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)
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)
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)
Article
Biochemistry & Molecular Biology
Yasset Perez-Riverol, Jingwen Bai, Chakradhar Bandla, David Garcia-Seisdedos, Suresh Hewapathirana, Selvakumar Kamatchinathan, Deepti J. Kundu, Ananth Prakash, Anika Frericks-Zipper, Martin Eisenacher, Mathias Walzer, Shengbo Wang, Alvis Brazma, Juan Antonio Vizcaino
Summary: PRIDE is the largest data repository of mass spectrometry-based proteomics data in the world, with around 500 datasets submitted per month. In addition to continuous improvements in data pipelines and infrastructure, PRIDE has developed the Spectra Archive and MAGE-TAB file format to enhance sample metadata annotation and access to mass spectra.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Andreas Digre, Cecilia Lindskog
Summary: Understanding the spatial distribution of proteins is crucial for comprehending the biology, molecular repertoire, and structure of human cells. The Human Protein Atlas (HPA) has evolved into one of the world's largest biological databases and recently underwent a major update, categorizing the data into 10 comprehensive sections that provide insights into different aspects of the human proteome and protein-coding genes. By integrating large datasets on a single-cell level, the HPA now offers refined information on tissue and cell type specificity, as well as detailed expression profiles in various cell states.
Article
Plant Sciences
Oindrila Bhattacharya, Irma Ortiz, Nathan Hendricks, Linda L. Walling
Summary: Tomato is a model species for studying fruit development, wounding, herbivory, and pathogen attack. This study identified the stromal proteome of tomato using protein isolation, analysis, and selection, providing insights into tomato chloroplast proteins.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Andreas Digre, Cecilia Lindskog
Summary: The Human Protein Atlas project aims to map the entire human proteome using antibody-based proteomics and other omics technologies. It is divided into six main sections focusing on different aspects of the human proteome, such as tissue distribution, subcellular localization, pathology impact on cancer patients, blood cell expression, brain protein distribution, and protein involvement in metabolism. This publicly available resource holds promise for further understanding human biology and integration with other single cell analysis efforts.
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)
Editorial Material
Genetics & Heredity
Michael Attwaters
Summary: Three papers published in Nature present the largest open-access plasma proteomics dataset to date, which serves as a valuable resource for understanding human diseases and identifying potential drug targets.
NATURE REVIEWS GENETICS
(2023)
Review
Biochemical Research Methods
Eric W. Deutsch, Gilbert S. Omenn, Zhi Sun, Michal Maes, Maria Pernemalm, Krishnan K. Palaniappan, Natasha Letunica, Yves Vandenbrouck, Virginie Brun, Sheng-ce Tao, Xiaobo Yu, Philipp E. Geyer, Vera Ignjatovic, Robert L. Moritz, Jochen M. Schwenk
Summary: The study of proteins circulating in blood presents significant opportunities for diagnosing, stratifying, or preventing diseases. Recent technological advancements have made the proteomic analysis of blood-derived serum and plasma increasingly important in understanding human biology and pathophysiology. By utilizing mass-spectrometry (MS) or affinity-based methods, valuable insights into SARS-CoV-2 infections, aging, and hemostasis have been gained, along with the potential to combine proteomics with genetic data for further insights. The ongoing challenges include translating plasma proteomics into precision medicine, with recent advances in the field providing impactful applications.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biology
Markus J. Sommer, Sooyoung Cha, Ales Varabyou, Natalia Rincon, Sukhwan Park, Ilia Minkin, Mihaela Pertea, Martin Steinegger, Steven L. Salzberg
Summary: The development of three-dimensional protein structure prediction methods has provided new opportunities for research on genomes and proteomes. By utilizing computational predictions of protein structures, it is possible to identify the functional protein product among multiple gene isoforms. In this study, we evaluated over 230,000 isoforms of human protein-coding genes using protein structure predictions, and identified several isoforms with more confidently predicted structures and potentially superior function compared to the canonical isoforms in the latest human gene database. We demonstrated the potential of protein structure prediction as a genome annotation tool and provided a resource of protein structures for better understanding the function of human genes and their isoforms.
Article
Biochemistry & Molecular Biology
Jan Schmitz, Lydia J. Kolaparambil Varghese, Felix Liebold, Moritz Meyer, Lukas Nerlich, Clement Starck, Seamus Thierry, Stefanie Jansen, Jochen Hinkelbein
Summary: The present study aims to investigate the time-dependent changes in protein expression due to hypobaric hypoxia. The results show that protein expression differs based on the duration of exposure, with significant differences in proteins associated with hemostasis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Aliki Xanthopoulou, Theodoros Moysiadis, Christos Bazakos, Evangelos Karagiannis, Ioanna Karamichali, George Stamatakis, Martina Samiotaki, Maria Manioudaki, Michail Michailidis, Panagiotis Madesis, Ioannis Ganopoulos, Athanassios Molassiotis, Georgia Tanou
Summary: The study provides new insights into plant biology through the integration of genomics and proteomics, identifying a large number of genes and proteins in sweet cherries. Analysis reveals differences between gene and protein quantities, key regulators of fruit development, and novel cherry proteins. Additionally, a new protein-level annotation and database were developed for further research in Prunus species.
Article
Parasitology
Klevia Dishnica, Chiara Piubelli, Marcello Manfredi, Ravi Teja Kondaveeti, Silvia Stefania Longoni, Monica Degani, Dora Buonfrate, Alejandro Giorgetti, Natalia Tiberti
Summary: This study aims to expand the characterization of S. stercoralis infective larvae (iL3) to explore the mechanisms of parasitism and identify novel serological diagnostic markers. The analysis identified 430 S. stercoralis proteins, with 187 (43%) being uncharacterized. Additionally, nine proteins with low homology to H. sapiens or other related pathogens and potential immunogenic properties were highlighted.
PARASITES & VECTORS
(2023)
Article
Multidisciplinary Sciences
Clement Bernard, Marie Locard-Paulet, Cyril Noel, Magalie Duchateau, Quentin Giai Gianetto, Bouziane Moumen, Thomas Rattei, Yann Hechard, Lars Juhl Jensen, Mariette Matondo, Ascel Samba-Louaka
Summary: This study provides detailed insights into the early stages of encystment of Acanthamoeba castellanii by integrating RNA-Seq, proteomics and phosphoproteomics data sets. The results reveal specific molecular details of processes such as cell proliferation shutdown, as well as rapid phospho-regulation of sites involved in cytoskeleton remodeling and translation regulation.
NATURE COMMUNICATIONS
(2022)
Correction
Biochemical Research Methods
Thibault Robin, Amos Bairoch, Markus Mueller, Frederique Lisacek, Lydie Lane
JOURNAL OF PROTEOME RESEARCH
(2019)
Article
Biochemical Research Methods
Paula Duek, Lydie Lane
JOURNAL OF PROTEOME RESEARCH
(2019)
Article
Biochemical Research Methods
Gilbert S. Omenn, Lydie Lane, Christopher M. Overall, Fernando J. Corrales, Jochen M. Schwenk, Young-Ki Paik, Jennifer E. Van Eyk, Siqi Liu, Stephen Pennington, Michael P. Snyder, Mark S. Baker, Eric W. Deutsch
JOURNAL OF PROTEOME RESEARCH
(2019)
Article
Biochemical Research Methods
Chengxin Zhang, Lydie Lane, Gilbert S. Omenn, Yang Zhang
JOURNAL OF PROTEOME RESEARCH
(2019)
Article
Biochemistry & Molecular Biology
Monique Zahn-Zabal, Pierre-Andre Michel, Alain Gateau, Frederic Nikitin, Mathieu Schaeffer, Estelle Audot, Pascale Gaudet, Paula D. Duek, Daniel Teixeira, Valentine Rech de Laval, Kasun Samarasinghe, Amos Bairoch, Lydie Lane
NUCLEIC ACIDS RESEARCH
(2020)
Editorial Material
Biochemical Research Methods
Monique Zahn-Zabal, Lydie Lane
EXPERT REVIEW OF PROTEOMICS
(2020)
Article
Multidisciplinary Sciences
Shan Zhang, Boris Reljic, Chao Liang, Baptiste Kerouanton, Joel Celio Francisco, Jih Hou Peh, Camille Mary, Narendra Suhas Jagannathan, Volodimir Olexiouk, Claire Tang, Gio Fidelito, Srikanth Nama, Ruey-Kuang Cheng, Caroline Lei Wee, Loo Chien Wang, Paula Duek Roggli, Prabha Sampath, Lydie Lane, Enrico Petretto, Radoslaw M. Sobota, Suresh Jesuthasan, Lisa Tucker-Kellogg, Bruno Reversade, Gerben Menschaert, Lei Sun, David A. Stroud, Lena Ho
NATURE COMMUNICATIONS
(2020)
Article
Biochemical Research Methods
Yves Vandenbrouck, Charles Pineau, Lydie Lane
JOURNAL OF PROTEOME RESEARCH
(2020)
Article
Biochemical Research Methods
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, Eric W. Deutsch
JOURNAL OF PROTEOME RESEARCH
(2020)
Article
Multidisciplinary Sciences
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 Uhlen, 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
(2020)
Article
Neurosciences
Laura Reiche, Peter Goettle, Lydie Lane, Paula Duek, Mina Park, Kasum Azim, Jana Schuette, Anastasia Manousi, Jessica Schira-Heinen, Patrick Kuery
Summary: The research revealed that the C21orf91 gene is crucial for accurate differentiation and myelination of oligodendroglial cells, and overexpression of C21orf91 leads to the coexpression of astroglial- and oligodendroglial markers, indicating an unbalanced glial cell population in the brains of individuals with Down syndrome.
FRONTIERS IN CELLULAR NEUROSCIENCE
(2021)
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)
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
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
Mathematical & Computational Biology
Paula Duek, Camille Mary, Monique Zahn-Zabal, Amos Bairoch, Lydie Lane
Summary: A workflow has been developed to generate hypotheses for the function of uncharacterized proteins, which has been applied to seven uncharacterized human proteins. The results of this study may contribute to filling gaps in the functional annotation of human proteins.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2021)