The PRIDE database and related tools and resources in 2019: improving support for quantification data

Perez‐Riverol, Yasset; Csordás, Attila; Bai, Jinwen; Bernal-Llinares, Manuel; Hewapathirana, Suresh; Kundu, Deepti Jaiswal; Inuganti, Avinash; Griss, Johannes; Mayer, Gerhard; Eisenacher, Martin; Pérez, Enrique; Uszkoreit, Julian; Pfeuffer, Julianus; Sachsenberg, Timo; Yılmaz, Şule; Tiwary, Shivani; Cox, Juergen; Audain, Enrique; Walzer, Mathias; Jarnuczak, Andrew F.; Ternent, Tobias; Brāzma, Alvis; Vizcaíno, Juan Antonio

doi:10.1093/nar/gky1106

Cited by 6,502 publications

(5,279 citation statements)

References 40 publications

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“…The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [79] partner repository with the dataset identifier PXD013688 (http://www.ebi.ac.uk/pride/ archive/projects/PXD013688).…”

Section: Data Availabilitymentioning

confidence: 99%

Extracellular vesicles impose quiescence on residual hematopoietic stem cells in the leukemic niche

et al. 2019

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Progressive remodeling of the bone marrow microenvironment is recognized as an integral aspect of leukemogenesis. Expanding acute myeloid leukemia (AML) clones not only alter stroma composition, but also actively constrain hematopoiesis, representing a significant source of patient morbidity and mortality. Recent studies revealed the surprising resistance of long‐term hematopoietic stem cells (LT‐HSC) to elimination from the leukemic niche. Here, we examine the fate and function of residual LT‐HSC in the BM of murine xenografts with emphasis on the role of AML‐derived extracellular vesicles (EV). AML‐EV rapidly enter HSC, and their trafficking elicits protein synthesis suppression and LT‐HSC quiescence. Mechanistically, AML‐EV transfer a panel of miRNA, including miR‐1246, that target the mTOR subunit Raptor, causing ribosomal protein S6 hypo‐phosphorylation, which in turn impairs protein synthesis in LT‐HSC. While HSC functionally recover from quiescence upon transplantation to an AML‐naive environment, they maintain relative gains in repopulation capacity. These phenotypic changes are accompanied by DNA double‐strand breaks and evidence of a sustained DNA‐damage response. In sum, AML‐EV contribute to niche‐dependent, reversible quiescence and elicit persisting DNA damage in LT‐HSC.

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Section: Data Availabilitymentioning

confidence: 99%

Extracellular vesicles impose quiescence on residual hematopoietic stem cells in the leukemic niche

et al. 2019

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“…The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (Perez‐Riverol et al, ) with the data set identifier PXD014052. Raw intensity values, results from LIMMA, GO enrichment and Phobius analyses and protein annotations are given in Appendix (combining quantitative with annotation data).…”

Section: Data Availability Statementmentioning

confidence: 99%

Comparative proteomics of stenotopic caddisfly Crunoecia irrorata identifies acclimation strategies to warming

2019

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Species' ecological preferences are often deduced from habitat characteristics thought to represent more or less optimal conditions for physiological functioning. Evolution has led to stenotopic and eurytopic species, the former having decreased niche breadths and lower tolerances to environmental variability. Species inhabiting freshwater springs are often described as being stenotopic specialists, adapted to the stable thermal conditions found in these habitats. Whether due to past local adaptation these species have evolved or have lost intra‐generational adaptive mechanisms to cope with increasing thermal variability has, to our knowledge, never been investigated. By studying how the proteome of a stenotopic species changes as a result of increasing temperatures, we investigate if the absence or attenuation of molecular mechanisms is indicative of local adaptation to freshwater springs. An understanding of compensatory mechanisms is especially relevant as spring specialists will experience thermal conditions beyond their physiological limits due to climate change. In this study, the stenotopic species Crunoecia irrorata (Trichoptera: Lepidostomatidae, Curtis 1834) was acclimated to 10, 15 and 20°C for 168 hr. We constructed a homology‐based database and via liquid chromatography‐tandem mass spectrometry (LC‐MS/MS)‐based shotgun proteomics identified 1,358 proteins. Differentially abundant proteins and protein norms of reaction revealed candidate proteins and molecular mechanisms facilitating compensatory responses such as trehalose metabolism, tracheal system alteration and heat‐shock protein regulation. A species‐specific understanding of compensatory physiologies challenges the characterization of species as having narrow tolerances to environmental variability if that characterization is based on occurrences and habitat characteristics alone.

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“…The MS proteomics data (DDA and DIA raw files, phosphopeptide spectral library, quantification files) have been deposited with the ProteomeXchange Consortium via the PRIDE partner repository (Perez‐Riverol et al, ) with the data set identifier PXD014076 (http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD014076; https://www.ebi.ac.uk/pride/archive/projects/PXD014076).…”

Section: Data Availability Statementmentioning

confidence: 99%

Evidence for a role of protein phosphorylation in the maintenance of the cnidarian–algal symbiosis

2019

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The endosymbiotic relationship between cnidarians and photosynthetic dinoflagellate algae provides the foundation of coral reef ecosystems. This essential interaction is globally threatened by anthropogenic disturbance. As such, it is important to understand the molecular mechanisms underpinning the cnidarian–algal association. Here we investigated phosphorylation‐mediated protein signalling as a mechanism of regulation of the cnidarian–algal interaction, and we report on the generation of the first phosphoproteome for the coral model system Aiptasia. Mass spectrometry‐based phosphoproteomics using data‐independent acquisition allowed consistent quantification of over 3,000 phosphopeptides totalling more than 1,600 phosphoproteins across aposymbiotic (symbiont‐free) and symbiotic anemones. Comparison of the symbiotic states showed distinct phosphoproteomic profiles attributable to the differential phosphorylation of 539 proteins that cover a broad range of functions, from receptors to structural and signal transduction proteins. A subsequent pathway enrichment analysis identified the processes of “protein digestion and absorption,” “carbohydrate metabolism,” and “protein folding, sorting and degradation,” and highlighted differential phosphorylation of the “phospholipase D signalling pathway” and “protein processing in the endoplasmic reticulum.” Targeted phosphorylation of the phospholipase D signalling pathway suggests control of glutamate vesicle trafficking across symbiotic compartments, and phosphorylation of the endoplasmic reticulum machinery suggests recycling of symbiosome‐associated proteins. Our study shows for the first time that changes in the phosphorylation status of proteins between aposymbiotic and symbiotic Aiptasia anemones may play a role in the regulation of the cnidarian–algal symbiosis. This is the first phosphoproteomic study of a cnidarian–algal symbiotic association as well as the first application of quantification by data‐independent acquisition in the coral field.

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The PRIDE database and related tools and resources in 2019: improving support for quantification data

Cited by 6,502 publications

References 40 publications

Extracellular vesicles impose quiescence on residual hematopoietic stem cells in the leukemic niche

Extracellular vesicles impose quiescence on residual hematopoietic stem cells in the leukemic niche

Comparative proteomics of stenotopic caddisfly Crunoecia irrorata identifies acclimation strategies to warming

Evidence for a role of protein phosphorylation in the maintenance of the cnidarian–algal symbiosis

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