Standard guidelines for the chromosome-centric human proteome project

Journal of Proteome Research

Volumn 11, Issue 4, 2012, Pages 2005-2013

  Paik, Young Ki ^a   Omenn, Gilbert S ^b   Uhlen, Mathias ^c   Hanash, Samir ^d   Marko Varga, György ^e   Aebersold, Ruedi ^f   Bairoch, Amos ^g   Yamamoto, Tadashi ^h   Legrain, Pierre ⁱ   Lee, Hyoung Joo ^a   Na, Keun ^a   Jeong, Seul Ki ^a   He, Fuchu ^j   Binz, Pierre Alain ^g   Nishimura, Toshihide ^k   Keown, Paul ^l   Baker, Mark S ^m   Yoo, Jong Shin ⁿ   Garin, Jerome ^o   Archakov, Alexander ^p   Bergeron, John ^q   Salekdeh, Ghasem Hosseini ^r   Hancock, William S ^a,s   more..

^a Yonsei University   (South Korea)

^b UNIVERSITY OF MICHIGAN   (United States)

^c ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^d Fred Hutchinson Cancer Research Center   (United States)

^e LUND UNIVERSITY   (Sweden)

^f UNIVERSITY OF ZURICH   (Switzerland)

^g UNIVERSITY OF GENEVA   (Switzerland)

^h NIIGATA UNIVERSITY GRADUATE SCHOOL OF MEDICAL AND DENTAL SCIENCES   (Japan)

ⁱ ECOLE POLYTECHNIQUE   (France)

^j Beijing Proteome Research Center   (China)

^k TOKYO MEDICAL UNIVERSITY   (Japan)

^l UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^m MACQUARIE UNIVERSITY   (Australia)

ⁿ Korea Basic Science Institute (KBSI)   (South Korea)

^o CEA GRENOBLE   (France)

^p INSTITUTE OF BIOMEDICAL CHEMISTRY   (Russian Federation)

^q MCGILL UNIVERSITY   (Canada)

^r ROYAN INSTITUTE FOR REPRODUCTIVE BIOMEDICINE   (Iran)

^s NORTHEASTERN UNIVERSITY   (United States)

more..

Author keywords

antibody; Biology Disease Driven Human Proteome Project; Chromosome Centric Human Proteome Project; Human Genome Project; Human Proteome Organization; Human Proteome Project; knowledge base; mass spectrometry

Indexed keywords

PROTEOME;

BIOINFORMATICS; CHROMOSOME; GENE LOCATION; HEALTH CARE INDUSTRY; HEALTH CARE POLICY; HUMAN; PEPTIDE MAPPING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; QUALITY CONTROL; REVIEW;

CHROMOSOMES, HUMAN; DATABASES, PROTEIN; GUIDELINES AS TOPIC; HUMAN GENOME PROJECT; HUMANS; MASS SPECTROMETRY; PROTEOME; PROTEOMICS; RESEARCH DESIGN;

EID: 84859622404     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr200824a     Document Type: Review

References (28)

1. Legrain, P.; Aebersold, R.; Archakov, A.; Bairoch, A. The human proteome project: Current state and future direction Mol. Cell. Proteomics 2011, 10, M111.009993
2. Hancock, W.; Omenn, G.; Legrain, P.; Paik, Y. K. Proteomics, human proteome project, and chromosomes J. Proteome Res. 2011, 10, 210
3. Paik, Y. K.; Jeong, S. K.; Omenn, G. S.; Uhlen, M.; Hanash, S. The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome Nat. Biotechnol. 2012, 30, 221-3
4. Uhlén, M.; Oksvold, P.; Algenas, C.; Hamsten, C. Antibody-based protein profiling of the human chromosome 21 Mol. Cell. Proteomics 2011, 10, M111.013458
5. Orchard, S.; Taylor, C.; Hermjakob, H.; Zhu, W. Current status of proteomic standards development Expert Rev. Proteomics 2005, 1, 179-83
6. Omenn, G. S.; States, D. J.; Adamski, M.; Blackwell, T. W. 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 Proteomics 2005, 5, 3226-45
7. He, F. Human liver proteome project: plan, progress, and perspectives Mol. Cell. Proteomics 2005, 4, 1841-8
8. Uhlen, M.; Ponten, F. Antibody-based proteomics for human tissue profiling Mol. Cell. Proteomics 2005, 4, 384-93
9. Hamacher, M.; Marcus, K.; Stephan, C.; Klose, J.; Park, Y. M.; Meyer, H. E. HUPO Brain Proteome Project: toward a code of conduct Mol. Cell. Proteomics 2008, 7, 457
10. Yamamoto, T.; Langham, R. G.; Ronco, P.; Knepper, M. A.; Thongboonkerd, V. Towards standard protocols and guidelines for urine proteomics: a report on the Human Kidney and Urine Proteome Project (HKUPP) symposium and workshop, 6 October 2007, Seoul, Korea and 1 November 2007, San Francisco, CA, USA Proteomics 2008, 8, 2156-9
11. Fingar, V. H.; Wieman, T. J.; Doak, K. W. Changes in tumor interstitial pressure induced by photodynamic therapy Photochem. Photobiol. 1991, 53, 763-8
12. Picotti, P.; Rinner, O.; Stallmach, R.; Dautel, F. High-throughput generation of selected reaction-monitoring assays for proteins and proteomes Nat. Methods 2010, 7, 43-6
13. Menon, R.; Omenn, G. S. Identification of alternatively spliced transcripts using a proteomic informatics approach Methods Mol. Biol. 2011, 696, 319-26
14. Im, K. M.; Kirchhoff, T; Wang, X; Green, T; Chow, C. Y. Haplotype structure in Ashkenazi Jewish BRCA1 and BRCA2 mutation carriers Hum. Genet. 2011, 130, 685-99
15. Swaney, D. L.; Wenger, C. D.; Coon, J. J. Value of using multiple proteases for large-scale mass spectrometry-based proteomics J. Proteome Res. 2010, 9, 1323-9
16. Horvatovich, P.; Hoekman, B.; Govorukhina, N.; Bischoff, R. Multidimensional chromatography coupled to mass spectrometry in analysing complex proteomics samples J. Sep. Sci. 2010, 33, 1421-37
17. Makarov, A.; Denisov, E.; Kholomeev, A.; Balschun, W.; Lange, O.; Strupat, K.; Horning, S. Performance evaluation of a hybrid linear ion trap/orbitrap mass spectrometer Anal. Chem. 2006, 78, 2113-20
18. Pichler, P.; Köcher, T.; Holzmann, J.; Mazanek, M.; Taus, T.; Ammerer, G.; Mechtler, K. Peptide labeling with isobaric tags yields higher identification rates using iTRAQ 4-plex compared to TMT 6-plex and iTRAQ 8-plex on LTQ Orbitrap Anal. Chem. 2010, 82, 6549-58
19. Kitteringham, N. R.; Jenkins, R. E.; Lane, C. S.; Elliott, V. L.; Park, B. K. Multiple reaction monitoring for quantitative biomarker analysis in proteomics and metabolomics J. Chromatogr., B: Anal. Technol. Biomed. Life Sci. 2009, 877, 1229-39
20. Schmidt, A.; Beck, M.; Malmström, J.; Lam, H.; Claassen, M.; Campbell, D.; Aebersold, R. Absolute quantification of microbial proteomes at different states by directed mass spectrometry Mol. Syst. Biol. 2011, 7, 510
21. Berglund, L.; Björling, E.; Oksvold, P.; Fagerberg, L.; Asplund, A.; Szigyarto, C. A.; Persson, A.; Ottosson, J.; Wernérus, H.; Nilsson, P.; Lundberg, E.; Sivertsson, A.; Navani, S.; Wester, K.; Kampf, C.; Hober, S.; Pontén, F.; Uhlén, M. A genecentric Human Protein Atlas for expression profiles based on antibodies Mol. Cell. Proteomics 2008, 7, 2019-27
22. Duncan, M. W.; Aebersold, R.; Caprioli, R. M. The pros and cons of peptide-centric proteomics Nat. Biotechnol. 2010, 28, 659-64
23. Kapp, E. A.; Schütz, F.; Connolly, L. M.; Chakel, J. A.; Meza, J. E. An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis Proteomics 2005, 5, 3475-90
24. Zhang, B.; Chambers, M. C.; Tabb, D. L. Proteomic parsimony through bipartite graph analysis improves accuracy and transparency J. Proteome Res. 2007, 6, 3549-57
25. Farrah, T.; Deutsch, E. W.; Omenn, G. S.; Campbell, D. S.; Sun, Z. A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas Mol. Cell. Proteomics 2011, 10, M110.006353
26. Bradshaw, R. A.; Burlingame, A. L.; Carr, S.; Aebersold, R. Reporting protein identification data: the next generation of guidelines Mol. Cell. Proteomics 2006, 5, 787-8
27. ENCODE Project Consortium; Myers, R. M.; Stamatoyannopoulos, J.; Snyder, M.; Dunham, I.; Hardison, R. C. Users guide to the encyclopedia of DNA elements (ENCODE) PLoS Biol. 2011, 9, e1001046
28. Conrad, D. F.; Keebler, J. E.; DePristo, M. A.; Lindsay, S. J.; Zhang, Y. Variation in genome-wide mutation rates within and between human families Nat. Genet. 2011, 43, 712-4