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The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition

Eric W. Deutsch, Attila Csordas, Zhi Sun, Andrew Jarnuczak, Yasset Perez-Riverol, Tobias Ternent, David S. Campbell, Manuel Bernal-Llinares, Shujiro Okuda, Shin Kawano, Robert L. Moritz, Jeremy J. Carver (+5 others)
2016 Nucleic Acids Research  
As demonstrated by data submission statistics, PX is supporting a change in culture of the proteomics field: public data sharing is now an accepted standard, supported by requirements for journal submissions  ...  The ProteomeXchange (PX) Consortium of proteomics resources (http://www.proteomexchange. org) was formally started in 2011 to standardize data submission and dissemination of mass spectrometry proteomics  ...  ACKNOWLEDGEMENTS The ProteomeXchange partners would like to thank all data submitters and collaborators for their contributions. The UK-Japan collaboration is funded by the BBSRC grant BB/N022440/1.  ... 
doi:10.1093/nar/gkw936 pmid:27924013 pmcid:PMC5210636 fatcat:nfs4hxhbozh45bmv4q75e5eqt4

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

2019 Nucleic Acids Research  
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  ...  Next, with current data submission statistics, we demonstrate that the proteomics field is now actively embracing public open data policies.  ...  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

Proteomics Standards Initiative: Fifteen Years of Progress and Future Work

Eric W. Deutsch, Sandra Orchard, Pierre-Alain Binz, Wout Bittremieux, Martin Eisenacher, Henning Hermjakob, Shin Kawano, Henry Lam, Gerhard Mayer, Gerben Menschaert, Yasset Perez-Riverol, Reza M. Salek (+5 others)
2017 Journal of Proteome Research  
One prominent example already mentioned is the ProteomeXchange Consortium 20 of proteomics data repositories, which is actively fostering a culture of open data deposition and sharing. 21 Crucial to  ...  All of the ProteomeXchange Consortium members participate actively in the PSI and rely on the products of the PSI to streamline the deposition and dissemination of data sets.  ... 
doi:10.1021/acs.jproteome.7b00370 pmid:28849660 pmcid:PMC5715286 fatcat:7oigf27kencedhbhmvtrbuv5a4

Defining the Akt1 interactome data and delineating alterations in its composition as a function of cell cycle progression

Shweta Duggal, Noor Jailkhani, Mukul Kumar Midha, Kanury V.S. Rao, Ajay Kumar
2017 Data in Brief  
Akt1 expressing HEK 293 cells were cultured in light, medium and heavy labeled SILAC media.  ...  The obtained Akt1 protein partners were observed to change as the cell cycle progressed from G0 to G1S and then to G2 phase. Additionally,  ...  Acknowledgements The study was supported by a Department of Biotechnology, Ministry of Science and Technology, Government of India grant to K.V.S.R.  ... 
doi:10.1016/j.dib.2017.02.018 pmid:28243621 pmcid:PMC5320063 fatcat:vnye5a4eifdobbxfxn7osaqls4

Dataset to delineate changes in association between Akt1 and its interacting partners as a function of active state of Akt1 protein

Nutan Gupta, Shweta Duggal, Noor Jailkhani, Samrat Chatterjee, Kanury V.S. Rao, Ajay Kumar
2017 Data in Brief  
Supplementary material Transparency data associated with this article can be found in the online version at http://dx.doi. org/10.1016/j.dib.2017.05.040.  ...  The study was supported by a Department of Biotechnology, Ministry of Science and Technology, Government of India grant to K.V.S.R. Transparency document.  ...  The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [4] partner repository with the dataset identifier PXD005976.  ... 
doi:10.1016/j.dib.2017.05.040 pmid:28603765 pmcid:PMC5454128 fatcat:sf7frwwnyncydnkwdzkt6y4bey

Unlocking Big Data for better health

Steven Munevar
2017 Nature Biotechnology  
ProteomeXchange In 2014 the ProteomeXchange consortium launched a public portal for exchanging proteomics data and information, highlighting a growing trend in the sharing of data generated in mass-spectrometry  ...  The rise of open proteomics In 2014 the ProteomeXchange consortium launched a public portal for exchanging proteomics data and information, highlighting a growing trend in the sharing of data generated  ... 
doi:10.1038/nbt.3918 pmid:28700551 fatcat:oqiurm5cgzec7lfenvjvlemxoy

Splice-Junction-Based Mapping of Alternative Isoforms in the Human Proteome

Edward Lau, Yu Han, Damon R. Williams, Cody T. Thomas, Rajani Shrestha, Joseph C. Wu, Maggie P.Y. Lam
2019 Cell Reports  
Using the custom databases to reanalyze ∼80 million mass spectra in public proteomics datasets, we identify more than 1,500 noncanonical protein isoforms across 12 human tissues, including ∼400 sequences  ...  The described approach may help elucidate functional consequences of alternative splicing and expand the scope of proteomics investigations in various systems.  ...  and R01 HL146690 to J.C.W.; and R01 GM117624, R01 HL141278, and The CU Consortium for Fibrosis Research and Translation Pilot Grant to M.P.Y.L.  ... 
doi:10.1016/j.celrep.2019.11.026 pmid:31825849 pmcid:PMC6961840 fatcat:niapkkyjofcxvm6zicijonehhe

A community proposal to integrate proteomics activities in ELIXIR

Juan Antonio Vizcaíno, Mathias Walzer, Rafael C. Jiménez, Wout Bittremieux, David Bouyssié, Christine Carapito, Fernando Corrales, Myriam Ferro, Albert J.R. Heck, Peter Horvatovich, Martin Hubalek, Lydie Lane (+14 others)
2017 F1000Research  
.: The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition. Nucleic Acids Res. 2017; 45(D1): D1100-D6.  ...  This white paper is the direct result of a strategy meeting on 'The Future of Proteomics in ELIXIR' that took place in March 2017 in Tübingen (Germany), and involved representatives of eleven ELIXIR nodes  ...  Velek (ELIXIR Hub) for his help in drafting Figure 2 . Supplementary material Supplementary File 1: Detailed minutes of the meeting "The future of proteomics in ELIXIR".  ... 
doi:10.12688/f1000research.11751.1 pmid:28713550 pmcid:PMC5499783 fatcat:whlty6rqcneedd2llpxmgsca7q

Proteomic analysis of extracellular vesicles from a Plasmodium falciparum Kenyan clinical isolate defines a core parasite secretome

Abdirahman Abdi, Lu Yu, David Goulding, Martin K. Rono, Philip Bejon, Jyoti Choudhary, Julian Rayner
2017 Wellcome Open Research  
The authors argue that EVs cannot be derived from the erythrocyte despite identifying components of the erythrocyte membrane in their proteome (e.g. band 3, top right paragraph on page 5).  ...  In combination with their conclusion that PfEVs are only comprised of exosomes, do the authors suggest that Maurer's clefts are multivesicular body like compartments?  ...  The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE 48 partner repository, with the dataset identifier PXD006925. .  ... 
doi:10.12688/wellcomeopenres.11910.2 pmid:28944300 pmcid:PMC5583745 fatcat:jgygerkl7nc2lke5lx5oq35tli

Quick 96FASP for high throughput quantitative proteome analysis

Yanbao Yu, Shiferaw Bekele, Rembert Pieper
2017 Journal of Proteomics  
We conclude that the q96FASP approach promises to be a promising cost-and time-effective method for shotgun proteomics and will be particularly useful in large scale biomarker discovery studies.  ...  We show that q96FASP allows the generation of protein digests derived from whole cell lysates and body fluids in a quality similar to that of the single FASP method.  ...  The PCR and Pall plates utilized in this study are generous gifts from Millipore and Pall Corporation, respectively.  ... 
doi:10.1016/j.jprot.2017.06.019 pmid:28669814 pmcid:PMC6029622 fatcat:ub4r3dixvbfttlxygm7pmp64xq

Quantitative proteomic characterization of lung-MSC and bone marrow-MSC using DIA-mass spectrometry

Sara Rolandsson Enes, Emma Åhrman, Anitha Palani, Oskar Hallgren, Leif Bjermer, Anders Malmström, Stefan Scheding, Johan Malmström, Gunilla Westergren-Thorsson
2017 Scientific Reports  
Recent advances in mass spectrometry (MS) based proteomics have made it possible to perform quantitative analysis of the MSC proteome using data-independent acquisition (DIA) MS, and improved bioinformatics  ...  Here, we present an in-depth mass spectrometry (MS) based strategy to investigate the proteomes of lung-MSC and bone marrow-MSC.  ...  This study was supported by the Swedish Foundation for Strategic Research, the Swedish Heart-Lung Foundation, the Alfred Österlund Foundation, the Royal Physiographical Society in Lund, and the Medical  ... 
doi:10.1038/s41598-017-09127-y pmid:28839187 pmcid:PMC5570998 fatcat:sgqpvnfmkjedjfqw7lf3rlhxmu

Quantitative Proteomics of Cerebrospinal Fluid in Paediatric Pneumococcal Meningitis

Guadalupe Gómez-Baena, Richard J. Bennett, Carmen Martínez-Rodríguez, Małgorzata Wnęk, Gavin Laing, Graeme Hickey, Lynn McLean, Robert J. Beynon, Enitan D. Carrol
2017 Scientific Reports  
Proteomics data are available via ProteomeXchange with identifier PXD004219.  ...  For a subset of proteins derived from the proteome analysis, we corroborated the proteomics data in a third cohort (hospital controls (n = 15), healthy controls (n = 5), cases (n = 20)) by automated quantitative  ...  G.L. was funded by the NIHR Biomedical Research Centre for Microbial Diseases. Instrumentation was in part supported by the University of Liverpool Technology Directorate.  ... 
doi:10.1038/s41598-017-07127-6 pmid:28765563 pmcid:PMC5539295 fatcat:xxvl2nd6mndebn2vkdgw5wf2zm

Improved growth rate in Clostridium thermocellum hydrogenase mutant via perturbed sulfur metabolism

Ranjita Biswas, Charlotte M. Wilson, Richard J. Giannone, Dawn M. Klingeman, Thomas Rydzak, Manesh B. Shah, Robert L. Hettich, Steven D. Brown, Adam M. Guss
2017 Biotechnology for Biofuels  
A similar pattern was seen with proteomics. Further physiological characterization demonstrated an increase in sulfide synthesis and elimination of cysteine consumption in C. thermocellum ΔhydG.  ...  Results: Addition of 5 mM acetate to the growth medium improved the growth rate in C. thermocellum ∆hydG, whereas wild type remained unaffected.  ...  Olson for his assistance with resequencing data analysis and helpful discussions.  ... 
doi:10.1186/s13068-016-0684-x pmid:28053665 pmcid:PMC5209896 fatcat:zplgcoev2rhgdek7rdrpf33c2u

Proteome and Secretome Analysis Reveals Differential Post-transcriptional Regulation of Toll-like Receptor Responses

Marijke Koppenol-Raab, Virginie Sjoelund, Nathan P. Manes, Rachel A. Gottschalk, Bhaskar Dutta, Zachary L. Benet, Iain D. C. Fraser, Aleksandra Nita-Lazar
2017 Molecular & Cellular Proteomics  
The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium via the PRIDE (46) partner repository with the data set identifier PXD004113.  ...  DATA AVAILABILITY The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (46) partner repository with the data set identifier PXD004113.  ... 
doi:10.1074/mcp.m116.064261 pmid:28235783 pmcid:PMC5393387 fatcat:hgh76unm7feexpiurcb6t7ijxe

Protein abundances can distinguish between naturally-occurring and laboratory strains of Yersinia pestis, the causative agent of plague

Eric D. Merkley, Landon H. Sego, Andy Lin, Owen P. Leiser, Brooke L. Deatherage Kaiser, Joshua N. Adkins, Paul S. Keim, David M. Wagner, Helen W. Kreuzer, Ramin M. Hakami
2017 PLoS ONE  
of how diverse genome changes lead to convergent phenotypes, difficulty in detecting certain types of mutations, or perhaps because some adaptive modifications are epigenetic.  ...  The methodology is able to discover signatures for laboratory facility and culture medium that are largely independent of the signature of laboratory adaptation.  ...  Acknowledgments The research is part of the Signature Discovery Initiative at Pacific Northwest National Labora  ... 
doi:10.1371/journal.pone.0183478 pmid:28854255 pmcid:PMC5576697 fatcat:uc4dllrfsjchrjxlwd5n7xfwlq
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