Advances in the Chromosome-Centric Human Proteome Project: looking to the future

References

• Legrain P, Aebersold R, Archakov A, et al. The human proteome project: current state and future direction. Mol Cell Proteomics. 2011;10:M111.009993.
   PubMed Web of Science ®Google Scholar
• Paik YK, Jeong SK, Omenn GS, et al. The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nat Biotechnol. 2012;30:221–223.
   PubMed Web of Science ®Google Scholar
• Paik YK, Omenn GS, Uhlen M, et al. Standard Guidelines for the Chromosome-Centric Human Proteome Project. J Proteome Res. 2012;11:2005–2013.
   PubMed Web of Science ®Google Scholar
• Paik YK, Overall CM, Deutsch EW, et al. Progress in the Chromosome-Centric Human Proteome Project as highlighted in the annual special issue IV. J Proteome Res. 2016;15:3945–3950.
   PubMed Web of Science ®Google Scholar
• Omenn GS, Lane L, Lundberg EK, et al. Progress on the HUPO draft human proteome: 2017 metrics of the Human Proteome Project. J Proteome Res. 2017 Aug 30. [Epub ahead of print] PubMed PMID: 28853897. DOI:10.1021/acs.jproteome.7b00375
   Google Scholar
• Collins FS, Morgan M, Patrinos A. The Human Genome Project: lessons from large-scale biology. Science. 2003;300:286–290.
   PubMed Web of Science ®Google Scholar
• Kim HS. Genomic impact, chromosomal distribution and transcriptional regulation of HERV elements. Mol Cells. 2012;33:539–544.
   PubMed Web of Science ®Google Scholar
• A Gene Centric Human Proteome Project - HUPO views. Mol Cell Proteomics. 2010;9:427–429.
   PubMed Web of Science ®Google Scholar
• Omenn GS. Report from the 2nd annual US HUPO meeting on the HUPO Human Plasma Proteome Project. Expert Rev Proteomics. 2006;3:165–168.
   PubMed Web of Science ®Google Scholar
• The HPP white paper. Vancouver, Canada. [accessed date: 2017 Oct 14]. Available from: https://www.hupo.org/publications. available from www.hupo.org.
   Google Scholar
• Services RF. Proteomics ponders prime time. Science. 2009;321:1758–1761.
   Web of Science ®Google Scholar
• Hancock WS, Omenn GS, Legrain P, et al. Proteomics, Human Proteome Project, and chromosomes. J Proteome Res. 2011;10:1.
   Web of Science ®Google Scholar
• Omenn GS, Lane L, Lundberg EK, et al. Metrics for the Human Proteome Project 2016: progress on identifying and characterizing the human proteome, including post-translational modifications. J Proteome Res. 2016;15:3951–3960.
   PubMed Web of Science ®Google Scholar
• Deutsch EW, Overall CM, Van Eyk JE, et al. Human Proteome Project mass spectrometry data interpretation guidelines 2.1. J Proteome Res. 2016;15:3961–3970.
   PubMed Web of Science ®Google Scholar
• Omenn GS, Lane L, Lundberg EK, et al. Metrics for the Human Proteome Project 2015: progress on the human proteome and guidelines for high-confidence protein identification. J Proteome Res. 2015;14:3452–3460.
   PubMed Web of Science ®Google Scholar
• Vizcaíno JA, Deutsch EW, Wang R, et al. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat Biotechnol. 2014;32:223–226.
   PubMed Web of Science ®Google Scholar
• Deutsch EW, Albar JP, Binz PA, et al. Development of data representation standards by the human proteome organization proteomics standards initiative. J Am Med Informatics Assoc. 2015;22:495–506.
   PubMed Web of Science ®Google Scholar
• Fenyö D, Beavis RC. The GPMDB REST interface. Bioinformatics. 2015;31:2056–2058.
   PubMed Web of Science ®Google Scholar
• 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;13:15–20.
   PubMed Web of Science ®Google Scholar
• Cox JT, Marginean I, Smith RD, et al. On the ionization and ion transmission efficiencies of different ESI-MS interfaces. J Am Soc Mass Spectrom. 2015;26:55–62.
   PubMed Web of Science ®Google Scholar
• Kim MS, Pinto SM, Getnet D, et al. A draft map of the human proteome. Nature. 2014;509:575–581.
   PubMed Web of Science ®Google Scholar
• Wilhelm M, Schlegl J, Hahne H, et al. Mass-spectrometry-based draft of the human proteome. Nature. 2014;509:582–587.
   PubMed Web of Science ®Google Scholar
• Ezkurdia I, Vázquez J, Valencia A, et al. Analyzing the first drafts of the human proteome. J Proteome Res. 2014;13:3854–3855.
   PubMed Web of Science ®Google Scholar
• Savitski MM, Wilhelm M, Hahne H, et al. A scalable approach for protein false discovery rate estimation in large proteomic data sets. Mol Cell Proteomics. 2015;14:2394–2404.
   PubMed Web of Science ®Google Scholar
• Schubert OT, Gillet LC, Collins BC, et al. Building high-quality assay libraries for targeted analysis of SWATH MS data. Nat Protoc. 2015;10:426–441.
   PubMed Web of Science ®Google Scholar
• Gaudet P, Argoud-Puy G, Cusin I, et al. NeXtProt: organizing protein knowledge in the context of human proteome projects. J Proteome Res. 2013;12:293–298.
   PubMed Web of Science ®Google Scholar
• Gaudet P, Michel PA, Zahn-Zabal M, et al. The neXtProt knowledgebase on human proteins: 2017 update. Nucleic Acids Res. 2017;45:D177–D182.
   PubMed Web of Science ®Google Scholar
• Schaeffer M, Gateau A, Teixeira D, et al. The neXtProt peptide uniqueness checker: a tool for the proteomics community. Bioinformatics. 2017. [Epub ahead of print]. DOI:10.1093/bioinformatics/btx318
   Web of Science ®Google Scholar
• Jeong SK, Hancock WS, Paik YK. GenomewidePDB 2.0: a newly upgraded versatile proteogenomic database for the Chromosome-Centric Human Proteome Project. J Proteome Res. 2015;14:3710–3719.
   PubMed Web of Science ®Google Scholar
• Yang S, Zhang X, Diao L, et al. CAPER 3.0: A scalable cloud-based system for data-intensive analysis of Chromosome-Centric Human Proteome Project data sets. J Proteome Res. 2015;14:3720–3728.
   PubMed Web of Science ®Google Scholar
• Krasnov GS, Dmitriev AA, Kudryavtseva AV, et al. PPLine: an automated pipeline for SNP, SAP, and splice variant detection in the context of proteogenomics. J Proteome Res. 2015;14:3729–3737.
   PubMed Web of Science ®Google Scholar
• Tabas-Madrid D, Alves-Cruzeiro J, Segura V, et al. Proteogenomics dashboard for the Human Proteome Project. J Proteome Res. 2015;14:3738–3749.
   PubMed Web of Science ®Google Scholar
• Panwar B, Menon R, Eksi R, et al. MI-PVT: A tool for visualizing the Chromosome-Centric Human Proteome. J Proteome Res. 2015;14:3762–3767.
   PubMed Web of Science ®Google Scholar
• Dong Q, Menon R, Omenn GS, et al. Structural bioinformatics inspection of neXtProt PE5 proteins in the human proteome. J Proteome Res. 2015;14:3750–3761.
   PubMed Web of Science ®Google Scholar
• Park GW, Hwang H, Kim KH, et al. Integrated proteomic pipeline using multiple search engines for a proteogenomic study with a controlled protein false discovery rate. J Proteome Res. 2016;15:4082–4090.
   PubMed Web of Science ®Google Scholar
• Deutsch EW, Sun Z, Campbell DS, et al. Tiered human integrated sequence search databases for shotgun proteomics. J Proteome Res. 2016;15:4091–4100.
   PubMed Web of Science ®Google Scholar
• Vandenbrouck Y, Lane L, Carapito C, et al. Looking for missing proteins in the proteome of human spermatozoa: an update. J Proteome Res. 2016;15:3998–4019.
   PubMed Web of Science ®Google Scholar
• Duek P, Bairoch A, Gateau A, et al. Missing protein landscape of human chromosomes 2 and 14: progress and current status. J Proteome Res. 2016;15:3971–3978.
   PubMed Web of Science ®Google Scholar
• Zhao M, Wei W, Cheng L, et al. Searching missing proteins based on the optimization of membrane protein enrichment and digestion process. J Proteome Res. 2016;15:4020–4029.
   PubMed Web of Science ®Google Scholar
• Atlas SRM. Systems biology, Seattle. [accessed date: 2017 Oct 14]. Availble from: www.srmatlas.org. available from http://www.peptideatlas.org/
   Google Scholar
• Human protein atlas. Stockholm, Sweden; [accessed date: 2017 Oct 14]. Available from: http://www.proteinatlas.org. available from http://www.scilifelab.se/.
   Google Scholar
• Uhlen M, Fagerberg L, Hallstrom BM, et al. Tissue-based map of the human proteome. Science. 2015;347:1260419.
   PubMed Web of Science ®Google Scholar
• Carapito C, Lane L, Benama M, et al. Computational and mass-spectrometry-based workflow for the discovery and validation of missing human proteins: application to chromosomes 2 and 14. J Proteome Res. 2015;14:3621–3634.
   PubMed Web of Science ®Google Scholar
• Jumeau F, Com E, Lane L, et al. Human spermatozoa as a model for detecting missing proteins in the context of the Chromosome-Centric Human Proteome Project. J Proteome Res. 2015;14:3606–3620.
   PubMed Web of Science ®Google Scholar
• Meyfour A, Ansari H, Pahlavan S, et al. Y chromosome missing protein, TBL1Y, may play an important role in cardiac differentiation. J Proteome Res. 2017 Sep 13 [Epub ahead of print] PubMed PMID: 28853286. DOI:10.1021/acs.jproteome.7b00391
   Google Scholar
• Mohamedali A, Ahn SB, Vka S, et al. Human prestin: a candidate PE1 protein lacking stringent mass spectrometric evidence? J Proteome Res. 2017 Sep 21. [Epub ahead of print] PubMed PMID: 28895742. DOI:10.1021/acs.jproteome.7b00354
   PubMedGoogle Scholar
• Calviello L, Mukherjee N, Wyler E, et al. Detecting actively translated open reading frames in ribosome profiling data. Nat Methods. 2016;13(2):165–170.
   PubMed Web of Science ®Google Scholar
• Wang T, Cui Y, Jin J, et al. Translating mRNAs strongly correlate to proteins in a multivariate manner and their translation ratios are phenotype specific. Nucleic Acids Res. 2013;41(9):4743–4754.
   PubMed Web of Science ®Google Scholar
• Verheggen K, Volders PJ, Mestdagh P, et al. Non-coding after all: biases in proteomics data do not explain observed absence of lncRNA translation products. J Proteome Res. 2017;16:2508–2515.
   PubMed Web of Science ®Google Scholar
• Slavoff SA, Mitchell AJ, Schwaid AG, et al. Peptidomic discovery of short open reading frame-encoded peptides in human cells. Nat Chem Biol. 2013;9(1):59–64.
   PubMed Web of Science ®Google Scholar
• Chang C, Li L, Zhang C, et al. Systematic analyses of the transcriptome, translatome, an proteome provide a global view and potential strategy for the C-HPP. J Proteome Res. 2014;13(1):38–49.
   PubMed Web of Science ®Google Scholar
• Vakilian H, Mirzaei M, Sharifi Tabar M, et al. DDX3Y, a male-specific region of Y chromosome gene, may modulate neuronal differentiation. J Proteome Res. 2015 Sep 4;14(9):3474–8341.
   PubMed Web of Science ®Google Scholar
• Yen CY, Houel S, Ahn NG, et al. Spectrum-to-spectrum searching using a proteome-wide spectral library. Mol Cell Proteomics. 2011;10:M111.007666.
   Web of Science ®Google Scholar
• Cho JY, Lee HJ, Jeong SK, et al. Combination of multiple spectral libraries improves the current search methods used to identify missing proteins in the Chromosome-Centric Human Proteome Project. J Proteome Res. 2015;14:4959–4966.
   PubMed Web of Science ®Google Scholar
• Wang BH, Reisman S, Bailey M, et al. Peptidomic profiles of post myocardial infarction rats affinity depleted plasma using matrix-assisted laser desorption/ionization time of flight (MALDI-ToF) mass spectrometry. Clin Transl Med. 2012 Jun 15;1(1):11. DOI:10.1186/2001-1326-1-11
   PubMedGoogle Scholar
• Paulo JA, Gaun A, Kadiyala V, et al. Subcellular fractionation enhances proteome coverage of pancreatic duct cells. Biochim Biophys Acta. 2013 Apr;1834(4):791–797.
   PubMed Web of Science ®Google Scholar
• Cox B, Emili A. Tissue subcellular fractionation and protein extraction for use in mass-spectrometry-based proteomics. Nat Protoc. 2006;1(4):1872–1878.
   PubMed Web of Science ®Google Scholar
• Moreda-Piñeiro A, García-Otero N, Bermejo-Barrera P. A review on preparative and semi-preparative offgel electrophoresis for multidimensional protein/peptide assessment. Anal Chim Acta. 2014 Jul 11;836: 1–17. DOI:10.1016/j.aca.2014.04.053
   PubMed Web of Science ®Google Scholar
• Segura V, Garin-Muga A, Guruceaga E, et al. Progress and pitfalls in finding the ‘missing proteins’ from the human proteome map. Expert Rev Proteomics. 2017 Jan;14(1):9–14. Epub 2016 Dec 2. PubMed PMID: 27885863. DOI:10.1080/14789450.2017.1265450
   PubMed Web of Science ®Google Scholar
• Cho JY, Lee HJ, Jeong SK, et al. Epsilon-Q: an automated analyzer interface for mass spectral library search and label-free protein quantification. J Proteome Res. 2017. (in press).
   Google Scholar
• Chen Y, Li Y, Zhong J, et al. Identification of missing proteins defined by Chromosome-Centric Proteome Project in the cytoplasmic detergent-insoluble proteins. J Proteome Res. 2015;14:3693–3709.
   PubMed Web of Science ®Google Scholar
• Eckhard U, Marino G, Abbey SR, et al. The human dental pulp proteome and N-terminome: levering the unexplored potential of semitryptic peptides enriched by TAILS to identify missing proteins in the Human Proteome Project in underexplored tissues. J Proteome Res. 2015 Feb;22(7):299–310.
   Google Scholar
• Wisniewski ES, Rees DK, Chege EW. Proteolytic-based method for the identification of human growth hormone. J Forensic Sci. 2009 Jan;54(1):122–127.
   PubMed Web of Science ®Google Scholar
• Menon R, Panwar B, Eksi R, et al. Computational inferences of the functions of alternative/noncanonical splice isoforms specific to HER2+/ER–/PR– breast cancers, a chromosome 17 C-HPP study. J Proteome Res. 2015;14:3519–3529.
   PubMed Web of Science ®Google Scholar
• Nesvizhskii AI. Proteogenomics: concepts, applications and computational strategies. Nat Methods. 2014;11:1114–1125.
   PubMed Web of Science ®Google Scholar
• Gu X, Karp PH, Brody SL, et al. Chemosensory functions for pulmonary neuroendocrine cells. A J Respir Cell Mol Biol. 2014;50:637–646.
   PubMed Web of Science ®Google Scholar
• Hallem EA, Dahanukar A, Carlson JR. Insect odor and taste receptors. Annu Rev Entomol. 2006;51:113–135.
   PubMed Web of Science ®Google Scholar
• Niimura Y. Evolutionary dynamics of olfactory receptor genes in chordates: interaction between environments and genomic contents. Hum Genomics. 2009;4:107–118.
   PubMedGoogle Scholar
• Gilad Y, Lancet D. Population differences in the human functional olfactory repertoire. Mol Biol Evol. 2003;20:307–314.
   PubMed Web of Science ®Google Scholar
• Gaillard I, Rouquier S, Giorgi D. Olfactory receptors. Cell Mol Life Sci. 2004;61:456–469.
   PubMed Web of Science ®Google Scholar
• Baker MS, Ahn SB, Mohamedali A, et al. Accelerating the search for the missing proteins in the human proteome. Nat Commun. 2017;8:14271.
   PubMed Web of Science ®Google Scholar
• Fan Y, Zhang Y, Xu S, et al. Insights from ENCODE on missing proteins: why β-defensin expression is scarcely detected. J Proteome Res. 2015;14:3635–3644.
   PubMed Web of Science ®Google Scholar
• Paik YK, Hancock WS. Uniting ENCODE with genome-wide proteomics. Nat Biotechnol. 2012;30:1065–1067.
   PubMed Web of Science ®Google Scholar
• Na K, Shin H, Cho JY, et al. A systematic proteogenomic approach to exploring a novel function of NHERF1 involved in human reproductive disorder: lessons for exploring missing proteins. J Proteome Res. (in press).
   Google Scholar
• Paik YK, Overall CM, Deutsch E, et al. Progress and future direction of chromosome-centric human proteome project. J Proteome Res. (being submitted; out on. [cited 2017 Dec 1].
   Google Scholar
• C-HPP Wiki Site. Groningen, The Netherlands; [accessed date: 2017 Oct 14]. Available from: http://c-hpp.webhosting.rug.nl/tiki-index.php. Available from c-hpp.org.
   Google Scholar
• Horvatovich P, Lundberg EKChen YJ, et al. Quest for missing proteins: update 2015 on chromosome-centric human proteome project. J Proteome Res. 2015;14:3415–3431.
   PubMed Web of Science ®Google Scholar