| | |  | | | | Record from Web of Science® | | | | | | |
| 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 |
|
|
| Author(s): Omenn GS, States DJ, Adamski M, Blackwell TW, Menon R, Hermjakob H, Apweiler R, Haab BB, Simpson RJ, Eddes JS, Kapp EA, Moritz RL, Chan DW, Rai AJ, Admon A, Aebersold R, Eng J, Hancock WS, Hefta SA, Meyer H, Paik YK, Yoo JS, Ping PP, Pounds J, Adkins J, Qian XH, Wang R, Wasinger V, Wu CY, Zhao XH, Zeng R, Archakov A, Tsugita A, Beer I, Pandey A, Pisano M, Andrews P, Tammen H, Speicher DW, Hanash SM |
| Source: PROTEOMICS Volume: 5 Issue: 13 Pages: 3226-3245 Published: AUG 2005 |
| Times Cited: 255 References: 64 |
| Abstract: HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms; (2) compared PPP reference specimens of human serum and EDTA, heparin, and citrate-anticoagulated plasma; and (3) created a publicly-available knowledge base (www.bioinformatics.med.umich.edu/hupo/ppp; www.ebi.ac.uk/pride). Thirty-five participating laboratories in 13 countries submitted datasets. Working groups addressed (a) specimen stability and protein concentrations; (b) protein identifications from 18 MS/MS datasets; (c) independent analyses from raw MS-MS spectra; (d) search engine performance, subproteome analyses, and biological insights; (e) antibody arrays; and (f) direct MS/SELDI analyses. MS-MS datasets had 15 710 different International Protein Index (IPI) protein IDs; our integration algorithm applied to multiple matches of peptide sequences yielded 9504 IPI proteins identified with one or more peptides and 3020 proteins identified with two or more peptides (the Core Dataset). These proteins have been characterized with Gene Ontology, InterPro, Novartis Atlas, OMIM, and immunoassay-based concentration determinations. The database permits examination of many other subsets, such as 1274 proteins identified with three or more peptides. Reverse protein to DNA matching identified proteins for 118 previously unidentified ORFs. We recommend use of plasma instead of serum, with EDTA (or citrate) for anticoagulation. To improve resolution, sensitivity and reproducibility of peptide identifications and protein matches, we recommend combinations of depletion, fractionation, and MS/MS technologies, with explicit criteria for evaluation of spectra, use of search algorithms, and integration of homologous protein matches.
This Special Issue of PROTEOMICS presents papers integral to the collaborative analysis plus many reports of supplementary work on various aspects of the PPP workplan. These PPP results on complexity, dynamic range, incomplete sampling, false-positive matches, and integration of diverse datasets for plasma and serum proteins lay a foundation for development and validation of circulating protein biomarkers in health and disease.
|
| Document Type: Article |
| Language: English |
| Reprint Address: Omenn, GS (reprint author), Univ Michigan, MSRB 1,1150 W Med Ctr Dr, Ann Arbor, MI 48109 USA |
Addresses:
1. Univ Michigan, Ann Arbor, MI 48109 USA
2. European Bioinformat Inst, Hinxton, England
3. Van Andel Res Inst, Grand Rapids, MI USA
4. Ludwig Inst Canc Res, Melbourne, Vic 3050 Australia
5. Johns Hopkins Univ, Baltimore, MD USA
6. Technion Israel Inst Technol, Haifa, Israel
7. Swiss Fed Inst Technol, ETH, Zurich, Switzerland
8. Inst Syst Biol, Seattle, WA USA
9. Northeastern Univ, Boston, MA 02115 USA
10. Ruhr Univ Bochum, D-4630 Bochum, Germany
11. Yonsei Res Ctr, Seoul, South Korea
12. Korea Basic Sci Inst, Seoul, South Korea
13. Univ Calif Los Angeles, Los Angeles, CA USA
14. Pacific NW Natl Lab, Richland, WA USA
15. Inst Radiat Med, Beijing, Peoples R China
16. CUNY Mt Sinai Sch Med, New York, NY 10029 USA
17. Univ New S Wales, Kensington, NSW 2033 Australia
18. Chinese Acad Med Sci, Beijing 100037, Peoples R China
19. Shanghai Inst Biol Sci, Shanghai, Peoples R China
20. Inst Biomed Chem, Moscow, Russia
21. NEC Proteom Res Lab, Tsukuba, Ibaraki Japan
22. IBM Corp, Haifa, Israel
23. Proteom Res Serv Inc, Ann Arbor, MI USA
24. BioVisioN AG, Hannover, Germany
25. Wistar Inst Anat & Biol, Philadelphia, PA 19104 USA
26. Fred Hutchinson Canc Res Ctr, Seattle, WA 98104 USA |
| Publisher: WILEY-V C H VERLAG GMBH, PO BOX 10 11 61, D-69451 WEINHEIM, GERMANY |
| Subject Category: Biochemical Research Methods; Biochemistry & Molecular Biology |
| IDS Number: 958VZ |
| ISSN: 1615-9853 |
| DOI: 10.1002/pmic.200500358 |
|
| | | | | | | | | Record from Web of Science® | | | | | | | | | |