Article
Biochemical Research Methods
Oceane Girard, Regis Lavigne, Simon Chevolleau, Constance Onfray, Emmanuelle Com, Pierre-Olivier Schmit, Manuel Chapelle, Thomas Freour, Lydie Lane, Laurent David, Charles Pineau
Summary: The Chromosome-centric Human Proteome Project aims to identify and characterize the proteins encoded by the human genome. They have confirmed the existence of proteins for 93.2% of genes and focus on studying reproductive processes and embryonic development. Through their research, they have discovered 4 new missing proteins and deposited the data on ProteomeXchange.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Gilbert S. Omenn, Lydie Lane, Christopher M. Overall, Charles Pineau, Nicolle H. Packer, Ileana M. Cristea, Cecilia Lindskog, Susan T. Weintraub, Sandra Orchard, Michael H. A. Roehrl, Edouard Nice, Siqi Liu, Nuno Bandeira, Yu-Ju Chen, Tiannan Guo, Ruedi Aebersold, Robert L. Moritz, Eric W. Deutsch
Summary: According to the 2022 metrics of the HUPO Human Proteome Project (HPP), protein expression has been detected for 93.2% of the predicted proteins in the human genome. The number of missing proteins has been reduced, indicating experimental progress and reclassification. Proteomics continues to yield significant findings in biological and clinical studies and integrates with other omics platforms.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Gilbert S. Omenn, Lydie Lane, Christopher M. Overall, Young-Ki Paik, Ileana M. Cristea, Fernando J. Corrales, Cecilia Lindskog, Susan Weintraub, Michael H. A. Roehrl, Siqi Liu, Nuno Bandeira, Sudhir Srivastava, Yu-Ju Chen, Ruedi Aebersold, Robert L. Moritz, Eric W. Deutsch
Summary: The 2021 Metrics of the HUPO Human Proteome Project (HPP) reveal significant progress in detecting protein expression in the human genome. The number of missing proteins has decreased, and the utilization of proteomics in biological and clinical research continues to expand and integrate effectively with other omics platforms. This represents a promising advancement in understanding the human proteome and its potential applications in healthcare.
JOURNAL OF PROTEOME RESEARCH
(2021)
Review
Biochemical Research Methods
Gilbert S. Omenn
Summary: The HUPO Human Proteome Project celebrates its 10th anniversary by achieving the milestone of confident detection of proteins from 90% of predicted protein-coding genes. This global project has influenced data-sharing, quality assurance, and issued stringent guidelines for detecting missing proteins. The project's impact is highlighted in special issues of Nature Communications and Journal of Proteome Research.
MOLECULAR & CELLULAR PROTEOMICS
(2021)
Review
Multidisciplinary Sciences
Lloyd M. Smith, Jeffrey N. Agar, Julia Chamot-Rooke, Paul O. Danis, Ying Ge, Joseph A. Loo, Ljiljana Pasa-Tolic, Yury O. Tsybin, Neil L. Kelleher
Summary: Understanding the structure and properties of proteins is crucial in deciphering biological functions. The concept of defining the human proteome as a reference set of proteoforms is proposed, with a call for improved technologies in a two-pronged strategy.
Article
Oncology
Lazaro Hiram Betancourt, Jeovanis Gil, Aniel Sanchez, Viktoria Doma, Magdalena Kuras, Jimmy Rodriguez Murillo, Erika Velasquez, Ugur Cakir, Yonghyo Kim, Yutaka Sugihara, Indira Pla Parada, Beata Szeitz, Roger Appelqvist, Elisabet Wieslander, Charlotte Welinder, Natalia Pinto de Almeida, Nicole Woldmar, Matilda Marko-Varga, Jonatan Eriksson, Krzysztof Pawlowski, Bo Baldetorp, Christian Ingvar, Hakan Olsson, Lotta Lundgren, Henrik Lindberg, Henriett Oskolas, Boram Lee, Ethan Berge, Marie Sjogren, Carina Eriksson, Dasol Kim, Ho Jeong Kwon, Beatrice Knudsen, Melinda Rezeli, Johan Malm, Runyu Hong, Peter Horvath, A. Marcell Szasz, Jozsef Timar, Sarolta Karpati, Peter Horvatovich, Tasso Miliotis, Toshihide Nishimura, Harubumi Kato, Erik Steinfelder, Madalina Oppermann, Ken Miller, Francesco Florindi, Quimin Zhou, Gilberto B. Domont, Luciana Pizzatti, Fabio C. S. Nogueira, Leticia Szadai, Istvan Balazs Nemeth, Henrik Ekedahl, David Fenyo, Gyorgy Marko-Varga
Summary: The MM500 meta-study aims to establish a knowledge basis of the tumor proteome as a complement to genome and transcriptome studies. By analyzing 505 well-annotated melanoma tumor samples, the study defined the melanoma proteome landscape, including thousands of proteins and mutated proteoforms. The study found a high degree of correlation between the melanoma transcriptome and proteome, increasing understanding of melanoma disease.
CLINICAL AND TRANSLATIONAL MEDICINE
(2021)
Article
Cell Biology
Yi-Rong Jiang, Le Zhu, Lan-Rui Cao, Qiong Wu, Jian-Bo Chen, Yu Wang, Jie Wu, Tian-Yu Zhang, Zhao-Lun Wang, Zhi-Ying Guan, Qin-Qin Xu, Qian-Xi Fan, Shao-Wen Shi, Hui-Feng Wang, Jian-Zhan Pan, Xu-Dong Fu, Yongcheng Wang, Qun Fang
Summary: A new single-cell analysis platform, capable of simultaneously analyzing the transcriptome and proteome, provides an important resource for understanding the relationship between transcription and translation in cells. By applying this platform to mouse oocytes, we investigated the correlation between RNA and protein, as well as the meiosis regulatory network, and identified specific oocyte maturational signatures.
Article
Nutrition & Dietetics
Wenming Wei, Bolun Cheng, Dan He, Yijing Zhao, Xiaoyue Qin, Qingqing Cai, Na Zhang, Xiaoge Chu, Sirong Shi, Feng Zhang
Summary: This study analyzes the genetic association between bitter or sweet beverage perception and human brain proteins. The results identify several candidate brain proteins for bitter or sweet beverage perception and support the potential effect of beverage perception on brain function.
Article
Multidisciplinary Sciences
Christine Olander, Jesper Edvardsson Rasmussen, Per Olof Eriksson, Goran Laurell, Helge Rask-Andersen, Jonas Bergquist
Summary: This study analyzed the proteomics of the endolymphatic sac using a refined sampling technique, identifying a total of 1656 non-redundant proteins, with 110 proteins unique to the endolymphatic sac. The results validate a strategy for in vivo and in situ human sampling during surgery and may form a platform for further investigations into the function of this intriguing part of the inner ear.
SCIENTIFIC REPORTS
(2021)
Article
Biochemical Research Methods
Deeptarup Biswas, Sanjyot Vinayak Shenoy, Chetanya Chetanya, Mercedes Lachen-Montes, Abhilash Barpanda, Arunachalam Paramasivan Athithyan, Susmita Ghosh, Karina Ausin, Maria Victoria Zelaya, Joaquin Fernandez-Irigoyen, Akash Manna, Sudesh Roy, Arunasu Talukdar, Graham Roy Ball, Enrique Santamaria, Sanjeeva Srivastava
Summary: This study presents the first draft of the human brain interhemispheric proteome, providing comprehensive coverage of 3300 experimentally measured proteins across multiple brain regions. Specific markers were identified in different brain regions, contributing to the understanding of brain disorders and synapse biology. An online portal, IBPM, was developed to facilitate research in neuroproteomics.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Martin D. Garlovsky, Jessica A. Sandler, Timothy L. Karr
Summary: This study provides an updated version of the Drosophila melanogaster sperm proteome (DmSP3) using improved methods and annotation, revealing reduced gene content and protein abundance on the X chromosome and supporting the meiotic sex-chromosome inactivation model.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Chemistry, Multidisciplinary
Jiaying Li, Jiahua Zhou, Kailu Tian, He Zhu, Yao Chen, Yangyu Huang, Guosheng Wang, Zhou Gong, Hongqiang Qin, Mingliang Ye, Hao Xu
Summary: The quantitative profiling of residue reactivity in proteins can help identify covalent druggable targets for precise therapy. In this study, a chemical proteomics platform was developed to analyze the reactivity of histidine (His) residues. Through this platform, the reactivity of His residues in the human proteome was characterized, and a large number of His residues with high reactivity were identified. The findings suggest that these highly reactive residues are less likely to be phosphorylation sites, which requires further research to understand the underlying mechanism. This comprehensive map of His residue reactivity provides potential bindable sites for disrupting protein activities and offers new opportunities for developing covalent inhibitors using acrolein derivatives as reactive warheads.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemical Research Methods
Kirill E. Medvedev, Jimin Pei, Nick Grishin
Summary: This study developed a database of human proteome IDRs that are significantly enriched in particular amino acids, providing information on function terms, disorder prediction, enriched IDR composition, and ranks of human proteins with similar enriched IDRs. The distribution analysis revealed significant overrepresentation of R- and Y-enriched IDRs in metabolic and enzymatic activities, and F-enriched IDRs in transport. Approximately 75% of functional categories contain IDPs with IDRs significantly enriched in hydrophobic residues important for protein-protein interactions.
Article
Biochemistry & Molecular Biology
Chih-Yi Gabriela Lin, Anna Christina Naeger, Thomas Lunardi, Aleksandra Vancevska, Gerald Lossaint, Joachim Lingner
Summary: Telomere shortening can lead to diseases and aging, often due to the lack of telomerase in cells. By developing a new isolation protocol, specific proteins associated with telomere replication can be purified, revealing their importance for maintaining telomere stability. This study provides a valuable resource for understanding the dynamic changes of the telomeric proteome during replication.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Genetics & Heredity
Yi Zhou, La Zhu, Yu Sun, Hui Zhang, Jiaojiao Wang, Weilin Qin, Wangchao He, Luojing Zhou, Qi Li, Rurong Zhao, Kaikun Luo, Chenchen Tang, Chun Zhang, Shaojun Liu
Summary: The study focused on changes in active sites of the testicular transcriptome of allotetraploid fish by analyzing RNA Pol II CTD YSPTSPS (phospho S5) and RNA-seq data. Results showed no significant difference in transcriptionally active sites between different types of fish, suggesting chromosome number increase did not affect transcriptionally active sites. RNA-seq analysis further indicated no significant changes in highly active sites in the genome regions, implying conservation of active transcriptome sites in allotetraploid fish compared to diploid fish.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Yongchao Dou, Emily A. Kawaler, Daniel Cui Zhou, Marina A. Gritsenko, Chen Huang, Lili Blumenberg, Alla Karpova, Vladislav A. Petyuk, Sara R. Savage, Shankha Satpathy, Wenke Liu, Yige Wu, Chia-Feng Tsai, Bo Wen, Zhi Li, Song Cao, Jamie Moon, Zhiao Shi, MacIntosh Cornwell, Matthew A. Wyczalkowski, Rosalie K. Chu, Suhas Vasaikar, Hua Zhou, Qingsong Gao, Ronald J. Moore, Kai Li, Sunantha Sethuraman, Matthew E. Monroe, Rui Zhao, David Heiman, Karsten Krug, Karl Clauser, Ramani Kothadia, Yosef Maruvka, Alexander R. Pico, Amanda E. Oliphant, Emily L. Hoskins, Samuel L. Pugh, Sean J. I. Beecroft, David W. Adams, Jonathan C. Jarman, Andy Kong, Hui-Yin Chang, Boris Reva, Yuxing Liao, Dmitry Rykunov, Antonio Colaprico, Xi Steven Chen, Andrzej Czekanski, Marcin Jedryka, Rafa Matkowski, Maciej Wiznerowicz, Tara Hiltke, Emily Boja, Christopher R. Kinsinger, Mehdi Mesri, Ana I. Robles, Henry Rodriguez, David Mutch, Katherine Fuh, Matthew J. Ellis, Deborah DeLair, Mathangi Thiagarajan, D. R. Mani, Gad Getz, Michael Noble, Alexey I. Nesvizhskii, Pei Wang, Matthew L. Anderson, Douglas A. Levine, Richard D. Smith, Samuel H. Payne, Kelly V. Ruggles, Karin D. Rodland, Li Ding, Bing Zhang, Tao Liu, David Fenyo
Article
Multidisciplinary Sciences
Shankha Satpathy, Eric J. Jaehnig, Karsten Krug, Beom-Jun Kim, Alexander B. Saltzman, Doug W. Chan, Kimberly R. Holloway, Meenakshi Anurag, Chen Huang, Purba Singh, Ari Gao, Noel Namai, Yongchao Dou, Bo Wen, Suhas V. Vasaikar, David Mutch, Mark A. Watson, Cynthia Ma, Foluso O. Ademuyiwa, Mothaffar F. Rimawi, Rachel Schiff, Jeremy Hoog, Samuel Jacobs, Anna Malovannaya, Terry Hyslop, Karl R. Clauser, D. R. Mani, Charles M. Perou, George Miles, Bing Zhang, Michael A. Gillette, Steven A. Carr, Matthew J. Ellis
NATURE COMMUNICATIONS
(2020)
Article
Biochemical Research Methods
Haifen Li, Ruo Zhou, Shaohang Xu, Xiaoping Chen, Yanbin Hong, Qing Lu, Hao Liu, Baojin Zhou, Xuandiang Liang
JOURNAL OF PROTEOME RESEARCH
(2020)
Article
Multidisciplinary Sciences
Chenwei Wang, Ke Shui, Shanshan Ma, Shaofeng Lin, Ying Zhang, Bo Wen, Wankun Deng, Haodong Xu, Hui Hu, Anyuan Guo, Yu Xue, Luoying Zhang
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Bo Wen, Kai Li, Yun Zhang, Bing Zhang
NATURE COMMUNICATIONS
(2020)
Article
Biochemistry & Molecular Biology
Michael A. Gillette, Shankha Satpathy, Song Cao, Saravana M. Dhanasekaran, Suhas V. Vasaikar, Karsten Krug, Francesca Petralia, Yize Li, Wen-Wei Liang, Boris Reva, Azra Krek, Jiayi Ji, Xiaoyu Song, Wenke Liu, Runyu Hong, Lijun Yao, Lili Blumenberg, Sara R. Savage, Michael C. Wendl, Bo Wen, Kai Li, Lauren C. Tang, Melanie A. MacMullan, Shayan C. Avanessian, M. Harry Kane, Chelsea J. Newton, MacIntosh Cornwell, Ramani B. Kothadia, Weiping Ma, Seungyeul Yoo, Rahul Mannan, Pankaj Vats, Chandan Kumar-Sinha, Emily A. Kawaler, Tatiana Omelchenko, Antonio Colaprico, Yifat Geffen, Yosef E. Maruvka, Felipe da Veiga Leprevost, Maciej Wiznerowicz, Zeynep H. Gumus, Rajwanth R. Veluswamy, Galen Hostetter, David Heiman, Matthew A. Wyczalkowski, Tara Hiltke, Mehdi Mesri, Christopher R. Kinsinger, Emily S. Boja, Gilbert S. Omenn, Arul M. Chinnaiyan, Henry Rodriguez, Qing Kay Li, Scott D. Jewell, Mathangi Thiagarajan, Gad Getz, Bing Zhang, David Fenyo, Kelly Ruggles, Marcin P. Cieslik, Ana Robles, Karl R. Clauser, Ramaswamy Govindan, Pei Wang, Alexey Nesvizhskii, Li Ding, D. R. Mani, Steven A. Carr
Review
Biochemical Research Methods
Bo Wen, Wen-Feng Zeng, Yuxing Liao, Zhiao Shi, Sara R. Savage, Wen Jiang, Bing Zhang
Article
Biochemical Research Methods
Kai Li, Antrix Jain, Anna Malovannaya, Bo Wen, Bing Zhang
Article
Oncology
Chen Huang, Lijun Chen, Sara R. Savage, Rodrigo Vargas Eguez, Yongchao Dou, Yize Li, Felipe da Veiga Leprevost, Eric J. Jaehnig, Jonathan T. Lei, Bo Wen, Michael Schnaubelt, Karsten Krug, Xiaoyu Song, Marcin Cieslik, Hui-Yin Chang, Matthew A. Wyczalkowski, Kai Li, Antonio Colaprico, Qing Kay Li, David J. Clark, Yingwei Hu, Liwei Cao, Jianbo Pan, Yuefan Wang, Kyung-Cho Cho, Zhiao Shi, Yuxing Liao, Wen Jiang, Meenakshi Anurag, Jiayi Ji, Seungyeul Yoo, Daniel Cui Zhou, Wen-Wei Liang, Michael Wendl, Pankaj Vats, Steven A. Carr, D. R. Mani, Zhen Zhang, Jiang Qian, Xi S. Chen, Alexander R. Pico, Pei Wang, Arul M. Chinnaiyan, Karen A. Ketchum, Christopher R. Kinsinger, Ana Robles, Eunkyung An, Tara Hiltke, Mehdi Mesri, Mathangi Thiagarajan, Alissa M. Weaver, Andrew G. Sikora, Jan Lubinski, Malgorzata Wierzbicka, Maciej Wiznerowicz, Shankha Satpathy, Michael A. Gillette, George Miles, Matthew J. Ellis, Gilbert S. Omenn, Henry Rodriguez, Emily S. Boja, Saravana M. Dhanasekaran, Li Ding, Alexey Nesvizhskii, Adel K. El-Naggar, Daniel W. Chan, Hui Zhang, Bing Zhang
Summary: This study presents a proteogenomic analysis of HPV-negative HNSCCs, identifying potential therapeutic targets and uncovering tumor characteristics such as immune status and resistance mechanisms. The findings suggest new strategies for stratifying HNSCC and improving treatment outcomes.
Article
Biochemical Research Methods
Zhiao Shi, Bo Wen, Qiang Gao, Bing Zhang
Summary: ProMS is a computational algorithm for selecting protein markers based on clustering, showing superior performance in two clinically relevant classification problems compared to existing feature selection methods. It can be extended to the multiomics setting through a constrained weighted k-medoids clustering algorithm, leading to improved performance on independent test data. In addition to performance, ProMS and ProMS_mo provide functional interpretation of selected protein markers and facilitate robust transition to verification and validation platforms.
MOLECULAR & CELLULAR PROTEOMICS
(2021)
Article
Biochemistry & Molecular Biology
Liwei Cao, Chen Huang, Daniel Cui Zhou, Yingwei Hu, T. Mamie Lih, Sara R. Savage, Karsten Krug, David J. Clark, Michael Schnaubelt, Lijun Chen, Felipe da Veiga Leprevost, Rodrigo Vargas Eguez, Weiming Yang, Jianbo Pan, Bo Wen, Yongchao Dou, Wen Jiang, Yuxing Liao, Zhiao Shi, Nadezhda Terekhanova, Song Cao, Rita Jui-Hsien Lu, Yize Li, Ruiyang Liu, Houxiang Zhu, Peter Ronning, Yige Wu, Matthew A. Wyczalkowski, Hariharan Easwaran, Ludmila Danilova, Arvind Singh Mer, Seungyeul Yoo, Joshua M. Wang, Wenke Liu, Benjamin Haibe-Kains, Mathangi Thiagarajan, Scott D. Jewell, Galen Hostetter, Chelsea J. Newton, Qing Kay Li, Michael H. Roehr, David Fenyo, Pei Wang, Alexey Nesvizhskii, D. R. Mani, Gilbert S. Omenn, Emily S. Boja, Mehdi Mesri, Ana Robles, Henry Rodriguez, Oliver F. Bathe, Daniel W. Chan, Ralph H. Hruban, Li Ding, Bing Zhang, Hui Zhang
Summary: This study conducted comprehensive proteogenomic analysis of PDAC to understand the molecular alterations that drive oncogenesis. Multiple analyses were performed on tissues from patients, providing valuable resources for early detection and identification of therapeutic targets.
Article
Biochemistry & Molecular Biology
Shankha Satpathy, Karsten Krug, Pierre M. Jean Beltran, Sara R. Savage, Francesca Petralia, Chandan Kumar-Sinha, Yongchao Dou, Boris Reva, M. Harry Kane, Shayan C. Avanessian, Suhas V. Vasaikar, Azra Krek, Jonathan T. Lei, Eric J. Jaehnig, Tatiana Omelchenko, Yifat Geffen, Erik J. Bergstrom, Vasileios Stathias, Karen E. Christianson, David Heiman, Marcin P. Cieslik, Song Cao, Xiaoyu Song, Jiayi Ji, Wenke Liu, Kai Li, Bo Wen, Yize Li, Zeynep H. Gumus, Myvizhi Esai Selvan, Rama Soundararajan, Tanvi H. Visal, Maria G. Raso, Edwin Roger Parra, Ozgun Babur, Pankaj Vats, Shankara Anand, Tobias Schraink, MacIntosh Cornwell, Fernanda Martins Rodrigues, Houxiang Zhu, Chia-Kuei Mo, Yuping Zhang, Felipe da Veiga Leprevost, Chen Huang, Arul M. Chinnaiyan, Matthew A. Wyczalkowski, Gilbert S. Omenn, Chelsea J. Newton, Stephan Schurer, Kelly Ruggles, David Fenyo, Scott D. Jewell, Mathangi Thiagarajan, Mehdi Mesri, Henry Rodriguez, Sendurai A. Mani, Namrata D. Udeshi, Gad Getz, James Suh, Qing Kay Li, Galen Hostetter, Paul K. Paik, Saravana M. Dhanasekaran, Ramaswamy Govindan, Li Ding, Ana Robles, Karl R. Clauser, Alexey Nesvizhskii, Pei Wang, Steven A. Carr, Bing Zhang, D. R. Mani, Michael A. Gillette
Summary: The proteogenomic analysis of LSCC reveals a deeper understanding of its biology and potential therapeutic directions. New therapeutic targets and rationale for further exploration have been identified, along with support for complex regulation of metabolic pathways and immune-related research directions. Furthermore, insights from triangulation with other cancers highlight unique and shared vulnerabilities, guiding future research into LSCC biology and treatment.
Article
Multidisciplinary Sciences
Xinpei Yi, Yuxing Liao, Bo Wen, Kai Li, Yongchao Dou, Sara R. Savage, Bing Zhang
Summary: A comprehensive immunopeptidome atlas of human cancer was constructed by analyzing 43 published immunopeptidomic datasets and standardized analysis of 81.6 million MS/MS spectra, expanding the current knowledge of MHC-bound antigens and providing unprecedented characterization of post-translationally modified antigens and their cancer-association. Systematic analysis of cancer-testis antigens, cancer-associated antigens, and neoantigens was performed, offering a central resource named caAtlas for selection and prioritization of MHC-bound peptides for in vitro HLA binding assay and immunogenicity testing, ultimately paving the way for the development of cancer immunotherapies.
Article
Biochemical Research Methods
Bo Wen, Eric J. Jaehnig, Bing Zhang
Summary: OmicsEV is an R package that evaluates the quality of omics data tables by using various methods to assess depth, normalization, biological signal, and other factors. It generates comprehensive visual and quantitative evaluation results to help assess data quality and determine the optimal data processing method and parameters.
Article
Computer Science, Artificial Intelligence
Seungyeul Yoo, Zhiao Shi, Bo Wen, SoonJye Kho, Renke Pan, Hanying Feng, Hong Chen, Anders Carlsson, Patrik Eden, Weiping Ma, Michael Raymer, Ezekiel J. Maier, Zivana Tezak, Elaine Johanson, Denise Hinton, Henry Rodriguez, Jun Zhu, Emily Boja, Pei Wang, Bing Zhang
Summary: Sample mislabeling or misannotation is a common problem in scientific research, especially in large-scale, multi-omic studies. A crowdsourced challenge was organized to identify and correct mislabels, resulting in the development of an open-source software named COSMO with high accuracy and robustness in multi-omic datasets.