Table of Contents

CHAPTER 1
Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database (Pages: 1-35)
Dr. Gilbert S. Omenn Dr. David J. States Marcin Adamski Thomas W. Blackwell Rajasree Menon Henning Hermjakob Rolf Apweiler Brian B. Haab Ph.D. Professor Richard J. Simpson James S. Eddes Eugene A. Kapp Robert L. Moritz Daniel W. Chan Dr. Alex J. Rai Professor Arie Admon Ruedi Aebersold Jimmy Eng Professor William S. Hancock Stanley A. Hefta Helmut Meyer Professor Young-Ki Paik Jong-Shin Yoo Peipei Ping Dr. Joel Pounds Joshua Adkins Dr. Xiaohong Qian Ph.D. Rong Wang Valerie Wasinger Chi Yue Wu Xiaohang Zhao Rong Zeng Alexander Archakov Akira Tsugita Ilan Beer Dr. Akhilesh Pandey Michael Pisano Philip Andrews Harald Tammen Dr. David W. Speicher Samir M. Hanash
CHAPTER 2
Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project (Pages: 37-61)
Marcin Adamski Thomas Blackwell Rajasree Menon Dr. Lennart Martens Henning Hermjakob Chris Taylor Dr. Gilbert S. Omenn Dr. David J. States
CHAPTER 3
HUPO Plasma Proteome Project specimen collection and handling: Towards the standardization of parameters for plasma proteome samples (Pages: 63-89)
Dr. Alex J. Rai Craig A. Gelfand Bruce C. Haywood David J. Warunek Jizu Yi Mark D. Schuchard Richard J. Mehigh Steven L. Cockrill Graham B. I. Scott Harald Tammen Peter Schulz-Knappe Dr. David W. Speicher Frank Vitzthum Brian B. Haab Ph.D. Gerard Siest Daniel W. Chan
CHAPTER 4
Immunoassay and antibody microarray analysis of the HUPO Plasma Proteome Project reference specimens: Systematic variation between sample types and calibration of mass spectrometry data (Pages: 91-113)
Brian B. Haab Ph.D. Bernhard H. Geierstanger George Michailidis Frank Vitzthum Sara Forrester Ryan Okon Petri Saviranta Achim Brinker Martin Sorette Lorah Perlee Shubha Suresh Garry Drwal Joshua N. Adkins Gilbert S. Omenn
CHAPTER 5
Depletion of multiple high-abundance proteins improves protein profiling capacities of human serum and plasma (Pages: 115-134)
Lynn A. Echan Hsin-Yao Tang Nadeem Ali-Khan KiBeom Lee Dr. David W. Speicher
CHAPTER 9
Efficient prefractionation of low-abundance proteins in human plasma and construction of a two-dimensional map (Pages: 201-219)
Sang Yun Cho Eun-Young Lee Joon Seok Lee Hye-Young Kim Jae Myun Park Min-Seok Kwon Young-Kew Park Hyoung-Joo Lee Min-Jung Kang Jin Young Kim Jong Shin Yoo Sung Jin Park Jin Won Cho Hyon-Suk Kim Professor Young-Ki Paik
CHAPTER 10
Comparison of alternative analytical techniques for the characterisation of the human serum proteome in HUPO Plasma Proteome Project (Pages: 221-247)
Xiaohai Li Yan Gong Ying Wang Songfeng Wu Yun Cai Ping He Zhuang Lu Wantao Ying Yangjun Zhang Liyan Jiao Hongzhi He Zisen Zhang Fuchu He Xiaohang Zhao Dr. Xiaohong Qian Ph.D.
CHAPTER 11
A proteomic study of the HUPO Plasma Proteome Project's pilot samples using an accurate mass and time tag strategy (Pages: 249-271)
Joshua N. Adkins Matthew E. Monroe Kenneth J. Auberry Yufeng Shen Jon M. Jacobs David G. Camp II Frank Vitzthum Karin D. Rodland Richard C. Zangar Richard D. Smith Dr. Joel G. Pounds
CHAPTER 12
Analysis of Human Proteome Organization Plasma Proteome Project (HUPO PPP) reference specimens using surface enhanced laser desorption/ionization-time of flight (SELDI-TOF) mass spectrometry: Multi-institution correlation of spectra and identification of biomarkers (Pages: 273-287)
Dr. Alex J. Rai Paul M. Stemmer Zhen Zhang Bao-Ling Adam William T. Morgan Rebecca E. Caffrey Vladimir N. Podust Manisha Patel Lih-Yin Lim Natalia V. Shipulina Daniel W. Chan O. John Semmes Hon-Chiu Eastwood Leung
CHAPTER 13
An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and specificity analysis (Pages: 289-315)
Eugene A. Kapp Frédéric Schütz Lisa M. Connolly John A. Chakel Jose E. Meza Christine A. Miller David Fenyo Jimmy K. Eng Joshua N. Adkins Dr. Gilbert S. Omenn Professor Richard J. Simpson
CHAPTER 14
Human Plasma PeptideAtlas (Pages: 317-322)
Dr. Eric W. Deutsch Jimmy K. Eng Hui Zhang Nichole L. King Alexey I. Nesvizhskii Biaoyang Lin Hookeun Lee Eugene C. Yi Reto Ossola Ruedi Aebersold
CHAPTER 15
Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories (Pages: 323-328)
Dr. Lennart Martens Alexey I. Nesvizhskii Henning Hermjakob Marcin Adamski Dr. Gilbert S. Omenn Joël Vandekerckhove Kris Gevaert
CHAPTER 16
A functional annotation of subproteomes in human plasma (Pages: 329-351)
Peipei Ping Thomas M. Vondriska Chad J. Creighton T. K. B. Gandhi Ziping Yang Rajasree Menon Min-Seok Kwon Sang Yun Cho Garry Drwal Markus Kellmann Suraj Peri Shubha Suresh Mads Gronborg Henrik Molina Raghothama Chaerkady B. Rekha Arun S. Shet Robert E. Gerszten Haifeng Wu Mark Raftery Valerie Wasinger Peter Schulz-Knappe Samir M. Hanash Professor Young-Ki Paik Professor William S. Hancock Dr. David J. States Dr. Gilbert S. Omenn Dr. Akhilesh Pandey
CHAPTER 17
Cardiovascular-related proteins identified in human plasma by the HUPO Plasma Proteome Project Pilot Phase (Pages: 353-370)
Beniam T. Berhane Chenggong Zong David A. Liem Aaron Huang Steven Le Ricky D. Edmondson Richard C. Jones Xin Qiao Julian P. Whitelegge Peipei Ping Thomas M. Vondriska