How to submit MS proteomics data to ProteomeXchange via the PRIDE database.
作者： Tobias Ternent , Attila Csordas , Da Qi , Guadalupe Gómez‐Baena , Robert J Beynon
关键词:
摘要: The ProteomeXchange (PX) consortium has been established to standardize and facilitate submission dissemination of MS-based proteomics data in the public domain. In consortium, PRIDE database at European Bioinformatics Institute, acts as initial point MS/MS sets. this manuscript, we explain step by process sets PX via PRIDE. We describe detail two available workflows: ‘complete’ ‘partial’ submissions, together with tools streamline process. Throughout will use one example set containing identification quantification data, which deposited PRIDE/ProteomeXchange accession number PXD000764 (http://proteomecentral.proteomexchange.org/dataset/PXD000764).
sci-hub.se 参考文章(24)
Ze-Qiang Ma, Surendra Dasari, Matthew C. Chambers, Michael D. Litton, Scott M. Sobecki, Lisa J. Zimmerman, Patrick J. Halvey, Birgit Schilling, Penelope M. Drake, Bradford W. Gibson, David L. Tabb, IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering. Journal of Proteome Research. ,vol. 8, pp. 3872- 3881 ,(2009) , 10.1021/PR900360J
Surendra Dasari, Matthew C Chambers, Robbert J Slebos, Lisa J Zimmerman, Amy-Joan L Ham, David L Tabb, None, TagRecon: high-throughput mutation identification through sequence tagging. Journal of Proteome Research. ,vol. 9, pp. 1716- 1726 ,(2010) , 10.1021/PR900850M
Juan A Vizcaíno, Eric W Deutsch, Rui Wang, Attila Csordas, Florian Reisinger, Daniel Ríos, José A Dianes, Zhi Sun, Terry Farrah, Nuno Bandeira, Pierre-Alain Binz, Ioannis Xenarios, Martin Eisenacher, Gerhard Mayer, Laurent Gatto, Alex Campos, Robert J Chalkley, Hans-Joachim Kraus, Juan Pablo Albar, Salvador Martinez-Bartolome, Rolf Apweiler, Gilbert S Omenn, Lennart Martens, Andrew R Jones, Henning Hermjakob, None, ProteomeXchange provides globally coordinated proteomics data submission and dissemination Nature Biotechnology. ,vol. 32, pp. 223- 226 ,(2014) , 10.1038/NBT.2839
Joseph M Foster, Sven Degroeve, Laurent Gatto, Matthieu Visser, Rui Wang, Johannes Griss, Rolf Apweiler, Lennart Martens, None, A posteriori quality control for the curation and reuse of public proteomics data. Proteomics. ,vol. 11, pp. 2182- 2194 ,(2011) , 10.1002/PMIC.201000602
Darren Kessner, Matt Chambers, Robert Burke, David Agus, Parag Mallick, ProteoWizard: open source software for rapid proteomics tools development Bioinformatics. ,vol. 24, pp. 2534- 2536 ,(2008) , 10.1093/BIOINFORMATICS/BTN323
Florent Gluck, Christine Hoogland, Paola Antinori, Xavier Robin, Frederic Nikitin, Anne Zufferey, Carla Pasquarello, Vanessa Fétaud, Loïc Dayon, Markus Müller, Frederique Lisacek, Laurent Geiser, Denis Hochstrasser, Jean-Charles Sanchez, Alexander Scherl, EasyProt--an easy-to-use graphical platform for proteomics data analysis. Journal of Proteomics. ,vol. 79, pp. 146- 160 ,(2013) , 10.1016/J.JPROT.2012.12.012
Jari Häkkinen, Gregory Vincic, Olle Månsson, Kristofer Wårell, Fredrik Levander, The proteios software environment: an extensible multiuser platform for management and analysis of proteomics data. Journal of Proteome Research. ,vol. 8, pp. 3037- 3043 ,(2009) , 10.1021/PR900189C
R. Cote, F. Reisinger, L. Martens, H. Barsnes, J. A. Vizcaino, H. Hermjakob, The Ontology Lookup Service: bigger and better Nucleic Acids Research. ,vol. 38, pp. 155- 160 ,(2010) , 10.1093/NAR/GKQ331
Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, Oliver Kohlbacher, OpenMS – An open-source software framework for mass spectrometry BMC Bioinformatics. ,vol. 9, pp. 163- 163 ,(2008) , 10.1186/1471-2105-9-163
David L. Tabb, Christopher G. Fernando, Matthew C. Chambers, MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. Journal of Proteome Research. ,vol. 6, pp. 654- 661 ,(2007) , 10.1021/PR0604054