Metrics for the Human Proteome Project 2013–2014 and Strategies for Finding Missing Proteins
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One year ago the Human Proteome Project (HPP) leadership designated the baseline metrics for the Human Proteome Project to be based on neXtProt with a total of 13,664 proteins validated at protein evidence level 1 (PE1) by mass spectrometry, antibody-capture, Edman sequencing, or 3D structures. Corresponding chromosome-specific data were provided from PeptideAtlas, GPMdb, and Human Protein Atlas. This year, the neXtProt total is 15,646 and the other resources, which are inputs to neXtProt, have high-quality identifications and additional annotations for 14,012 in PeptideAtlas, 14,869 in GPMdb, and 10,976 in HPA. We propose to remove 638 genes from the denominator that are "uncertain" or "dubious" in Ensembl, UniProt/SwissProt, and neXtProt. That leaves 3844 "missing proteins", currently having no or inadequate documentation, to be found from a new denominator of 19,490 protein-coding genes. We present those tabulations and web links and discuss current strategies to find the missing proteins.
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The HPP uses a coordinated neXtProt and UniProtKB system that attributes five levels of supporting evidence for protein existence (PE1-PE5).
“The HPP relies upon a coordinated system developed by neXtProt and UniProtKB, which attributes five levels of supporting evidence for protein existence (PE)6.”
From A high-stringency blueprint of the human proteome (2020) · cites this paper as [6]
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The Pfam Protein Families Database
Bateman, A. G. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.276 · Cited by 14,062 · see citing works
The Pfam protein families database
Punta, M., Coggill, P. C., Eberhardt, R. Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr1065 · Cited by 3,719 · see citing works
Deep proteome and transcriptome mapping of a human cancer cell line
Nagaraj, N., Wisniewski, J. R., Geiger, T., Cox, J., Kircher, M., Kelso, J., Pääbo, S., & Mann, M. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.81 · Cited by 979 · see citing works
Data growth and its impact on the SCOP database: new developments
Andreeva, A. E., Howorth, D., Chandonia, J., Brenner, S. E., Hubbard, T., Chothia, C., & Murzin, A. G. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm993 · Cited by 933 · see citing works
The quantitative proteome of a human cell line
Beck, M., Schmidt, A., Malmstroem, J., Claassen, M., Ori, A., Szymborska, A., Herzog, F., Rinner, O., Ellenberg, J., & Aebersold, R. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.82 · Cited by 816 · see citing works
Geiger, T., Wehner, A., Schaab, C., Cox, J., & Mann, M. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.014050 · Cited by 797 · see citing works
The quantitative proteomes of human‐induced pluripotent stem cells and embryonic stem cells
Muñoz, J., Low, T. Y., Kok, Y. J., Chin, A. C. P., Frese, C. K., Ding, V., Choo, A. B. H., & Heck, A. J. R. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.84 · Cited by 132 · see citing works
Tang, H., Ali‐Khan, N., Echan, L. A., Levenkova, N., Rux, J. J., & Speicher, D. W. (2005) · PROTEOMICS · doi:10.1002/pmic.200401275 · Cited by 125 · see citing works
neXtProt: Organizing Protein Knowledge in the Context of Human Proteome Projects
Gaudet, P., Argoud-Puy, G., Cusin, I., Duek, P., Evalet, O., Gateau, A., Gleizes, A., Pereira, M., Zahn-Zabal, M., Zwahlen, C., et al. (2013) · Journal of Proteome Research · doi:10.1021/pr300830v · Cited by 124 · see citing works
Self-citationThe State of the Human Proteome in 2012 as Viewed through PeptideAtlas
Farrah, T., Deutsch, E. W., Hoopmann, M. R., Hallows, J. L., Sun, Z., Huang, C., & Moritz, R. L. (2012) · Journal of Proteome Research · doi:10.1021/pr301012j · Cited by 120 · see citing works
Self-citationAebersold, R. H., Bader, G. D., Edwards, A. M., Eyk, J. E. V., Kussmann, M., Qin, J., & Omenn, G. S. (2012) · Journal of Proteome Research · doi:10.1021/pr301151m · Cited by 102 · see citing works
Self-citationA First Step Toward Completion of a Genome-Wide Characterization of the Human Proteome
Marko‐Varga, G., Omenn, G. S., Paik, Y., & Hancock, W. S. (2012) · Journal of Proteome Research · doi:10.1021/pr301183a · Cited by 79 · see citing works
Self-citationPeppy: Proteogenomic Search Software
Risk, B. A., Spitzer, W. J., & Giddings, M. C. (2013) · Journal of Proteome Research · doi:10.1021/pr400208w · Cited by 79 · see citing works
Zgoda, V. G., Kopylov, A. T., Tikhonova, O. V., Moisa, A. A., Pyndyk, N. V., Farafonova, T. E., Novikova, S. E., Лисица, А. В., Ponomarenko, E. A., Poverennaya, E. V., et al. (2012) · Journal of Proteome Research · doi:10.1021/pr300821n · Cited by 63 · see citing works
Hood, L., Omenn, G. S., Moritz, R. L., Aebersold, R. H., Yamamoto, K. R., Amos, M. D., Hunter‐Cevera, J., Locascio, L. E., & Participants, W. (2012) · PROTEOMICS · doi:10.1002/pmic.201270086 · Cited by 59 · see citing works
Self-citationFagerberg, L., Oksvold, P., Skogs, M., Älgenäs, C., Lundberg, E. K., Pontén, F., Sivertsson, Å., Odeberg, J., Klevebring, D., Kampf, C., et al. (2012) · Journal of Proteome Research · doi:10.1021/pr300924j · Cited by 50 · see citing works
Self-citationZhong, J., Cui, Y., Guo, J., Chen, Z., Yang, L., He, Q., Zhang, G., & Wang, T. (2013) · Journal of Proteome Research · doi:10.1021/pr4007409 · Cited by 45 · see citing works
Liu, S., Im, H., Bairoch, A., Cristofanilli, M., Chen, R., Deutsch, E. W., Dalton, S., Fenyö, D., Fanayan, S., Gates, C., et al. (2012) · Journal of Proteome Research · doi:10.1021/pr300985j · Cited by 38 · see citing works
Self-citationNeuhauser, N., Nagaraj, N., McHardy, P., Zanivan, S. R., Scheltema, R. A., Cox, J., & Mann, M. (2013) · Journal of Proteome Research · doi:10.1021/pr400181q · Cited by 38 · see citing works
Lee, H., Jeong, S.-K., Na, K., Lee, M. J., Lee, S. H., Lim, J.-S., Cha, H.-J., Cho, J.-Y., Kwon, J., Kim, H., et al. (2013) · Journal of Proteome Research · doi:10.1021/pr301040g · Cited by 33 · see citing works
The Proteome Browser Web Portal
Goode, R. J. A., Yu, S., Kannan, A., Christiansen, J. H., Beitz, A., Hancock, W. S., Nice, E. C., & Smith, A. I. (2012) · Journal of Proteome Research · doi:10.1021/pr3010056 · Cited by 28 · see citing works
CAPER: a Chromosome-Assembled human Proteome browsER
Guo, F., Wang, D., Liu, Z., Lu, L., Zhang, W., Sun, H., Zhang, H., Ma, J., Wu, S., Li, N., et al. (2012) · Journal of Proteome Research · doi:10.1021/pr300831z · Cited by 24 · see citing works
Jeong, S.-K., Lee, H., Na, K., Cho, J.-Y., Lee, M. J., Kwon, J., Kim, H., Park, Y. M., Yoo, J. S., Hancock, W. S., et al. (2012) · Journal of Proteome Research · doi:10.1021/pr3009447 · Cited by 20 · see citing works
Muraoka, S., Kume, H., Adachi, J., Shiromizu, T., Watanabe, S., Masuda, T., Ishihama, Y., & Tomonaga, T. (2012) · Journal of Proteome Research · doi:10.1021/pr300824m · Cited by 19 · see citing works
Martins‐de‐Souza, D., Carvalho, P. C., Schmitt, A., Junqueira, M., Nogueira, F. C. S., Turck, C. W., & Domont, G. B. (2013) · Journal of Proteome Research · doi:10.1021/pr4009157 · Cited by 16 · see citing works
Danielsson, F., Wiking, M., Mahdessian, D., Skogs, M., Blal, H. A., Hjelmare, M., Stadler, C., Uhlén, M., & Lundberg, E. K. (2012) · Journal of Proteome Research · doi:10.1021/pr3009308 · Cited by 13 · see citing works
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Sorted by citations
A draft map of the human proteome
Kim, M.-S., Pinto, S. M., Getnet, D., Nirujogi, R. S., Manda, S. S., Chaerkady, R., Madugundu, A. K., Kelkar, D. S., Isserlin, R., Jain, S., et al. (2014) · Nature · doi:10.1038/nature13302 · Cited by 2,198 · see citing works
Mass-spectrometry-based draft of the human proteome
Wilhelm, M., Schlegl, J., Hahne, H., Gholami, A. M., Lieberenz, M., Savitski, M. M., Ziegler, E., Butzmann, L., Gessulat, S., Marx, H., et al. (2014) · Nature · doi:10.1038/nature13319 · Cited by 1,820 · see citing works
Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes
Ezkurdia, I., Juan, D., Rodrı́guez, J. M., Frankish, A., Diekhans, M., Harrow, J., Vázquez, J., Valencia, A., & Tress, M. L. (2014) · Human Molecular Genetics · doi:10.1093/hmg/ddu309 · Cited by 551 · see citing works
A repository of assays to quantify 10,000 human proteins by SWATH-MS
Rosenberger, G., Koh, C. C., Guo, T., Röst, H. L., Kouvonen, P., Collins, B. C., Heusel, M., Liu, Y., Caron, E., Vichalkovski, A., et al. (2014) · Scientific Data · doi:10.1038/sdata.2014.31 · Cited by 413 · see citing works
Self-citationA high-stringency blueprint of the human proteome
Adhikari, S., Nice, E. C., Deutsch, E. W., Lane, L., Omenn, G. S., Pennington, S. R., Paik, Y.-K., Overall, C. M., Corrales, F. J., Cristea, I. M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19045-9 · Cited by 210 · see citing works
Self-citationPérez‐Riverol, Y., Alpi, E., Wang, R., Hermjakob, H., & Vizcaíno, J. A. (2014) · PROTEOMICS · doi:10.1002/pmic.201400302 · Cited by 197 · see citing works
A hidden human proteome encoded by ‘non-coding’ genes
Lu, S., Zhang, J., Lian, X., Sun, L., Meng, K., Chen, Y., Sun, Z., Yin, X., Li, Y., Zhao, J., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz646 · Cited by 197 · see citing works
Transformative Impact of Proteomics on Cardiovascular Health and Disease
Lindsey, M. L., Mayr, M., Gomes, A. V., Delles, C., Arrell, D. K., Murphy, A. M., Lange, R. A., Costello, C. E., Jin, Y.-F., Laskowitz, D. T., et al. (2015) · Circulation · doi:10.1161/cir.0000000000000226 · Cited by 174 · see citing works
Quality control in mass spectrometry‐based proteomics
Bittremieux, W., Tabb, D. L., Impens, F., Staes, A., Timmerman, E., Martens, L., & Laukens, K. (2017) · Mass Spectrometry Reviews · doi:10.1002/mas.21544 · Cited by 127 · see citing works
Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0
Deutsch, E. W., Lane, L., Overall, C. M., Bandeira, N., Baker, M. S., Pineau, C., Moritz, R. L., Corrales, F., Orchard, S., Van Eyk, J. E., et al. (2019) · Journal of Proteome Research · doi:10.1021/acs.jproteome.9b00542 · Cited by 122 · see citing works
Self-citationAnalyzing the First Drafts of the Human Proteome
Ezkurdia, I., Vázquez, J., Valencia, A., & Tress, M. L. (2014) · Journal of Proteome Research · doi:10.1021/pr500572z · Cited by 102 · see citing works
Lange, P. F., Huesgen, P. F., Nguyen, K., & Overall, C. M. (2014) · Journal of Proteome Research · doi:10.1021/pr401191w · Cited by 97 · see citing works
Omenn, G. S., Lane, L., Lundberg, E. K., Beavis, R. C., Nesvizhskii, A. I., & Deutsch, E. W. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00499 · Cited by 93 · see citing works
Self-citationAbascal, F., Ezkurdia, I., Rodriguez-Rivas, J., Rodrı́guez, J. M., del Pozo, Á., Vázquez, J., Valencia, A., & Tress, M. L. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004325 · Cited by 84 · see citing works
The Human Eye Proteome Project: Updates on an Emerging Proteome
Ahmad, M. T., Zhang, P., Dufresne, C. P., Ferrucci, L., & Semba, R. D. (2018) · PROTEOMICS · doi:10.1002/pmic.201700394 · Cited by 83 · see citing works
Deutsch, E. W., Sun, Z., Campbell, D., Kusebauch, U., Chu, C. S., Mendoza, L., Shteynberg, D., Omenn, G. S., & Moritz, R. L. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00500 · Cited by 80 · see citing works
Self-citationKrasnov, G. S., Dmitriev, A. A., Kudryavtseva, A. V., Shargunov, A., Karpov, D. S., Урошлев, Л. А., Melnikova, N. V., Blinov, V. M., Poverennaya, E. V., Archakov, A. I., et al. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00490 · Cited by 81 · see citing works
Looking for Missing Proteins in the Proteome of Human Spermatozoa: An Update
Vandenbrouck, Y., Lane, L., Carapito, C., Duek, P., Rondel, K., Bruley, C., Macron, C., Gonzalez de Peredo, A., Couté, Y., Chaoui, K., et al. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00400 · Cited by 77 · see citing works
Self-citationOmenn, G. S., Lane, L., Lundberg, E. K., Beavis, R. C., Overall, C. M., & Deutsch, E. W. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00511 · Cited by 77 · see citing works
Self-citationN‐terminome analysis of the human mitochondrial proteome
Jácome, A. S. V., Rabilloud, T., Schaeffer‐Reiss, C., Rompais, M., Ayoub, D., Lane, L., Bairoch, A., DORSSELAER, A. V., & Carapito, C. (2015) · PROTEOMICS · doi:10.1002/pmic.201400617 · Cited by 74 · see citing works
Self-citationJumeau, F., Com, E., Lane, L., Duek, P. D., Lagarrigue, M., Lavigne, R., Laetitia Guillot, D., Rondel, K., Gateau, A., Melaine, N., et al. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00170 · Cited by 70 · see citing works
Self-citationSelenoprotein K and Protein Palmitoylation
Fredericks, G. J., & Hoffmann, P. R. (2015) · Antioxidants and Redox Signaling · doi:10.1089/ars.2015.6375 · Cited by 69 · see citing works
Omenn, G. S., Lane, L., Overall, C. M., Corrales, F. J., Schwenk, J. M., Paik, Y., Eyk, J. E. V., Liu, S., Snyder, M. P., Baker, M. S., et al. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00441 · Cited by 68 · see citing works
Self-citationEnhancing bottom‐up and top‐down proteomic measurements with ion mobility separations
Baker, E. S., Burnum-Johnson, K., Ibrahim, Y., Orton, D., Monroe, M. E., Kelly, R., Moore, R. J., Zhang, X., Théberge, R., Costello, C. E., et al. (2015) · PROTEOMICS · doi:10.1002/pmic.201500048 · Cited by 64 · see citing works
Prudova, A., Serrano, K., Eckhard, U., Fortelny, N., Devine, D. V., & Overall, C. M. (2014) · Blood · doi:10.1182/blood-2014-04-569640 · Cited by 64 · see citing works
Deutsch, E. W., Albar, J. P., Binz, P., Eisenacher, M., Jones, A. R., Mayer, G., Omenn, G. S., Orchard, S. E., Vizcaíno, J. A., & Hermjakob, H. (2015) · Journal of the American Medical Informatics Association · doi:10.1093/jamia/ocv001 · Cited by 56 · see citing works
Self-citationProgress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project
Omenn, G. S., Lane, L., Lundberg, E. K., Overall, C. M., & Deutsch, E. W. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00375 · Cited by 55 · see citing works
Self-citationQuest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project
Horvatovich, P. L., Lundberg, E. K., Chen, Y., Sung, T.-Y., He, F., Nice, E. C., Goode, R. J. A., Yu, S., Ranganathan, S., Baker, M. S., et al. (2015) · Journal of Proteome Research · doi:10.1021/pr5013009 · Cited by 54 · see citing works
Self-citationLiu, W., Xiang, L., Zheng, T., Jin, J., & Zhang, G. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1034 · Cited by 53 · see citing works
Paik, Y., Lane, L., Kawamura, T., Chen, Y., Cho, J., LaBaer, J., Yoo, J. S., Domont, G. B., Corrales, F. J., Omenn, G. S., et al. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00383 · Cited by 49 · see citing works
Self-citationTissue-Based Proteogenomics Reveals that Human Testis Endows Plentiful Missing Proteins
Zhang, Y., Li, Q., Wu, F., Zhou, R., Qi, Y., Su, N., Chen, L., Xu, S., Jiang, T., Zhang, C., et al. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00435 · Cited by 47 · see citing works
Eckhard, U., Marino, G., Abbey, S. R., Tharmarajah, G., Matthew, I., & Overall, C. M. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00579 · Cited by 46 · see citing works
Carapito, C., Lane, L., Benama, M., Opsomer, A., Mouton‐Barbosa, E., Garrigues, L., de Peredo, A. G., Burel, A., Bruley, C., Gateau, A., et al. (2015) · Journal of Proteome Research · doi:10.1021/pr5010345 · Cited by 44 · see citing works
Self-citationOmenn, G. S., Guan, Y., & Menon, R. (2014) · Journal of Proteomics · doi:10.1016/j.jprot.2014.04.012 · Cited by 44 · see citing works
Self-citationOmenn, G. S., Lane, L., Overall, C. M., Cristea, I. M., Corrales, F. J., Lindskog, C., Paik, Y., Eyk, J. E. V., Liu, S., Pennington, S. R., et al. (2020) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00485 · Cited by 41 · see citing works
Self-citationOmenn, G. S., Lane, L., Overall, C. M., Corrales, F. J., Schwenk, J. M., Paik, Y.-K., Van Eyk, J. E., Liu, S., Pennington, S., Snyder, M. P., et al. (2019) · Journal of Proteome Research · doi:10.1021/acs.jproteome.9b00434 · Cited by 40 · see citing works
Self-citationThe Quest of the Human Proteome and the Missing Proteins: Digging Deeper
Reddy, P. J., Ray, S., & Srivastava, S. (2015) · OMICS A Journal of Integrative Biology · doi:10.1089/omi.2015.0035 · Cited by 39 · see citing works
Wei, W., Luo, W., Wu, F., Peng, X., Zhang, Y., Zhang, M., Zhao, Y., Su, N., Qi, Y., Chen, L., et al. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00390 · Cited by 38 · see citing works
Integration of omics sciences to advance biology and medicine
Boja, E. S., Kinsinger, C. R., Rodriguez, H., & Srinivas, P. R. (2014) · Clinical Proteomics · doi:10.1186/1559-0275-11-45 · Cited by 35 · see citing works
Defining the proteome of human iris, ciliary body, retinal pigment epithelium, and choroid
Zhang, P., Kirby, D. J., Dufresne, C. P., Chen, Y., Turner, R. L., Ferri, S., Edward, D. P., Eyk, J. E. V., & Semba, R. D. (2016) · PROTEOMICS · doi:10.1002/pmic.201500188 · Cited by 33 · see citing works
Kitata, R. B., Dimayacyac-Esleta, B. R. T., Choong, W.-K., Tsai, C.-F., Lin, T., Tsou, C., Weng, S.-H., Chen, Y., Yang, P.-C., Arco, S. D., et al. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00477 · Cited by 32 · see citing works
Fenyö, D., & Beavis, R. C. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv107 · Cited by 32 · see citing works
Self-citationChen, Y., Li, Y., Zhong, J., Zhang, J., Chen, Z., Yang, L., Cao, X., He, Q., Zhang, G., & Wang, T. (2015) · Journal of Proteome Research · doi:10.1021/pr501103r · Cited by 31 · see citing works
Functional Annotation of Proteome Encoded by Human Chromosome 22
Pinto, S. M., Manda, S. S., Kim, M., Taylor, K., Selvan, L. D. N., Balakrishnan, L., Subbannayya, T., Yan, F., Prasad, T. S. K., Gowda, H., et al. (2014) · Journal of Proteome Research · doi:10.1021/pr401169d · Cited by 28 · see citing works
Li, H.-D., Menon, R., Govindarajoo, B., Panwar, B., Zhang, Y., Omenn, G. S., & Guan, Y. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00494 · Cited by 27 · see citing works
Self-citationNavas-Carrillo, D., Marín, F. R., Valdés, M., & Orenes‐Piñero, E. (2016) · Critical Reviews in Clinical Laboratory Sciences · doi:10.1080/10408363.2016.1241214 · Cited by 26 · see citing works
Advances in the Chromosome-Centric Human Proteome Project: looking to the future
Paik, Y., Omenn, G. S., Hancock, W. S., Lane, L., & Overall, C. M. (2017) · Expert Review of Proteomics · doi:10.1080/14789450.2017.1394189 · Cited by 25 · see citing works
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Sivertsson, Å., Lindström, E., Oksvold, P., Katona, B., Hikmet, F., Vuu, J., Gustavsson, J., Sjöstedt, E., von Feilitzen, K., Kampf, C., et al. (2020) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00486 · Cited by 26 · see citing works
Bell, P. A., Solis, N., Kizhakkedathu, J. N., Matthew, I., & Overall, C. M. (2019) · Journal of Proteome Research · doi:10.1021/acs.jproteome.9b00445 · Cited by 25 · see citing works
Carapito, C., Duek, P. D., Macron, C., Seffals, M., Rondel, K., Delalande, F., Lindskog, C., Fréour, T., Vandenbrouck, Y., Lane, L., et al. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00374 · Cited by 24 · see citing works
Self-citationGupta, M. K., Jayaram, S., Madugundu, A. K., Chavan, S., Advani, J., Pandey, A., Thongboonkerd, V., & Sirdeshmukh, R. (2014) · Journal of Proteome Research · doi:10.1021/pr500023p · Cited by 22 · see citing works
Yang, L., Lian, X., Zhang, W., Guo, J., Wang, Q., Li, Y., Chen, Y., Yin, X., Yang, P., Lan, F., et al. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00480 · Cited by 23 · see citing works
Poverennaya, E. V., Ilgisonis, E. V., Ponomarenko, E. A., Kopylov, A. T., Zgoda, V. G., Radko, S. P., Лисица, А. В., & Archakov, A. I. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00348 · Cited by 23 · see citing works
Robin, T., Bairoch, A., Müller, M., Lisacek, F., & Lane, L. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00392 · Cited by 22 · see citing works
Self-citationGenome-wide Proteomics, Chromosome-centric Human Proteome Project (C-HPP), Part II
Paik, Y., Omenn, G. S., Thongboonkerd, V., Marko‐Varga, G., & Hancock, W. S. (2013) · Journal of Proteome Research · doi:10.1021/pr4011958 · Cited by 22 · see citing works
Self-citationHigh spatial resolution proteomic comparison of the brain in humans and chimpanzees
Bauernfeind, A. L., Reyzer, M. L., Caprioli, R. M., Ely, J. J., Babbitt, C. C., Wray, G. A., Hof, P. R., & Sherwood, C. C. (2015) · The Journal of Comparative Neurology · doi:10.1002/cne.23777 · Cited by 21 · see citing works
Fu, S., Liu, X., Luo, M., Xie, K., Nice, E. C., Zhang, H., & Huang, C. (2017) · Expert Review of Proteomics · doi:10.1080/14789450.2017.1299006 · Cited by 21 · see citing works
Lichti, C. F., Mostovenko, E., Wadsworth, P. A., Lynch, G. C., Pettitt, B. M., Sulman, E. P., Wang, Q., Lang, F. F., Rezeli, M., Marko‐Varga, G., et al. (2014) · Journal of Proteome Research · doi:10.1021/pr500810g · Cited by 21 · see citing works
Identification of Missing Proteins in the Phosphoproteome of Kidney Cancer
Peng, X., Xu, F., Liu, S., Li, S., Huang, Q., Chang, L., Wang, L., Ma, X., He, F., & Xu, P. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00332 · Cited by 21 · see citing works
Sun, J., Shi, J., Wang, Y., Chen, Y., Li, Y., Kong, D., Chang, L., Liu, F., Lv, Z., Zhou, Y., et al. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00397 · Cited by 20 · see citing works
A peptide resource for the analysis of Staphylococcus aureus in host–pathogen interaction studies
Depke, M., Michalik, S., Rabe, A., Surmann, K., Brinkmann, L., Jehmlich, N., Bernhardt, J., Hecker, M., Wollscheid, B., Sun, Z., et al. (2015) · PROTEOMICS · doi:10.1002/pmic.201500091 · Cited by 20 · see citing works
Prediction of a Missing Protein Expression Map in the Context of the Human Proteome Project
Guruceaga, E., del Pino, M. M. S., Corrales, F. J., & Segura, V. (2015) · Journal of Proteome Research · doi:10.1021/pr500850u · Cited by 19 · see citing works
Paik, Y., Overall, C. M., Deutsch, E. W., Hancock, W. S., & Omenn, G. S. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00803 · Cited by 18 · see citing works
Self-citationProteomic Analysis of Embryonic and Young Human Vitreous
Yee, K. M. P., Feener, E. P., Madigan, M. C., JACKSON, N. J., Gao, B., Ross‐Cisneros, F. N., Provis, J. M., Aiello, L. P., Sadun, A. A., & Sebag, J. (2015) · Investigative Ophthalmology & Visual Science · doi:10.1167/iovs.15-16809 · Cited by 18 · see citing works
Use of ENCODE Resources to Characterize Novel Proteoforms and Missing Proteins in the Human Proteome
Nilsson, C. L., Mostovenko, E., Lichti, C. F., Ruggles, K. V., Fenyö, D., Rosenbloom, K. R., Hancock, W. S., Paik, Y., Omenn, G. S., LaBaer, J., et al. (2014) · Journal of Proteome Research · doi:10.1021/pr500564q · Cited by 17 · see citing works
Self-citationStructural Bioinformatics Inspection of neXtProt PE5 Proteins in the Human Proteome
Dong, Q., Menon, R., Omenn, G. S., & Zhang, Y. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00516 · Cited by 17 · see citing works
Self-citationMissing Protein Landscape of Human Chromosomes 2 and 14: Progress and Current Status
Duek, P., Bairoch, A., Gateau, A., Vandenbrouck, Y., & Lane, L. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00443 · Cited by 17 · see citing works
Self-citationMalm, J., Lindberg, H., Erlinge, D., Appelqvist, R., Yakovleva, M., Welinder, C., Steinfelder, E., Fehniger, T. E., & Marko‐Varga, G. (2015) · Clinical and Translational Medicine · doi:10.1186/s40169-015-0067-0 · Cited by 16 · see citing works
Vít, O., Man, P., Kádek, A., Hausner, J., Sklenář, J., Harant, K., Novák, P., Ščigelová, M., Woffendin, G., & Petrák, J. (2016) · Journal of Proteomics · doi:10.1016/j.jprot.2016.03.016 · Cited by 16 · see citing works
Detection of Missing Proteins Using the PRIDE Database as a Source of Mass Spectrometry Evidence
Garín-Muga, A., Odriozola, L., Martínez‐Val, A., del‐Toro, N., Martínez, R., Molina, M., Cantero, L., Rivera, R., Garrido, N., Domı́nguez, F., et al. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00437 · Cited by 16 · see citing works
He, C., Sun, J., Shi, J., Wang, Y., Jialing, Z., Wu, S., Chang, L., Gao, H., Liu, F., Lv, Z., et al. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00398 · Cited by 16 · see citing works
Sjöstedt, E., Sivertsson, Å., Hikmet, F., Katona, B., Näsström, Å., Vuu, J., Kesti, D., Oksvold, P., Edqvist, P.-H. D., Olsson, I., et al. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00406 · Cited by 16 · see citing works
Toward defining the anatomo‐proteomic puzzle of the human brain: An integrative analysis
Fernández‐Irigoyen, J., Labarga, A., Zabaleta, A., de Morentin, X. M., Pérez‐Valderrama, E., Zelaya, M. V., & Santamaría, E. (2014) · PROTEOMICS - CLINICAL APPLICATIONS · doi:10.1002/prca.201400127 · Cited by 16 · see citing works
Proteomic Validation of Transcript Isoforms, Including Those Assembled from RNA-Seq Data
Tay, A. P., Pang, C. N. I., Twine, N. A., Hart‐Smith, G., Harkness, L., Kassem, M. S., & Wilkins, M. R. (2015) · Journal of Proteome Research · doi:10.1021/pr5011394 · Cited by 16 · see citing works
Cho, J.-Y., Lee, H., Jeong, S.-K., Kim, K.-Y., Kwon, K., Yoo, J. S., Omenn, G. S., Baker, M. S., Hancock, W. S., & Paik, Y. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00578 · Cited by 15 · see citing works
Self-citationCom, E., Melaine, N., Chalmel, F., & Pineau, C. (2014) · Journal of Proteomics · doi:10.1016/j.jprot.2014.04.013 · Cited by 15 · see citing works
Recent Advances in the Chromosome-Centric Human Proteome Project: Missing Proteins in the Spot Light
Paik, Y., Omenn, G. S., Overall, C. M., Deutsch, E. W., & Hancock, W. S. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00785 · Cited by 15 · see citing works
Self-citationElguoshy, A., Hirao, Y., Xu, B., Saito, S., Quadery, A. F., Yamamoto, K., Mitsui, T., Yamamoto, T., & Chromosome X Project Team of JProS (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00423 · Cited by 14 · see citing works
Objective: biochemical function
Anton, B. P., Kasif, S., Roberts, R. J., & Steffen, M. A. (2014) · Frontiers in Genetics · doi:10.3389/fgene.2014.00210 · Cited by 14 · see citing works
Informatics View on the Challenges of Identifying Missing Proteins from Shotgun Proteomics
Choong, W.-K., Chang, H.-Y., Chen, C.-T., Tsai, C.-F., Hsu, W.-L., Chen, Y., & Sung, T.-Y. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00482 · Cited by 14 · see citing works
Aebersold, R. H., Bader, G. D., Edwards, A. M., Eyk, J. E. V., Kussman, M., Qin, J., & Omenn, G. S. (2014) · PROTEOMICS · doi:10.1002/pmic.201400041 · Cited by 14 · see citing works
Self-citationGirard, O., Lavigne, R., Chevolleau, S., Onfray, C., Com, E., Schmit, P.-O., Chapelle, M., Fréour, T., Lane, L., David, L., et al. (2022) · Journal of Proteome Research · doi:10.1021/acs.jproteome.2c00496 · Cited by 14 · see citing works
Self-citationAbdul-Khalek, N., Picciani, M., Shouman, O., Wimmer, R., Overgaard, M. T., Wilhelm, M., & Gregersen Echers, S. (2025) · Journal of Proteome Research · doi:10.1021/acs.jproteome.4c00973 · Cited by 13 · see citing works
Genomic variability and protein species — Improving sequence coverage for proteogenomics
Bischoff, R., Permentier, H. P., Guryev, V., & Horvatovich, P. L. (2015) · Journal of Proteomics · doi:10.1016/j.jprot.2015.09.021 · Cited by 13 · see citing works
Deciphering the Dark Proteome: Use of the Testis and Characterization of Two Dark Proteins.
Melaine, N., Com, E., Bellaud, P., Guillot, L., Lagarrigue, M., Morrice, N., Guével, B., Lavigne, R., de la Calle, J. V., Dojahn, J., et al. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00387 · Cited by 11 · see citing works
Na, K., Shin, H., Cho, J.-Y., Jung, S. H., Lim, J., Lim, J.-S., Kim, E. A., Kim, H. S., Kang, A. R., Kim, J. H., et al. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00146 · Cited by 12 · see citing works
Self-citationLarge Scale Identification of Variant Proteins in Glioma Stem Cells
Mostovenko, E., Végvári, Á., Rezeli, M., Lichti, C. F., Fenyö, D., Wang, Q., Lang, F. F., Sulman, E. P., Sahlin, K. B., Marko‐Varga, G., et al. (2017) · ACS Chemical Neuroscience · doi:10.1021/acschemneuro.7b00362 · Cited by 12 · see citing works
Expanding and Enriching the LncRNA Gene–Disease Landscape Using the GeneCaRNA Database
Aggarwal, S., Rosenblum, C., Gould, M., Ziman, S., Barshir, R., Zelig, O., Guan‐Golan, Y., Stein, T. I., Safran, M., Pietrokovski, S., et al. (2024) · Biomedicines · doi:10.3390/biomedicines12061305 · Cited by 11 · see citing works
Can “Normal” Protein Expression Ranges Be Estimated with High-Throughput Proteomics?
Higdon, R., & Kolker, E. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00176 · Cited by 11 · see citing works
Jeong, S.-K., Kim, C.-Y., & Paik, Y. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00548 · Cited by 11 · see citing works
Xu, A., Li, G., Yang, D. C., Wu, S., Ouyang, H., Xu, P., & He, F. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00450 · Cited by 10 · see citing works
Jones, M. K., Lü, B., Chen, D. Z., Spivia, W. R., Mercado, A. T., Ljubimov, A. V., Svendsen, C. N., Eyk, J. E. V., & Wang, S. (2018) · PROTEOMICS · doi:10.1002/pmic.201800213 · Cited by 9 · see citing works
The Challenge of Human Spermatozoa Proteome: A Systematic Review.
Gilany, K., Minai‐Tehrani, A., Amini, M., Agharezaee, N., & Arjmand, B. (2017) · Europe PMC (PubMed Central) · Cited by 9 · see citing works
Characterization of human pineal gland proteome
Yelamanchi, S. D., Kumar, M., Madugundu, A. K., Gopalakrishnan, L., Dey, G., Chavan, S., Sathe, G. J., Mathur, P. P., Gowda, H., Mahadevan, A., et al. (2016) · Molecular BioSystems · doi:10.1039/c6mb00507a · Cited by 9 · see citing works
Protocol for Increasing the Sensitivity of MS-Based Protein Detection in Human Chorionic Villi
Shkrigunov, T., Pogodin, P. V., Zgoda, V. G., Larina, O. B., Kisrieva, Y. S., Klimenko, M., Александрович, Л. О., Klimenko, P., Lisitsa, A., & Petushkova, N. A. (2022) · Current Issues in Molecular Biology · doi:10.3390/cimb44050140 · Cited by 8 · see citing works
Jeong, S.-K., Hancock, W. S., & Paik, Y. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00541 · Cited by 8 · see citing works
Siddiqui, O., Zhang, H., Guan, Y., & Omenn, G. S. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00442 · Cited by 8 · see citing works
Self-citationThe Russian part of the human proteome project:first results and prospects
Ponomarenko, E. A., Zgoda, V. G., Kopylov, A. T., Poverennaya, E. V., Ilgisonis, E. V., Лисица, А. В., & Archakov, A. I. (2015) · Biomeditsinskaya Khimiya · doi:10.18097/pbmc20156102169 · Cited by 8 · see citing works
Insights from ENCODE on Missing Proteins: Why β-Defensin Expression Is Scarcely Detected
Yang, F., Zhang, Y., Xu, S., Kong, N., Zhou, Y., Ren, Z., Deng, Y., Lin, L., Ren, Y., Wang, Q., et al. (2015) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00565 · Cited by 7 · see citing works
Nishimura, T., Kawamura, T., Sugihara, Y., Bando, Y., Sakamoto, S., Nomura, M., Ikeda, N., Ohira, T., Fujimoto, J., Tojo, H., et al. (2014) · Clinical and Translational Medicine · doi:10.1186/s40169-014-0038-x · Cited by 7 · see citing works
- Authors
- Lane, L., Bairoch, A., Beavis, R. C., Deutsch, E. W., Gaudet, P., Lundberg, E., & Omenn, G. S.
- Affiliations
- SIB Swiss Institute of Bioinformatics (CH)
- University of British Columbia (CA)
- Institute for Systems Biology (US)
- AlbaNova (SE)
- University of Michigan (US)
- Corresponding author
- Omenn, Gilbert S.
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2013-12-23
- Volume
- 13
- Issue
- 1
- Pages
- 15-20
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- PMC
- PMC3928647
- OpenAlex
- W2074956188
- Cited by
- 129
- References
- 26
- Citations by year
- 2025: 2 · 2024: 2 · 2023: 1 · 2022: 2 · 2020: 4 · 2019: 6 · 2018: 14 · 2017: 15 · 2016: 14 · 2015: 45 · 2014: 23 · 2013: 1
- FWCI
- 12.40
- Type
- journal article
- Language
- en
- Open access
- Licence
- other-oa
- Locations
- Journal of Proteome Research (publishedVersion)
- PubMed (publishedVersion)
- Archive ouverte UNIGE (University of Geneva) (publishedVersion, other-oa)
- PubMed Central (acceptedVersion)
- Archive ouverte UNIGE (University of Geneva) (submittedVersion, cc-by)
- Funders
- Kommission für Technologie und Innovation
- Knut och Alice Wallenbergs Stiftelse
- National Institutes of Health (RM-08-029)
- National Human Genome Research Institute (RC2HG005805, HG005805)
- National Cancer Institute (R01CA144043)
- National Institute of General Medical Sciences (GM087221, R01GM087221, GM 076547, P50GM076547)
- National Institute of Environmental Health Sciences (U54 ES017885, P30ES017885)
- National Center for Research Resources (UL1RR024986, UL1 RR24986)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced Biosensing Techniques and Applications
- Keywords
- Human Proteome Project, human proteome, missing proteins, neXtProt, PeptideAtlas, Human Protein Atlas, protein-coding genes
- MeSH terms
- Chromosomes, Human, Humans, Mass Spectrometry, Proteome
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