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The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics

2019 Nucleic Acids Research  
In parallel, an unprecedented increase of data re-use activities in the field, including 'big data' approaches, is enabling novel research and new data resources.  ...  The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) has standardized data submission and dissemination of mass spectrometry proteomics data worldwide since 2012  ...  ACKNOWLEDGEMENTS The ProteomeXchange partners would like to thank all data submitters and collaborators for their contributions. FUNDING  ... 
doi:10.1093/nar/gkz984 pmid:31686107 pmcid:PMC7145525 fatcat:nvick5so3bgcndkofvl2irwzgy

A Small Effort for Researchers, a Big Gain for Soil Metaproteomics

Marco Chiapello, Elisa Zampieri, Antonietta Mello
2020 Frontiers in Microbiology  
The main repository for proteomics data, since 2012, is the proteomeXchange (PX) consortium (Vizcaíno et al., 2014) .  ...  The aims of the consortium are the data submission standardization and the dissemination of the proteomics data.  ...  AM has critically read, corrected, and covered the costs to publish in open access.  ... 
doi:10.3389/fmicb.2020.00088 pmid:32117118 pmcid:PMC7010931 fatcat:bh3jtdywvbc3hfpl3r3nmsf4yu

Rumen metaproteomics: closer to linking rumen microbial function to animal productivity traits

Thea Os Andersen, Benoit J. Kunath, Live H. Hagen, Magnus Ø. Arntzen, Phillip B. Pope
2020 Methods  
While many of the major microbial members of the rumen microbiome are acknowledged, advances in modern culture-independent meta-omic techniques, such as metaproteomics, enable deep exploration into active  ...  We present and discuss current methods in sample handling, protein extraction and data analysis for rumen metaproteomics, and finally emphasize the potential of (meta)genome-integrated metaproteomics for  ...  ACKNOWLEDGEMENTS 634 We are grateful for support from The Research Council of Norway (Project no. 250479), the 635  ... 
doi:10.1016/j.ymeth.2020.07.011 pmid:32758682 fatcat:yimq4kqz6reutprbf4ampujfzu

KDClassifier: Urinary Proteomic Spectra Analysis Based on Machine Learning for Classification of Kidney Diseases [article]

Wanjun Zhao, Yong Zhang, Xinming Li, Yonghong Mao, Changwei Wu, Lijun Zhao, Fang Liu, Jingqiang Zhu, Jingqiu Cheng, Hao Yang, Guisen Li
2020 medRxiv   pre-print
We divided the mass spectrum data into a training dataset (80%) and a validation dataset (20%).  ...  urinary proteomics.  ...  The mass spectra data on the urinary proteomics were deposited into the ProteomeXchange Consortium through the PRIDE partner repository using the dataset identifier PXD018996. RESULTS .  ... 
doi:10.1101/2020.12.01.20242198 fatcat:zjmhxv7cfbfuvod5xm2krshp6u

Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line

Michal Levin, Marion Scheibe, Falk Butter
2020 BMC Genomics  
While satisfactory annotation has been made feasible for well-studied model organisms through great efforts of big consortia, for most systems this kind of data is either absent or not adequately precise  ...  Furthermore using spatial proteomics, we establish the subcellular localization of thousands of these proteins.  ...  We thank Mario Dejung from the Proteomics Core Facility at the Institute of Molecular Biology for setting up the web-server and the dedicated data viewer on the website http://butterlab.org/ bombyxviewer  ... 
doi:10.1186/s12864-020-07088-7 pmid:33023468 fatcat:wbimstkyeja6lfdi4pcwmx4r3u

Membrane Modulation of Super-Secreting "midiBacillus" Expressing the Major Staphylococcus aureus Antigen – A Mass-Spectrometry-Based Absolute Quantification Approach

Minia Antelo-Varela, Rocío Aguilar Suárez, Jürgen Bartel, Margarita Bernal-Cabas, Tim Stobernack, Thomas Sura, Jan Maarten van Dijl, Sandra Maaß, Dörte Becher
2020 Frontiers in Bioengineering and Biotechnology  
However, the secretion potential of this organism is not fully utilized yet, mostly due to a limited understanding of critical rearrangements in the membrane proteome upon high-level protein secretion.  ...  We quantitatively characterize the membrane proteome adaptation of midiBacillus during production stress on the level of molecules per cell for more than 400 membrane proteins, including determination  ...  The MS proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (Deutsch et al., 2017; Perez-Riverol et al., 2019) partner repository with the dataset identifier PXD015496.  ... 
doi:10.3389/fbioe.2020.00143 pmid:32185169 pmcid:PMC7059095 fatcat:wopn7th6qjgifm3zh5thrhq6m4

E-RIHS PP D5.3 Data Curation Policy

Holly Wright, Julian Richards, Olivia Foster, Jessica Hendy, Carrie Wright, Paul Northrup, Troy Rasbury, Ashley Coutu
2020 Zenodo  
It provides a policy framework to be implemented by E-RIHS, but the report is designed to be of use to all those with interests in data within the heritage science domain.  ...  The report follows the structure of the FAIR principles (Findable, Accessible, Interoperable and Re-usable) but interprets them in the context of heritage science.  ...  The ProteomeXchange Consortium: established to provide globally coordinated standard data submission and dissemination pipelines involving the main proteomics repositories, and to encourage open data  ... 
doi:10.5281/zenodo.3946201 fatcat:xond5mdv5nhxzmbjzuii3jywda

Comparative Proteomics Analysis Reveals Unique Early Signaling Response of Saccharomyces cerevisiae to Oxidants with Different Mechanism of Action

Prajita Pandey, Khadiza Zaman, Laszlo Prokai, Vladimir Shulaev
2020 International Journal of Molecular Sciences  
Our discovery driven comparative proteomics analysis revealed unique early signaling response of the yeast Saccharomyces cerevisiae on the proteome level to oxidants with a different mechanism of action  ...  The early signaling events involved in oxidant recognition and triggering of oxidant-specific defense mechanisms to counteract oxidative stress still remain largely elusive.  ...  We uploaded our data to the ProteomeXchange Consortium [61] by the PRIDE partner repository (assigned dataset identifier: PXD022685).  ... 
doi:10.3390/ijms22010167 pmid:33375274 fatcat:z2j537f2jnbvbm2bazgy6yvmji

Comprehensive draft of the mouse embryonic fibroblast lysosomal proteome by mass spectrometry based proteomics

Srigayatri Ponnaiyan, Fatema Akter, Jasjot Singh, Dominic Winter
2020 Scientific Data  
Using the combined data, we generated a benchmark lysosomal proteome data set for mouse embryonic fibroblasts as well as a spectral library for the analysis of lysosomes by data independent acquisition  ...  In the current study, we used samples enriched for lysosomes by paramagnetic nanoparticles and systematically evaluated experimental parameters for the analysis of the lysosomal proteome.  ...  J.S. performed DIA mass spectrometry analyses and edited the manuscript. D.W. conceptualized the study, analyzed the data, and wrote the manuscript. All authors reviewed and approved the manuscript.  ... 
doi:10.1038/s41597-020-0399-5 pmid:32103020 pmcid:PMC7044164 fatcat:l4pnw6fn7bhqldgs6gstgm6he4

Standardization and harmonization of distributed multi-center proteotype analysis supporting precision medicine studies

Yue Xuan, Nicholas W. Bateman, Sebastien Gallien, Sandra Goetze, Yue Zhou, Pedro Navarro, Mo Hu, Niyati Parikh, Brian L. Hood, Kelly A. Conrads, Christina Loosse, Reta Birhanu Kitata (+21 others)
2020 Nature Communications  
Here we conceived and standardized a proteotype data generation and analysis workflow enabling distributed data generation and evaluated the quantitative data generated across laboratories of the international  ...  Cancer Moonshot consortium.  ...  and data analysis in the Spectronaut; Christoph Henrich and Alexander Tiegel for discussion about the data visualization; David Sarracino for the discussion about the study design.  ... 
doi:10.1038/s41467-020-18904-9 pmid:33067419 fatcat:xo66u443fjbr3gag2d4md43fza

Standardization and Harmonization of Distributed Multi-National Proteotype Analysis supporting Precision Medicine Studies [article]

Yue Xuan, Nicholas W. Bateman, Sebastien Gallien, Sandra Goetze, Yue Zhou, Pedro Navarro, Mo Hu, Niyati Parikh, Brian L. Hood, Kelly A. Conrads, Christina Loosse, Reta Birhanu Kitata (+21 others)
2020 bioRxiv   pre-print
Here we conceived and standardized a proteotype data generation and analysis workflow enabling distributed data generation and evaluated the quantitative data generated across laboratories of the international  ...  Cancer Moonshot consortium.  ...  and data analysis in the Spectronaut; Christoph Henrich and Alexander Tiegel for discussion about the data visualization; David Sarracino for the discussion about the study design.  ... 
doi:10.1101/2020.03.12.988089 fatcat:n772njjpindmth6tnx7xghlbj4

KDClassifier: A urinary proteomic spectra analysis tool based on machine learning for the classification of kidney diseases

Wanjun Zhao, Department of Thyroid Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
2021 Aging Pathobiology and Therapeutics  
The training data set (80%) was used to create a diagnostic model using XGBoost, random forest (RF), a support vector machine (SVM), and artificial neural networks (ANNs).  ...  We aimed to establish a novel diagnostic model for kidney diseases by combining artificial intelligence with complete mass spectrum information from urinary proteomics.  ...  The mass spectrometric data from the urinary proteomics were deposited in the ProteomeXchange Consortium through the PRIDE partner repository with the dataset identifier PXD018996.  ... 
doi:10.31491/apt.2021.09.064 fatcat:r3ycilqyzbg6rfa7a77cozanye

The bovine cumulus proteome is influenced by maturation condition and maturational competence of the oocyte

J. Walter, C. Monthoux, C. Fortes, J. Grossmann, B. Roschitzki, T. Meili, B. Riond, R. Hofmann-Lehmann, H. Naegeli, U. Bleul
2020 Scientific Reports  
Therefore, this study analysed the cumulus proteome of individual cumulus-oocyte complexes (COCs) with and without maturational competence, matured under in vivo or in vitro conditions (n = 5 per group  ...  The detected cumulus proteome included 2226 quantifiable proteins and was highly influenced by the maturation condition (479 differentially expressed proteins) as well as maturational competence of the  ...  Acknowledgements The laboratory work was partly (ELISA) performed using the logistics of the Center for Clinical Studies at the Vetsuisse Faculty of the University of Zurich.  ... 
doi:10.1038/s41598-020-66822-z pmid:32555221 fatcat:3pzxjnb2zbaz7ln3rla2inr4yy

Identification of proteins from the secretory/excretory products (SEPs) of the branchiuran ectoparasite Argulus foliaceus (Linnaeus, 1758) reveals unique secreted proteins amongst haematophagous ecdysozoa

Aisha AmbuAli, Sean J. Monaghan, Kevin McLean, Neil F. Inglis, Michaël Bekaert, Stefanie Wehner, James E. Bron
2020 Parasites & Vectors  
The work described in the present study is the first undertaken with the objective of identifying and partially characterising the components secreted from these glands using a proteomic approach.  ...  Proteins within the SEPs were identified and characterised using LC-ESI-MS/MS analysis. Data are available via ProteomeXchange with identifier PXD016226.  ...  Acknowledgments The authors would like to acknowledge the contributions of Mr Jimmy Poole on Isle of Bute for his enormous assistance in providing Argulus samples throughout the duration of this study.  ... 
doi:10.1186/s13071-020-3964-z pmid:32070416 fatcat:kubqd3cmpzburiz7rplnp7zhni

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 (+34 others)
2020 Nature Communications  
The Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate  ...  This knowledge is essential for discerning molecular processes in health and disease, as we demonstrate by highlighting potential roles the human proteome plays in our understanding, diagnosis and treatment  ...  A full alphabetical listing of the Human Proteome Project members appears in the Supplementary Information.  ... 
doi:10.1038/s41467-020-19045-9 pmid:33067450 fatcat:eqth2b7nhfgsfmon7vdopgvlxq
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