2019
DOI: 10.1093/nar/gkz984
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Abstract: 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. In this paper, we describe the main developments since the previous update manuscript was published in Nucleic Acids Research in 2017. Since then, in addition to the four PX existing members at the time (PRIDE, PeptideAtlas including the PASSEL resource, MassIVE and jPOST), two new resources have joined PX: iPr… Show more

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Cited by 543 publications
(499 citation statements)
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“…The adaptive Benjamini-Hochberg procedure was applied to adjust the p-values and FDR values under 1per cent were achieved. Complete dataset has been deposited to the ProteomeXchange Consortium via the PRIDE partner repos-itory5 with the dataset identifier PXD020180 (Deutsch et al, 2020).…”
Section: R a F Tmentioning
confidence: 99%
“…The adaptive Benjamini-Hochberg procedure was applied to adjust the p-values and FDR values under 1per cent were achieved. Complete dataset has been deposited to the ProteomeXchange Consortium via the PRIDE partner repos-itory5 with the dataset identifier PXD020180 (Deutsch et al, 2020).…”
Section: R a F Tmentioning
confidence: 99%
“…The RAW files were processed via MaxQuant [ 98 ] using a FASTA file containing protein sequences of S. lycopersicum (via Uniprot [ 99 ]), ToMoV DNA A (NC_001939.1), and DNA B (NC_001938.1). The raw data have been submitted to the ProteomeXchange ( , identifier PXD019197) [ 100 ]. With few exceptions, the default MaxQuant spectral search parameters were left, and they included the variable oxidation of methionine and N-termini as well as a fixed carbamidomethylation with a maximum number of 5 modifications per peptide.…”
Section: Methodsmentioning
confidence: 99%
“…The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (55,56) Data were exported to Microsoft Excel and unannotated effector proteins manually annotated. Data were imported into the R framework (https://www.r-project.org) integrated with R studio (https://rstudio.com/products/rstudio/) for generation for comparison with C. burnetii protein enrichment alongside purified mitochondria and generation of graphics.…”
Section: Data Availabilitymentioning
confidence: 99%