2020
- Research on the Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project. Gilbert S. Omenn, Lydie Lane, Christopher M. Overall, Ileana M. Cristea, Fernando J. Corrales, Cecilia Lindskog, Young-Ki Paik, Jennifer E. Van Eyk, Siqi Liu, Stephen R. Pennington, Michael P. Snyder, Mark S. Baker, Nuno Bandeira, Ruedi Aebersold, Robert L. Moritz, and Eric W. Deutsch. J. Proteome Res.
- A high-stringency blueprint of the human proteome. Subash Adhikari, Edouard C. Nice, Eric W. Deutsch, Lydie Lane, Gilbert S. Omenn, Stephen R. Pennington, Young-Ki Paik, Christopher M. Overall, Fernando J. Corrales, Ileana M. Cristea, Jennifer E. Van Eyk, Mathias Uhlén, Cecilia Lindskog, Daniel W. Chan, Amos Bairoch, James C. Waddington, Joshua L. Justice, Joshua LaBaer, Henry Rodriguez, Fuchu He, Markus Kostrzewa, Peipei Ping, Rebekah L. Gundry, Peter Stewart, Sanjeeva Srivastava, Sudhir Srivastava, Fabio C. S. Nogueira, Gilberto B. Domont, Yves Vandenbrouck, Maggie P. Y. Lam, Sara Wennersten, Juan Antonio Vizcaino, Marc Wilkins, Jochen M. Schwenk, Emma Lundberg, Nuno Bandeira, Gyorgy Marko-Varga, Susan T. Weintraub, Charles Pineau, Ulrike Kusebauch, Robert L. Moritz, Seong Beom Ahn, Magnus Palmblad, Michael P. Snyder, Ruedi Aebersold & Mark S. Baker. Nature Communications volume 11, Article number: 5301 (2020)
2019
- Proteomics identifies new therapeutic targets of early-stage hepatocellular carcinoma. Ying Jiang, Aihua Sun, Yang Zhao, Wantao Ying, Huichuan Sun, Xinrong Yang, Baocai Xing, Wei Sun, Liangliang Ren, Bo Hu, Chaoying Li, Li Zhang, Guangrong Qin, Menghuan Zhang, Ning Chen, Manli Zhang, Yin Huang, Jinan Zhou, Yan Zhao, Mingwei Liu, Xiaodong Zhu, Yang Qiu, Yanjun Sun, Cheng Huang, Meng Yan, Mingchao Wang, Wei Liu, Fang Tian, Huali Xu, Jian Zhou, Zhenyu Wu, Tieliu Shi, Weimin Zhu, Jun Qin, Lu Xie, Jia Fan, Xiaohong Qian, Fuchu He & Chinese Human Proteome Project (CNHPP) Consortium Nature 567, 257-261 (2019). Published: 27 February 2019
2018
Systemic and ocular fluid compounds as potential biomarkers in age-related macular degeneration. Kersten E, Paun CC, Schellevis RL, Hoyng CB, Delcourt C, Lengyel I, Peto T, Ueffing M, Klaver CCW, Dammeier S, den Hollander AI, de Jong EK.Surv Ophthalmol. 2018 Jan - Feb;63(1):9-39.
- Integrated omics dissection of proteome dynamics during cardiac remodeling. Lau E, Cao Q, Lam MPY, Wang J, Ng DCM, Bleakley BJ, Lee JM, Liem DA, Wang D, Hermjakob H, Ping P. 2018;9(1):120. doi: 10.1038/s41467-017-02467-3. PubMed PMID: 29317621; PMCID: PMC5760723. (accepted 2017)
Proteomic and Metaproteomic Approaches to Understand Host-Microbe Interactions. Starr AE, Deeke SA, Li L, Zhang X, Daoud R, Ryan J, Ning Z, Cheng K, Nguyen LVH, Abou-Samra E, Lavallée-Adam M, Figeys D. Anal Chem. 2018 Jan 2;90(1):86-109. doi: 10.1021/acs.analchem.7b04340.
The SysteMHC Atlas project. Shao W, Pedrioli PGA, Wolski W, Scurtescu C, Schmid E, Vizcaíno JA, et al. Nucleic Acids Res. 2018 Jan 4;46(D1):D1237-D1247. doi: 10.1093/nar/gkx664.
2017
- Designer proteases for post-translational modifications. Rita Strack Nature Methods 14, 106–107 (2017) doi:10.1038/nmeth.4173. Published online 31 January 2017
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A large-scale targeted proteomics assay resource based on an in vitro human proteome. Matsumoto M, Matsuzaki F, Oshikawa K, Goshima N, Mori M, Kawamura Y, Ogawa K, Fukuda E, Nakatsumi H, Natsume T, Fukui K, Horimoto K, Nagashima T, Funayama R, Nakayama K, Nakayama KI. Nat Methods. 2017 Mar;14(3):251-258. doi: 10.1038/nmeth.4116. Epub 2016 Dec 26.
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Building ProteomeTools based on a complete synthetic human proteome. Zolg DP, Wilhelm M, Schnatbaum K, Zerweck J, Knaute T, Delanghe B, Bailey DJ, Gessulat S, Ehrlich HC, Weininger M, Yu P, Schlegl J, Kramer K, Schmidt T, Kusebauch U, Deutsch EW, Aebersold R, Moritz RL, Wenschuh H, Moehring T, Aiche S, Huhmer A, Reimer U, Kuster B. Nat Methods. 2017 Mar;14(3):259-262. doi: 10.1038/nmeth.4153. Epub 2017 Jan 30.
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jPOSTrepo: an international standard data repository for proteomes. Okuda S, Watanabe Y, Moriya Y, Kawano S, Yamamoto T, Matsumoto M, Takami T, Kobayashi D, Araki N, Yoshizawa AC, Tabata T, Sugiyama N, Goto S, Ishihama Y. Nucleic Acids Res. 2017 Jan 4;45(D1):D1107-D1111. doi: 10.1093/nar/gkw1080.
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Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction. Wang J, Ma Z, Carr SA, Mertins P, Zhang H, Zhang Z, Chan DW, Ellis MJ, Townsend RR, Smith RD, McDermott JE, Chen X, Paulovich AG, Boja ES, Mesri M, Kinsinger CR, Rodriguez H, Rodland KD, Liebler DC, Zhang B. Mol Cell Proteomics. 2017 Jan;16(1):121-134. doi: 10.1074/mcp.M116.06030
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Age-related neurodegenerative disease associated pathways identified in retinal and vitreous proteome from human glaucoma eyes. Mehdi Mirzaei, Veer B. Gupta, Joel M. Chick, Todd M. Greco, Yunqi Wu, Nitin Chitranshi, Roshana Vander Wall, Eugene Hone, Liting Deng, Yogita Dheer, Mojdeh Abbasi, Mahdie Rezaeian, Nady Braidy, Yuyi You, Ghasem Hosseini Salekdeh, Paul A. Haynes, Mark P. Molloy, Ralph Martins, Ileana M. Cristea, Steven P. Gygi, Stuart L. Graham & Vivek K. Gupta. Scientific Reportsvolume 7, Article number: 12685 (2017) doi:10.1038/s41598-017-12858-7
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Prioritizing Popular Proteins in Liver Cancer: Remodelling One-Carbon Metabolism. Mora MI, Molina M, Odriozola L, Elortza F, Mato JM, Sitek B, Zhang P, He F, Latasa MU, Ávila MA, Corrales FJ.J Proteome Res. 2017 Oct 2. doi:10.1021/acs.jproteome.7b00390.
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Multicentric study of the effect of pre-analytical variables in the quality of plasma samples stored in biobanks using different complementary proteomic methods. Mateos J, Carneiro I, Corrales F, Elortza F, Paradela A, Del Pino MS, Iloro I, Marcilla M, Mora MI, Valero L, Ciordia S, Fernández V, Fortuño MA, García-Sánchez I, Martínez R, Muñoz MA, Rodriguez C, Doménech N; ProteoRed Spanish Biobanks Network.J Proteomics. 2017 Jan 6;150:109-120. doi: 10.1016/j.jprot.2016.09.003. Epub 2016 Sep 9.
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Introducing plasma/serum glycodepletion for the targeted proteomics analysis of cytolysis biomarkers. Maes P, Donadio-Andréi S, Louwagie M, Couté Y, Picard G, Lacoste C, Bruley C, Garin J, Ichai P, Faivre J, Jaquinod M, Brun V.Talanta. 2017 Aug 1;170:473-480. doi: 10.1016/j.talanta.2017.04.042. Epub 2017 Apr 19.
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Serum extracellular vesicles contain protein biomarkers for primary sclerosing cholangitis and cholangiocarcinoma. Arbelaiz A, Azkargorta M, Krawczyk M, Santos-Laso A, Lapitz A, Perugorria MJ, Erice O, Gonzalez E, Jimenez-Agüero R, Lacasta A, Ibarra C, Sanchez-Campos A, Jimeno JP, Lammert F, Milkiewicz P, Marzioni M, Macias RIR, Marin JJG, Patel T, Gores GJ, Martinez I, Elortza F, Falcon-Perez JM, Bujanda L, Banales JM. Hepatology. 2017 Oct;66(4):1125-1143. doi: 10.1002/hep.29291. Epub 2017 Aug 26.
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Bioinformatic Analysis of Coronary Disease Associated SNPs and Genes to Identify Proteins Potentially Involved in the Pathogenesis of Atherosclerosis. Chunhong Mao, Timothy D. Howard, Dan Sullivan,Zongming Fu, Guoqiang Yu,Sarah J. Parker, Rebecca Will,Richard S. Vander Heide, Yue Wang,James Hixson, Jennifer Van Eyk, and David M. Herrington. J Proteom Genom Res. 2017;2(1):1-12. doi: 10.14302/issn.2326-0793.jpgr-17-1447. PubMed PMID: 29367937; PMCID: PMC5777528.
- Plasma Proteomics for Epidemiology: Increasing Throughput With Standard-Flow Rates. Yin X, Baig F, Haudebourg E, Blankley RT, Gandhi T, Muller S, Reiter L, Hinterwirth H, Pechlaner R, Tsimikas S, Santer P, Willeit J, Kiechl S, Witztum JL, Sullivan A, Mayr M.Circ Cardiovasc Genet. 2017;10(6). doi: 10.1161/CIRCGENETICS.117.001808. PubMed PMID: 29237681.
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Bacillus spp. Isolated from Puba as a Source of Biosurfactants and Antimicrobial Lipopeptides.Perez KJ, Viana JD, Lopes FC, Pereira JQ, Dos Santos DM, Oliveira JS, Velho RV, Crispim SM, Nicoli JR, Brandelli A, Nardi RM. Front Microbiol. 2017 Jan 31;8:61. doi: 10.3389/fmicb.2017.00061
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jPOSTrepo: an international standard data repository for proteomes. Okuda S, Watanabe Y, Moriya Y, Kawano S, Yamamoto T, Matsumoto M, Takami T, Kobayashi D, Araki N, Yoshizawa AC, Tabata T, Sugiyama N, Goto S, Ishihama Y.Nucleic Acids Res. 2017 Jan 4;45(D1):D1107-D1111. doi: 10.1093/nar/gkw1080. PMID: 27899654 Free PMC Article.
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Quality Assessments of Long-term Quantitative Proteomic Analysis of Breast Cancer Xenograft Tissues. Jian-Ying Zhou, Lijun Chen, Bai Zhang, Yuan Tian, Tao Liu, Stefani N Thomas, Li Chen, Michael Schnaubelt, Emily Boja, Tara Hiltke, Christopher R Kinsinger, Henry Rodriguez, Sherri R Davies, Shunqiang Li, Jacqueline E Snider, Petra Erdmann-Gilmore, David L Tabb, R Reid Townsend, Matthew J Ellis, Karin D Rodland, Richard D Smith, Steven A Carr, Zhen Zhang, Daniel W Chan, Hui Zhang. Journal of Proteome Research, 2017; 16 (12): 4523-4530.
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Novel stool-based protein biomarkers for improved colorectal cancer screening: a case-control study. Linda JW Bosch, Meike de Wit, Thang V Pham, Veerle HM Coupé, Annemieke C Hiemstra, Sander R Piersma, Gideon Oudgenoeg, George L Scheffer, Sandra Mongera, Jochim Terhaar Sive Droste, Frank A Oort, Sietze T van Turenhout, Ilhame Ben Larbi, Joost Louwagie, Wim van Criekinge, Rene WM van der Hulst, Chris JJ Mulder, Beatriz Carvalho, Remond JA Fijneman, Connie R Jimenez*, Gerrit A Meijer. Annals of Internal Med, 2017 Dec 19;167(12):855-866. doi: 10.7326/M17-1068. Epub 2017 Nov 21.
- Identification of Differentially Expressed Splice Variants by the Proteogenomic Pipeline Splicify. Komor MA, Pham TV, Hiemstra AC, Piersma SR, Bolijn AS, Schelfhorst T, Delis-van Diemen PM, Tijssen M, Sebra RP, Ashby M, Meijer GA, Jimenez CR, Fijneman RJA. Mol Cell Proteomics. 2017 Oct;16(10):1850-1863. doi: 10.1074/mcp.TIR117.000056. Epub 2017 Jul 26.
- Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction. Wang J, Ma Z, Carr SA, Mertins P, Zhang H, Zhang Z, Chan DW, Ellis MJ, Townsend RR, Smith RD, McDermott JE, Chen X, Paulovich AG, Boja ES, Mesri M, Kinsinger CR, Rodriguez H, Rodland KD, Liebler DC, Zhang B. Mol Cell Proteomics. 2017 Jan;16(1):121-134. doi: 10.1074/mcp.M116.060301. Epub 2016 Nov 11.
- The target landscape of clinical kinase drugs. Klaeger S, Heinzlmeir S, Wilhelm M, Polzer H, Vick B, Koenig PA, Reinecke M, Ruprecht B, Petzoldt S, Meng C, Zecha J, Reiter K, Qiao H, Helm D, Koch H, Schoof M, Canevari G, Casale E, Depaolini SR, Feuchtinger A, Wu Z, Schmidt T, Rueckert L, Becker W, Huenges J, Garz AK, Gohlke BO, Zolg DP, Kayser G, Vooder T, Preissner R, Hahne H, Tõnisson N, Kramer K, Götze K, Bassermann F, Schlegl J, Ehrlich HC, Aiche S, Walch A, Greif PA, Schneider S, Felder ER, Ruland J, Médard G, Jeremias I, Spiekermann K, Kuster B. Science. 2017 Dec 1;358(6367). pii: eaan4368. doi: 10.1126/science.aan4368.
- Proteogenomic integration reveals therapeutic targets in breast cancer xenografts. Huang K, Li S, Mertins P, Cao S, Gunawardena HP, Ruggles KV, Mani DR, Clauser KR, Tanioka M, Usary J, Kavuri SM, Xie L, Yoon C, Qiao JW, Wrobel J, Wyczalkowski MA, Erdmann-Gilmore P, Snider JE, Hoog J, Singh P, Niu B, Guo Z, Sun SQ, Sanati S, Kawaler E, Wang X, Scott A, Ye K, McLellan MD, Wendl MC, Malovannaya A, Held JM, Gillette MA, Fenyö D, Kinsinger CR, Mesri M, Rodriguez H, Davies SR, Perou CM, Ma C, Townsend RR, Chen X, Carr SA, Matthew J. Ellis, and Li Ding. Nat Commun. 2017 Mar 28;8(14864). doi10.1038/ncomms14864
- Distinct metabolomic signature in cerebrospinal fluid in early parkinson's disease. Trezzi JP, Galozzi S, Jaeger C, Barkovits K, Brockmann K, Maetzler W, Berg D, Marcus K, Betsou F, Hiller K, Mollenhauer B (2017), Mov Disord., 32(10):1401-1408
- Untargeted screening for novel autoantibodies with prognostic value in first-episode psychosis. A Zandian, L Wingård, H Nilsson, E Sjöstedt, D X Johansson, D Just, C Hellström, M Uhlén, J M Schwenk, A Häggmark-Månberg, O Norbeck, B Owe-Larsson, P Nilsson, M A A Persson (2017), Translational Psychiatry, 7(7):e1177
- A Case for a Human Immuno-Peptidome Project Consortium. Caron,E., Aebersold,R., Banaei-Esfahani,A., Chong,C. and Bassani-Sternberg, M. (2017)Immunity, 47, 203–208.
- Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction. Abelin,J.G., Keskin,D.B., Sarkizova,S., Hartigan,C.R., Zhang,W., Sidney,J., Stevens,J., Lane,W., Zhang,G.L., Eisenhaure,T.M., et al.(2017) Immunity, 46, 315–326.
- Direct Pharmacological Targeting of a Mitochondrial Ion Channel Selectively Kills Tumor Cells In Vivo. Leanza L, Romio M, Becker KA, Azzolini M, Trentin L, Managò A, Venturini E, Zaccagnino A, Mattarei A, Carraretto L, Urbani A, Kadow S, Biasutto L, Martini V, Severin F, Peruzzo R, Trimarco V, Egberts JH, Hauser C, Visentin A, Semenzato G, Kalthoff H, Zoratti M, Gulbins E, Paradisi C, Szabo I. Cancer Cell. 2017 Apr 10;31(4):516-531.e10. doi: 10.1016/j.ccell.2017.03.003.
- Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens. Khodadoust,M.S, Olsson,N, Wagar,L.E, Haabeth,O.A.W, Chen,B, Swaminathan,K, Rawson,K, Liu,C.L, Steiner,D, Lund,P, et al. Nature. 2017 Mar 30;543(7647):723-727. doi: 10.1038/nature21433. Epub 2017 Mar 22.
- Dominant protection from HLA-linked autoimmunity by antigen-specific regulatory T cells. Ooi,J.D, Petersen,J, Tan,Y.H, Huynh,M, Willett,Z.J, Ramarathinam,S.H, Eggenhuizen,P.J, Loh,K.L, Watson,K.A, Gan,P.Y, et al. (2017) Nature. 2017 May 11;545(7653):243-247. doi: 10.1038/nature22329. Epub 2017 May 3.
- The immunopeptidomic landscape of ovarian carcinomas. Proceedings of the National Academy of Science. Schuster,H., Peper,J.K., Bösmüller,H.-C., Röhle,K., Backert,L., Bilich,T., Ney,B., Löffler,M.W., Kowalewski,D.J., Trautwein,N., et al. PNAS November 1, 2017. 201707658; published ahead of print November 1, 2017.
- Proteomic and metabolomic characterization of streptozotocin-induced diabetic nephropathy in TIMP3-deficient mice. Rossi C, Marzano V, Consalvo A, Zucchelli M, Levi Mortera S, Casagrande V, Mavilio M, Sacchetta P, Federici M, Menghini R, Urbani A, Ciavardelli D. Acta Diabetol. 2018 Feb;55(2):121-129. doi: 10.1007/s00592-017-1074-y. Epub 2017 Nov 13.
- A Map of Human Mitochondrial Protein Interactions Linked to Neurodegeneration Reveals New Mechanisms of Redox Homeostasis and NF-κB Signaling. Malty RH, Aoki H, Kumar A, Phanse S, Amin S, Zhang Q, Minic Z, Goebels F, Musso G, Wu Z, Abou-Tok H, Meyer M, Deineko V, Kassir S, Sidhu V, Jessulat M, Scott NE, Xiong X, Vlasblom J, Prasad B, Foster LJ, Alberio T, Garavaglia B, Yu H, Bader GD, Nakamura K, Parkinson J, Babu M. Cell Syst. 2017 Dec 27;5(6):564-577.e12. doi:10.1016/j.cels.2017.10.010
- Toward the Standardization of Mitochondrial Proteomics: The Italian Mitochondrial Human Proteome Project Initiative. Alberio T, Pieroni L, Ronci M, Banfi C, Bongarzone I, Bottoni P, Brioschi M,Caterino M, Chinello C, Cormio A, Cozzolino F, Cunsolo V, Fontana S, Garavaglia B, Giusti L, Greco V, Lucacchini A, Maffioli E, Magni F, Monteleone F, Monti M, Monti V, Musicco C, Petrosillo G, Porcelli V, Saletti R, Scatena R, Soggiu A, Tedeschi G, Zilocchi M, Roncada P, Urbani A, Fasano M. J Proteome Res. 2017 Dec 1;16(12):4319-4329. doi:10.1021/acs.jproteome.7b00350.
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Palmitate-induced lipotoxicity alters acetylation of multiple proteins in clonal β cells and human pancreatic islets. Ciregia F, Bugliani M, Ronci M, Giusti L, Boldrini C, Mazzoni MR, Mossuto S, Grano F, Cnop M, Marselli L, Giannaccini G, Urbani A, Lucacchini A, Marchetti P. Sci Rep. 2017 Oct 18;7(1):13445. doi:10.1038/s41598-017-13908-w.
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Efficacy of sterile fecal filtrate transfer for treating patients with Clostridium diffcicile infection. Ott SJ, Waetzig GH, Rehman A, Moltzau-Anderson J, Bharti R, Grasis JA, Cassidy L, Tholey A, Fickenscher H, Seegert D, Rosenstiel P, Schreiber S (2017). Gastroenterology, 152: 799-811.
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Screening and Validation of Novel Biomarkers in Osteoarticular Pathologies by Comprehensive Combination of Protein Array Technologies. Sierra-Sánchez, Álvaro; Garrido-Martín, Diego; Lourido, Lucía; González-González, María; Díez, Paula; Ruiz-Romero, Cristina; Sjöberg, Ronald; Droste, Conrad; De Las Rivas, Javier; Nilsson, Peter; Blanco García, Francisco; Fuentes, Manuel J Proteome Res 2017; 16(5): 1890-99.
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