biology. All Rights Reserved
Project funding: