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Deutsch, Eric W.; Perez-Riverol, Yasset; Carver, Jeremy; Kawano, Shin; Mendoza, Luis; Van Den Bossche, Tim; Gabriels, Ralf; Binz, Pierre-Alain; Pullman, Benjamin; Sun, Zhi; et al (, Nature Methods)
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Dai, Chengxin; Füllgrabe, Anja; Pfeuffer, Julianus; Solovyeva, Elizaveta M.; Deng, Jingwen; Moreno, Pablo; Kamatchinathan, Selvakumar; Kundu, Deepti Jaiswal; George, Nancy; Fexova, Silvie; et al (, Nature Communications)Abstract The amount of public proteomics data is rapidly increasing but there is no standardized format to describe the sample metadata and their relationship with the dataset files in a way that fully supports their understanding or reanalysis. Here we propose to develop the transcriptomics data format MAGE-TAB into a standard representation for proteomics sample metadata. We implement MAGE-TAB-Proteomics in a crowdsourcing project to manually curate over 200 public datasets. We also describe tools and libraries to validate and submit sample metadata-related information to the PRIDE repository. We expect that these developments will improve the reproducibility and facilitate the reanalysis and integration of public proteomics datasets.more » « less
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Ramsbottom, Kerry A.; Prakash, Ananth; Riverol, Yasset Perez; Camacho, Oscar Martin; Martin, Maria-Jesus; Vizcaíno, Juan Antonio; Deutsch, Eric W.; Jones, Andrew R. (, Journal of Proteome Research)
