The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

Perez‐Riverol, Yasset; Bai, Jinwen; Bandla, Chakradhar; García-Seisdedos, David; Hewapathirana, Suresh; Kamatchinathan, Selvakumar; Kundu, Deepti Jaiswal; Prakash, Ananth; Frericks-Zipper, Anika; Eisenacher, Martin; Walzer, Mathias; Wang, Shengbo; Brāzma, Alvis; Vizcaíno, Juan Antonio

doi:10.1093/nar/gkab1038

Cited by 4,413 publications

(3,099 citation statements)

References 59 publications

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“…Elsewhere, the GproteinDb ( 37 ) curates a wealth of information, especially information on the selectivity of their coupling to GPCRs, for a family of great importance to therapeutic design. Among databases reporting updates is PRIDE ( 38 ) where around 500 proteomics datasets are processed each month. After processing by improved data pipelines, the results are increasingly disseminated to other key databases such as UniProt ( 33 ), Ensembl ( 39 ) and Expression Atlas ( 40 ).…”

Section: New and Updated Databasesmentioning

confidence: 99%

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

Rigden

Fernández

2021

Nucleic Acids Research

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The 2022 Nucleic Acids Research Database Issue contains 185 papers, including 87 papers reporting on new databases and 85 updates from resources previously published in the Issue. Thirteen additional manuscripts provide updates on databases most recently published elsewhere. Seven new databases focus specifically on COVID-19 and SARS-CoV-2, including SCoV2-MD, the first of the Issue's Breakthrough Articles. Major nucleic acid databases reporting updates include MODOMICS, JASPAR and miRTarBase. The AlphaFold Protein Structure Database, described in the second Breakthrough Article, is the stand-out in the protein section, where the Human Proteoform Atlas and GproteinDb are other notable new arrivals. Updates from DisProt, FuzDB and ELM comprehensively cover disordered proteins. Under the metabolism and signalling section Reactome, ConsensusPathDB, HMDB and CAZy are major returning resources. In microbial and viral genomes taxonomy and systematics are well covered by LPSN, TYGS and GTDB. Genomics resources include Ensembl, Ensembl Genomes and UCSC Genome Browser. Major returning pharmacology resource names include the IUPHAR/BPS guide and the Therapeutic Target Database. New plant databases include PlantGSAD for gene lists and qPTMplants for post-translational modifications. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). Our latest update to the NAR online Molecular Biology Database Collection brings the total number of entries to 1645. Following last year's major cleanup, we have updated 317 entries, listing 89 new resources and trimming 80 discontinued URLs. The current release is available at http://www.oxfordjournals.org/nar/database/c/.

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Section: New and Updated Databasesmentioning

confidence: 99%

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

Rigden

Fernández

2021

Nucleic Acids Research

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“…For protein identification (FDR < 1%) and label free quantification, the MaxQuant software platform 68 was used in combination with the Human subset of the UniProt database. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD031539 69 .…”

Section: Methodsmentioning

confidence: 99%

Valosin-containing protein-regulated endoplasmic reticulum stress causes NOD2-dependent inflammatory responses

Ghalandary

Fröhlich³

et al. 2022

Sci Rep

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NOD2 polymorphisms may affect sensing of the bacterial muramyl dipeptide (MDP) and trigger perturbed inflammatory responses. Genetic screening of a patient with immunodeficiency and enteropathy revealed a rare homozygous missense mutation in the first CARD domain of NOD2 (ENST00000300589; c.160G > A, p.E54K). Biochemical assays confirmed impaired NOD2-dependent signaling and proinflammatory cytokine production in patient’s cells and heterologous cellular models with overexpression of the NOD2 mutant. Immunoprecipitation-coupled mass spectrometry unveiled the ATPase valosin-containing protein (VCP) as novel interaction partner of wildtype NOD2, while the binding to the NOD2 variant p.E54K was abrogated. Knockdown of VCP in coloncarcinoma cells led to impaired NF-κB activity and IL8 expression upon MDP stimulation. In contrast, tunicamycin-induced ER stress resulted in increased IL8, CXCL1, and CXCL2 production in cells with knockdown of VCP, while enhanced expression of these proinflammatory molecules was abolished upon knockout of NOD2. Taken together, these data suggest that VCP-mediated inflammatory responses upon ER stress are NOD2-dependent.

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“…The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al, 2022) partner repository with the dataset identifier PXD031159 and 10.6019/PXD031159.…”

Section: Data Availability Statementmentioning

confidence: 99%

Uncover New Reactivity of Genetically Encoded Alkyl Bromide Non-Canonical Amino Acids

et al. 2022

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Genetically encoded non-canonical amino acids (ncAAs) with electrophilic moieties are excellent tools to investigate protein-protein interactions (PPIs) both in vitro and in vivo. These ncAAs, including a series of alkyl bromide-based ncAAs, mainly target cysteine residues to form protein-protein cross-links. Although some reactivities towards lysine and tyrosine residues have been reported, a comprehensive understanding of their reactivity towards a broad range of nucleophilic amino acids is lacking. Here we used a recently developed OpenUaa search engine to perform an in-depth analysis of mass spec data generated for Thioredoxin and its direct binding proteins cross-linked with an alkyl bromide-based ncAA, BprY. The analysis showed that, besides cysteine residues, BprY also targeted a broad range of nucleophilic amino acids. We validated this broad reactivity of BprY with Affibody/Z protein complex. We then successfully applied BprY to map a binding interface between SUMO2 and SUMO-interacting motifs (SIMs). BprY was further applied to probe SUMO2 interaction partners. We identified 264 SUMO2 binders, including several validated SUMO2 binders and many new binders. Our data demonstrated that BprY can be effectively used to probe protein-protein interaction interfaces even without cysteine residues, which will greatly expand the power of BprY in studying PPIs.

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The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

Cited by 4,413 publications

References 59 publications

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

Valosin-containing protein-regulated endoplasmic reticulum stress causes NOD2-dependent inflammatory responses

Uncover New Reactivity of Genetically Encoded Alkyl Bromide Non-Canonical Amino Acids

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