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Using the Human Plasma PeptideAtlas to Study Human Plasma Proteins

  • Terry FarrahEmail author
  • Eric W. Deutsch
  • Ruedi Aebersold
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 728)

Abstract

PeptideAtlas is a web-accessible database of LC–MS/MS shotgun proteomics results from hundreds of experiments conducted in diverse laboratories, with all data processed via a uniform analysis pipeline. A total of 91 experiments on human plasma and serum are included. Using the PeptideAtlas web interface, users can browse and search the Human Plasma PeptideAtlas for identified peptides and identified proteins, view spectra, and select proteotypic peptides. Users can easily view supporting information such as chromosomal mapping, estimated abundances, and sequence alignments. Herein, the reader is instructed in the use of the Human Plasma PeptideAtlas through an illustrated exploration of cytokine receptors in plasma.

Key words

Plasma PeptideAtlas 

Notes

Acknowledgments

The PeptideAtlas Project has involved a great many contributors. The authors would like to thank the following persons for their contributions to the design and implementation of PeptideAtlas: Dave Campbell, Nichole King, Luis Mendoza, David Shteynberg, Natalie Tasman, Abhishek Pratap, Pat Moss, Jimmy Eng, Ning Zhang, Frank Desiere, Zhi Sun, and Michael Johnson. The authors would also like to thank Christopher Paulse and Robert West for reviewing this chapter and Julie Bletz for editing.

The authors have been funded in part with Federal funds from the National Heart, Lung, and Blood Institute, and the National Institutes of Health, under contract No. N01-HV-28179, and from PM50 GMO76547/Center for Systems Biology.

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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.Institute for Systems BiologySeattleUSA

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