The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013 von Vizcaíno, Juan Antonio, Côté, Richard G, Csordas, Attila, Dianes, José A, Fabregat, Antonio, Foster, Joseph M, Griss, Johannes, Alpi, Emanuele, Birim, Melih, Contell, Javier, O'Kelly, Gavin, Schoenegger, Andreas, Ovelleiro, David, Pérez-Riverol, Yasset, Reisinger, Florian, Ríos, Daniel, Wang, Rui, Hermjakob, Henning

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guide to the Proteomics Identifications Database proteomics data repository von Vizcaíno, Juan Antonio, Côté, Richard, Reisinger, Florian, Foster, Joseph M, Mueller, Michael, Rameseder, Jonathan, Hermjakob, Henning, Martens, Lennart

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PRIDE Cluster: building a consensus of proteomics data von Griss, Johannes, Foster, Joseph M, Hermjakob, Henning, Vizcaíno, Juan Antonio

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Genomic complexity of urothelial bladder cancer revealed in urinary cfDNA von Togneri, Fiona S, Ward, Douglas G, Foster, Joseph M, Devall, Adam J, Wojtowicz, Paula, Alyas, Sofia, Vasques, Fabiana Ramos, Oumie, Assa, James, Nicholas D, Cheng, K K, Zeegers, Maurice P, Deshmukh, Nayneeta, O'Sullivan, Brendan, Taniere, Philippe, Spink, Karen G, McMullan, Dominic J, Griffiths, Mike, Bryan, Richard T

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LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics von Foster, Joseph M, Moreno, Pablo, Fabregat, Antonio, Hermjakob, Henning, Steinbeck, Christoph, Apweiler, Rolf, Wakelam, Michael J O, Vizcaíno, Juan Antonio

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PRIDE Inspector: a tool to visualize and validate MS proteomics data von Wang, Rui, Fabregat, Antonio, Ríos, Daniel, Ovelleiro, David, Foster, Joseph M, Côté, Richard G, Griss, Johannes, Csordas, Attila, Perez-Riverol, Yasset, Reisinger, Florian, Hermjakob, Henning, Martens, Lennart, Vizcaíno, Juan Antonio

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Chromatographic retention time prediction for posttranslationally modified peptides von Moruz, Luminita, Staes, An, Foster, Joseph M., Hatzou, Maria, Timmerman, Evy, Martens, Lennart, Käll, Lukas

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Proteomics data repositories: Providing a safe haven for your data and acting as a springboard for further research von Vizcaíno, Juan Antonio, Foster, Joseph M., Martens, Lennart

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HER2 overexpression and amplification as a potential therapeutic target in colorectal cancer: analysis of 3256 patients enrolled in the QUASAR, FOCUS and PICCOLO colorectal cancer... von Richman, Susan D, Southward, Katie, Chambers, Philip, Cross, Debra, Barrett, Jennifer, Hemmings, Gemma, Taylor, Morag, Wood, Henry, Hutchins, Gordon, Foster, Joseph M, Oumie, Assa, Spink, Karen G, Brown, Sarah R, Jones, Marc, Kerr, David, Handley, Kelly, Gray, Richard, Seymour, Matthew, Quirke, Philip

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Proteomics Identifications database: 2010 update von Vizcaíno, Juan Antonio, Côté, Richard, Reisinger, Florian, Barsnes, Harald, Foster, Joseph M, Rameseder, Jonathan, Hermjakob, Henning, Martens, Lennart

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From Peptidome to PRIDE: Public proteomics data migration at a large scale von Csordas, Attila, Wang, Rui, Ríos, Daniel, Reisinger, Florian, Foster, Joseph M., Slotta, Douglas J., Vizcaíno, Juan Antonio, Hermjakob, Henning

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Cross-laboratory validation of the OncoScan® FFPE Assay, a multiplex tool for whole genome tumour profiling von Foster, Joseph M, Oumie, Assa, Togneri, Fiona S, Vasques, Fabiana Ramos, Hau, Debra, Taylor, Morag, Tinkler-Hundal, Emma, Southward, Katie, Medlow, Paul, McGreeghan-Crosby, Keith, Halfpenny, Iris, McMullan, Dominic J, Quirke, Phil, Keating, Katherine E, Griffiths, Mike, Spink, Karen G, Brew, Fiona

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A posteriori quality control for the curation and reuse of public proteomics data von Foster, Joseph M., Degroeve, Sven, Gatto, Laurent, Visser, Matthieu, Wang, Rui, Griss, Johannes, Apweiler, Rolf, Martens, Lennart

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Comparing mutation calls in fixed tumour samples between the affymetrix OncoScan® array and PCR based next-generation sequencing von Wood, Henry M, Foster, Joseph M, Taylor, Morag, Tinkler-Hundal, Emma, Togneri, Fiona S, Wojtowicz, Paula, Oumie, Assa, Spink, Karen G, Brew, Fiona, Quirke, Philip

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PRIDE: quality control in a proteomics data repository von Csordas, Attila, Ovelleiro, David, Wang, Rui, Foster, Joseph M, Ríos, Daniel, Vizcaíno, Juan Antonio, Hermjakob, Henning

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From Peptidome to PRIDE : P ublic proteomics data migration at a large scale von Csordas, Attila, Wang, Rui, Ríos, Daniel, Reisinger, Florian, Foster, Joseph M., Slotta, Douglas J., Vizcaíno, Juan Antonio, Hermjakob, Henning

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Bioinformatics Challenges in the Proteomic Analysis of Human Plasma von Foster, Joseph M., Martens, Lennart

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Abstract 626: Cross-site reproducibility and orthogonal validation of copy number and somatic mutation calls of OncoScan® FFPE Assay Kit in solid tumors von Foster, Joseph M., Oumie, Assa, Togneri, Fiona S., Taylor, Morag, Alyas, Sofia, Wojtowicz, Paula, Wood, Henry, Tinkler-Hundal, Emma, Southward, Katie, McMullan, Dominic, Quirke, Phil, Keating, Katherine E., Griffiths, Mike, Spink, Karen G., Brew, Fiona, Fung, Eric, Schmidt, Jeanette

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Chromatographic retention time prediction for posttranslationally modified peptides: TARGETED PROTEOMICS von MORUZ, Luminita, STAES, An, FOSTER, Joseph M, HATZOU, Maria, TIMMERMAN, Evy, MARTENS, Lennart, KÄLL, Lukas

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Proteomics data repositories: Providing a safe haven for your data and acting as a springboard for further research: Model Organism Proteomics von VIZCAINO, Juan Antonio, FOSTER, Joseph M, MARTENS, Lennart

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