Abstract
Undoubtedly, one of the greatest achievements of scientific research was the completion of sequencing the human genome in 2003 that is still unmatched in size of collaborative efforts (International Human Genome Sequencing Consortium 2004). The social benefit of the knowledge generated is better understanding the expressions of genes in healthy and diseased conditions, which in turn can lead to better diagnosis and treatment of many diseases, including various forms of cancer. Notably, the technological developments have continuously delivered efficient tools to overcome the difficulties of mapping about three billion base pair long genetic codes. As an additional outcome, today, we know that the human chromosomes hold about 20,300 genes coding for all functional proteins in the wide versatility of biological activities of cells.
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Aebersold R, Bader GD, Edwards AM, et al. The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community. J Proteome Res. 2013;12(1):23–7.
Anderson NL, Anderson NG. The human plasma proteome – history, character, and diagnostic prospects. Mol Cell Proteomics. 2002;1(11):845–67.
Anderson NL, Anderson NG, Haines LR, Hardie DB, Olafson RW, Pearson TW. Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA). J Proteome Res. 2004;3(2):235–44.
Berglund L, Bjorling E, Oksvold P, et al. A genecentric human protein atlas for expression profiles based on antibodies. Mol Cell Proteomic MCP. 2008;7(10):2019–27.
Björling E, Uhlén M. Antibodypedia, a portal for sharing antibody and antigen validation data. Mol Cell Proteomics. 2008;7(10):2028–37.
Craig R, Cortens JP, Beavis RC. Open source system for analyzing, validating, and storing protein identification data. J Proteome Res. 2004;3(6):1234–42.
Desiere F, Deutsch EW, King NL, et al. The PeptideAtlas project. Nucleic Acids Res. 2006;34 Suppl 1:D655–8.
Domon B, Aebersold R. Review – mass spectrometry and protein analysis. Science. 2006;312(5771):212–7.
Fenyo D, Eriksson J, Beavis R. Mass spectrometric protein identification using the global proteome machine. Methods Mol Biol. 2010;673:189–202.
Gaudet P, Argoud-Puy G, Cusin I, et al. neXtProt: organizing protein knowledge in the context of Human Proteome Projects. J Proteome Res. 2013;12(1):293–8.
Goode RJ, Yu S, Kannan A, et al. The proteome browser web portal. J Proteome Res. 2013;12(1):172–8.
Guo F, Wang D, Liu Z, et al. CAPER: a chromosome-assembled human proteome browsER. J Proteome Res. 2013;12(1):179–86.
International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature. 2004;431(7011):931–45.
Islam MT, Garg G, Hancock WS, Risk BA, Baker MS, Ranganathan S. Protannotator: a semiautomated pipeline for chromosome-wise functional annotation of the “Missing”. J Proteome Res. 2014;13(1):76–83.
Jeong S-K, Lee H-J, Na K, et al. GenomewidePDB, a proteomic database exploring the comprehensive protein parts list and transcriptome landscape in human chromosomes. J Proteome Res. 2013;12(1):106–11.
Lane L, Argoud-Puy G, Britan A, et al. neXtProt: a knowledge platform for human proteins. Nucleic Acids Res. 2012;40(Database issue):D76–83.
Lane L, Bairoch A, Beavis RC, et al. Metrics for the Human Proteome Project 2013–2014 and strategies for finding missing proteins. J Proteome Res. 2014;13(1):15–20.
Lange V, Picotti P, Domon B, Aebersold R. Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol. 2008;4:222.
Legrain P, Aebersold R, Archakov A, et al. The human proteome project: current state and future direction. Mol Cell Proteomic MCP. 2011;10(7):M111.009993.
Lilja H, Ulmert D, Bjork T, et al. Long-term prediction of prostate cancer up to 25 years before diagnosis of prostate cancer using prostate kallikreins measured at age 44 to 50 years. J Clin Oncol. 2007;25(4):431–6.
Lopez MF, Rezai T, Sarracino DA, et al. Selected reaction monitoring-mass spectrometric immunoassay responsive to parathyroid hormone and related variants. Clin Chem. 2010;56(2):281–90.
Mann M. Comparative analysis to guide quality improvements in proteomics. Nat Methods. 2009;6(10):717–9.
Martens L, Hermjakob H, Jones P, et al. PRIDE: the proteomics identifications database. Proteomics. 2005;5(13):3537–45.
Munoz J, Low TY, Kok YJ, et al. The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells. Mol Syst Biol. 2011;7:550.
Olsen JV, Schwartz JC, Griep-Raming J, et al. A dual pressure linear ion trap orbitrap instrument with very high sequencing speed. Mol Cell Proteomics. 2009;8(12):2759–69.
Paik YK, Jeong SK, Omenn GS, et al. The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nat Biotechnol. 2012a;30(3):221–3.
Paik YK, Omenn GS, Uhlen M, et al. Standard guidelines for the Chromosome-Centric Human Proteome Project. J Proteome Res. 2012b;11(4):2005–13.
Paik Y-K, Omenn GS, Thongboonkerd V, Marko-Varga G, Hancock WS. Genome-wide proteomics, chromosome-Centric Human Proteome Project (C-HPP), Part II. J Proteome Res. 2014;13(1):1–4.
Picotti P, Rinner O, Stallmach R, et al. High-throughput generation of selected reaction-monitoring assays for proteins and proteomes. Nat Methods. 2010;7(1):43–6.
Ranganathan S, Khan JM, Garg G, Baker MS. Functional annotation of the human chromosome 7 “Missing” proteins: a bioinformatics approach. J Proteome Res. 2013;12(6):2504–10.
Schmidt A, Claassen M, Aebersold R. Directed mass spectrometry: towards hypothesis-driven proteomics. Curr Opin Chem Biol. 2009;13(5–6):510–7.
Shi T, Fillmore TL, Sun X, et al. Antibody-free, targeted mass-spectrometric approach for quantification of proteins at low picogram per milliliter levels in human plasma/serum. Proc Natl Acad Sci U S A. 2012;109(38):15395–400.
Shiromizu T, Adachi J, Watanabe S, et al. Identification of missing proteins in the neXtProt database and unregistered phosphopeptides in the PhosphoSitePlus database as part of the Chromosome-Centric Human Proteome Project. J Proteome Res. 2013;12(6):2414–21.
Smith BE, Hill JA, Gjukich MA, Andrews PC. Tranche distributed repository and ProteomeCommons.org. Methods Mol Biol. 2011;696:123–45.
Song C, Wang F, Cheng K, et al. Large-scale quantification of single amino-acid variations by a variation-associated database search strategy. J Proteome Res. 2014;13(1):241–8.
The UniProt Consortium. Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res. 2011;39(Database issue):D214–9.
Végvári Á, Sjödin K, Rezeli M, et al. Identification of a novel proteoform of prostate specific antigen (SNP-L132I) in clinical samples by multiple reaction monitoring. Mol Cell Proteomic MCP. 2013;12(10):2761–73.
Wang D, Liu Z, Guo F, et al. CAPER 2.0: an interactive, configurable, and extensible workflow-based platform to analyze data sets from the Chromosome-Centric Human Proteome Project. J Proteome Res. 2014;13(1):99–106.
Whiteaker JR, Zhao L, Zhang HY, et al. Antibody-based enrichment of peptides on magnetic beads for mass-spectrometry-based quantification of serum biomarkers. Anal Biochem. 2007;362(1):44–54.
Whiteaker JR, Zhao L, Abbatiello SE, et al. Evaluation of large scale quantitative proteomic assay development using peptide affinity-based mass spectrometry. Mol Cell Proteomic MCP. 2011;10(4):M110.005645.
Zgoda VG, Kopylov AT, Tikhonova OV, et al. Chromosome 18 transcriptome profiling and targeted proteome mapping in depleted plasma, liver tissue and HepG2 Cells. J Proteome Res. 2013;12(1):123–34.
Zhong J, Cui Y, Guo J, et al. Resolving chromosome-centric human proteome with translating mRNA analysis: a strategic demonstration. J Proteome Res. 2014;13(1):50–9.
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Végvári, Á. (2014). Identification of Missing Proteins: Toward the Completion of Human Proteome. In: Marko-Varga, G. (eds) Genomics and Proteomics for Clinical Discovery and Development. Translational Bioinformatics, vol 6. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-9202-8_2
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DOI: https://doi.org/10.1007/978-94-017-9202-8_2
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