The PRIDE database and related tools and resources in 2019: improving support for quantification data.
Yasset Perez-Riverol,Attila Csordas,Jingwen Bai,Manuel Bernal-Llinares,Suresh Hewapathirana,Deepti J. Kundu,Avinash Inuganti,Johannes Griss,Johannes Griss,Gerhard Mayer,Martin Eisenacher,Enrique Perez,Julian Uszkoreit,Julianus Pfeuffer,Timo Sachsenberg,Şule Yılmaz,Shivani Tiwary,Juergen Cox,Enrique Audain,Mathias Walzer,Andrew F. Jarnuczak,Tobias Ternent,Alvis Brazma,Juan Antonio Vizcaíno +23 more
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TLDR
Key statistics on the current data contents and volume of downloads are outlined, and how PRIDE data are starting to be disseminated to added-value resources including Ensembl, UniProt and Expression Atlas are outlined.Citations
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The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences.
Yasset Perez-Riverol,Jingwen Bai,Chakradhar Bandla,David García-Seisdedos,Suresh Hewapathirana,Selvakumar Kamatchinathan,Deepti J. Kundu,Ananth Prakash,Anika Frericks-Zipper,Martin Eisenacher,Mathias Walzer,Shengbo Wang,Alvis Brazma,Juan Antonio Vizcaíno +13 more
TL;DR: The PRIDE database as discussed by the authors is the world's largest data repository of mass spectrometry-based proteomics data and is one of the founding members of the global ProteomeXchange (PX) consortium.
Journal ArticleDOI
Metabolic regulation of gene expression by histone lactylation
Di Zhang,Zhanyun Tang,He Huang,He Huang,Guolin Zhou,Chang Cui,Yejing Weng,Wenchao Liu,Sunjoo Kim,Sangkyu Lee,Mathew Perez-Neut,Jun Ding,Daniel M. Czyż,Rong Hu,Zhen Ye,Maomao He,Y. George Zheng,Howard A. Shuman,Lunzhi Dai,Lunzhi Dai,Bing Ren,Robert G. Roeder,Lev Becker,Yingming Zhao +23 more
TL;DR: The results suggest that an endogenous ‘lactate clock’ in bacterially challenged M1 macrophages turns on gene expression to promote homeostasis, and represents an opportunity to improve the understanding of the functions of lactate and its role in diverse pathophysiological conditions, including infection and cancer.
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Proteomics of SARS-CoV-2-infected host cells reveals therapy targets.
Denisa Bojkova,Kevin Klann,Benjamin Koch,Marek Widera,David Krause,Sandra Ciesek,Jindrich Cinatl,Christian Münch +7 more
TL;DR: The cellular infection profile of SARS-CoV-2 is revealed and the identification of drugs that inhibit viral replication is enabled, enabling the development of therapies for the treatment of COVID-19.
Journal ArticleDOI
The Global Phosphorylation Landscape of SARS-CoV-2 Infection.
Mehdi Bouhaddou,Danish Memon,Bjoern Meyer,Kris M. White,Veronica V. Rezelj,Miguel Correa Marrero,Benjamin J. Polacco,James E. Melnyk,Svenja Ulferts,Robyn M. Kaake,Jyoti Batra,Alicia L. Richards,Erica Stevenson,David E. Gordon,Ajda Rojc,Kirsten Obernier,Jacqueline M. Fabius,Margaret Soucheray,Lisa Miorin,Elena Moreno,Cassandra Koh,Quang Dinh Tran,Alexandra Hardy,Rémy Robinot,Thomas Vallet,Benjamin E. Nilsson-Payant,Claudia Hernandez-Armenta,Alistair Dunham,Sebastian Weigang,Julian Knerr,Maya Modak,Diego Quintero,Yuan Zhou,Aurelien Dugourd,Alberto Valdeolivas,Trupti Patil,Qiongyu Li,Ruth Hüttenhain,Merve Cakir,Monita Muralidharan,Minkyu Kim,Gwendolyn M. Jang,Beril Tutuncuoglu,Joseph Hiatt,Jeffrey Z. Guo,Jiewei Xu,Sophia Bouhaddou,Christopher J.P. Mathy,Anna Gaulton,Emma J. Manners,Eloy Felix,Ying Shi,Marisa Goff,Jean K. Lim,Timothy McBride,Michael C. O’Neal,Yiming Cai,Jason C.J. Chang,David J. Broadhurst,Saker Klippsten,Emmie de Wit,Andrew R. Leach,Tanja Kortemme,Brian K. Shoichet,Melanie Ott,Julio Saez-Rodriguez,Benjamin R. tenOever,R. Dyche Mullins,Elizabeth R. Fischer,Georg Kochs,Robert Grosse,Adolfo García-Sastre,Marco Vignuzzi,Jeffery R. Johnson,Kevan M. Shokat,Danielle L. Swaney,Pedro Beltrao,Nevan J. Krogan +77 more
TL;DR: A quantitative mass spectrometry-based phosphoproteomics survey of SARS-CoV-2 infection in Vero E6 cells reveals dramatic rewiring of phosphorylation on host and viral proteins, revealing potential COVID-19 therapies.
Journal ArticleDOI
DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput.
Vadim Demichev,Vadim Demichev,Christoph B. Messner,Spyros I. Vernardis,Kathryn S. Lilley,Markus Ralser,Markus Ralser +6 more
TL;DR: DIA-NN improves the identification and quantification performance in conventional DIA proteomic applications, and is particularly beneficial for high-throughput applications, as it is fast and enables deep and confident proteome coverage when used in combination with fast chromatographic methods.
References
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Journal ArticleDOI
Probability-based protein identification by searching sequence databases using mass spectrometry data.
TL;DR: A new computer program, Mascot, is presented, which integrates all three types of search for protein identification by searching a sequence database using mass spectrometry data, and the scoring algorithm is probability based.
Journal ArticleDOI
UniProt: the Universal Protein knowledgebase
Rolf Apweiler,Amos Marc Bairoch,Cathy H. Wu,Winona C. Barker,Brigitte Boeckmann,Serenella Ferro,Elisabeth Gasteiger,Hongzhan Huang,Rodrigo Lopez,Michele Magrane,Maria Jesus Martin,Darren A. Natale,Claire O'Donovan,Nicole Redaschi,Lai-Su L. Yeh +14 more
TL;DR: The Swiss-Prot, TrEMBL and PIR protein database activities have united to form the Universal Protein Knowledgebase (UniProt), which is to provide a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and query interfaces.
Journal ArticleDOI
2016 update of the PRIDE database and its related tools
Juan Antonio Vizcaíno,Attila Csordas,Noemi del-Toro,José A. Dianes,Johannes Griss,Ilias Lavidas,Gerhard Mayer,Yasset Perez-Riverol,Florian Reisinger,Tobias Ternent,Qing Wei Xu,Rui Wang,Henning Hermjakob +12 more
TL;DR: The developments in PRIDE resources and related tools are summarized and a brief update on the resources under development 'PRIDE Cluster' and 'PRide Proteomes', which provide a complementary view and quality-scored information of the peptide and protein identification data available inPRIDE Archive are given.
Journal ArticleDOI
The MaxQuant computational platform for mass spectrometry-based shotgun proteomics.
TL;DR: An updated protocol covering the most important basic computational workflows for mass-spectrometry-based proteomics data analysis, including those designed for quantitative label-free proteomics, MS1-level labeling and isobaric labeling techniques is presented.
Journal ArticleDOI
The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition
Eric W. Deutsch,Attila Csordas,Zhi Sun,Andrew F. Jarnuczak,Yasset Perez-Riverol,Tobias Ternent,David S. Campbell,Manuel Bernal-Llinares,Shujiro Okuda,Shin Kawano,Robert L. Moritz,Jeremy Carver,Mingxun Wang,Mingxun Wang,Yasushi Ishihama,Nuno Bandeira,Nuno Bandeira,Henning Hermjakob,Henning Hermjakob,Juan Antonio Vizcaíno +19 more
TL;DR: The ProteomeXchange Consortium of proteomics resources was formally started in 2011 to standardize data submission and dissemination of mass spectrometry proteomics data worldwide and is supporting a change in culture of the proteomics field.
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MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.
Jiirgen Cox,Matthias Mann +1 more