{"data":[{"id":"10.25345/c5z60cg60","type":"dois","attributes":{"doi":"10.25345/c5z60cg60","identifiers":[],"creators":[{"name":"Brasier, Allan R.","nameType":"Personal","givenName":"Allan R.","familyName":"Brasier","affiliation":["University of Wisconsin-Madison"],"nameIdentifiers":[]}],"titles":[{"lang":"en-US","title":"MassIVE MSV000102037 - Epigenetic role for the interferon-stimulated RNA-binding protein IFIT1 in interferon regulatory factor 1-driven anti-viral gene expression"},{"lang":"en-US","title":"Immunoprecipitation mass spectrometry (IP-MS) bottom-up proteomics data collected from respiratory syncytial virus (RSV)-infected A549 cells including FLAG-tagged IRF1-expressing and empty vector control transductants. Collected on timsTOF Pro coupled to NanoElute LC system.","titleType":"Subtitle"}],"publisher":"MassIVE","container":{},"publicationYear":2026,"subjects":[],"contributors":[],"dates":[{"date":"2026","dateType":"Issued"}],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Mass Spectrometry","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[],"descriptions":[],"geoLocations":[],"fundingReferences":[],"url":"https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?accession=MSV000102037","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2026-06-04T01:19:08Z","registered":"2026-06-04T01:19:09Z","published":null,"updated":"2026-06-04T01:19:09Z"},"relationships":{"client":{"data":{"id":"cdl.ucsd","type":"clients"}}}},{"id":"10.25345/c52z13406","type":"dois","attributes":{"doi":"10.25345/c52z13406","identifiers":[],"creators":[{"name":"Johnson, Michael D L","nameType":"Personal","givenName":"Michael D L","familyName":"Johnson","affiliation":["The University of Arizona"],"nameIdentifiers":[]}],"titles":[{"lang":"en-US","title":"MassIVE MSV000102036 - Iron and its import systems enhance copper accumulation in Streptococcus pneumoniae"},{"lang":"en-US","title":"Metal ions strongly influence bacterial metabolism, where fluctuations in metal availability can shape enzyme function and cellular fitness. In Streptococcus pneumoniae (pneumococcus), iron and copper play important yet contrasting biochemical roles. Iron is essential for growth, serving as a cofactor for enzymes involved in DNA synthesis and energy metabolism. In contrast, copper is toxic, as excess intracellular copper promotes mismetallation and induces oxidative stress. While the pneumococcus has dedicated systems for exporting copper, how copper enters cells remains unclear. Here, we show that iron enhances copper accumulation in the pneumococcus, an effect not observed with other trace metals such as zinc or manganese. Similar results were observed in a capsule-deficient strain. Metal-specific interactions were consistent with copper accessing the cell through iron uptake pathways. In support of this interpretation, the deletion of selected iron transport proteins significantly reduces copper association. Further, RNA-seq analysis revealed upregulation of the copper export system, suggesting that copper triggers the detoxification pathways. Biochemically, we demonstrate that iron substrate-binding proteins can interact with both iron and copper, supporting the idea of mismetallation. Together, these findings highlight how overlapping in metal-binding chemistry can shape metal homeostasis and reveal how essential metal uptake pathways facilitate toxic metal accumulation","titleType":"Subtitle"}],"publisher":"MassIVE","container":{},"publicationYear":2026,"subjects":[],"contributors":[],"dates":[{"date":"2026","dateType":"Issued"}],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Mass Spectrometry","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[],"descriptions":[],"geoLocations":[],"fundingReferences":[],"url":"https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?accession=MSV000102036","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2026-06-03T23:42:16Z","registered":"2026-06-03T23:42:17Z","published":null,"updated":"2026-06-03T23:42:17Z"},"relationships":{"client":{"data":{"id":"cdl.ucsd","type":"clients"}}}},{"id":"10.25345/c56m33j04","type":"dois","attributes":{"doi":"10.25345/c56m33j04","identifiers":[],"creators":[{"name":"Barnaba, Carlo","nameType":"Personal","givenName":"Carlo","familyName":"Barnaba","affiliation":["University of Kansas"],"nameIdentifiers":[]}],"titles":[{"lang":"en-US","title":"MassIVE MSV000102035 - Metformin Redirects Autophagy from Bulk Turnover to Mitochondrial Clearance"},{"lang":"en-US","title":"Affinity purification of Halo-ULK1 under various conditions followed by phosphopeptide enrichment to understand the changes in phosphorylation which may affect autophagy with metformin use.","titleType":"Subtitle"}],"publisher":"MassIVE","container":{},"publicationYear":2026,"subjects":[],"contributors":[],"dates":[{"date":"2026","dateType":"Issued"}],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Mass Spectrometry","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[],"descriptions":[],"geoLocations":[],"fundingReferences":[],"url":"https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?accession=MSV000102035","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2026-06-03T21:20:23Z","registered":null,"published":null,"updated":"2026-06-03T21:20:24Z"},"relationships":{"client":{"data":{"id":"cdl.ucsd","type":"clients"}}}},{"id":"10.25345/c5bc3tb3d","type":"dois","attributes":{"doi":"10.25345/c5bc3tb3d","identifiers":[],"creators":[{"name":"Barnaba, Carlo","nameType":"Personal","givenName":"Carlo","familyName":"Barnaba","affiliation":["University of Kansas"],"nameIdentifiers":[]}],"titles":[{"lang":"en-US","title":"MassIVE MSV000102034 - Metformin Redirects Autophagy from Bulk Turnover to Mitochondrial Clearance"},{"lang":"en-US","title":"Affinity purification of Halo-ULK1 under various conditions to understand the changes in protein complex conformation which may affect autophagy with metformin use.","titleType":"Subtitle"}],"publisher":"MassIVE","container":{},"publicationYear":2026,"subjects":[],"contributors":[],"dates":[{"date":"2026","dateType":"Issued"}],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Mass Spectrometry","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[],"descriptions":[],"geoLocations":[],"fundingReferences":[],"url":"https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?accession=MSV000102034","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2026-06-03T20:30:47Z","registered":"2026-06-03T20:30:47Z","published":null,"updated":"2026-06-03T20:30:47Z"},"relationships":{"client":{"data":{"id":"cdl.ucsd","type":"clients"}}}},{"id":"10.25345/c5g44j481","type":"dois","attributes":{"doi":"10.25345/c5g44j481","identifiers":[],"creators":[{"name":"Barrero, Maria J.","nameType":"Personal","givenName":"Maria J.","familyName":"Barrero","affiliation":["Instituto de Salud Carlos III"],"nameIdentifiers":[]}],"titles":[{"lang":"en-US","title":"MassIVE MSV000102033 - EHMT2 variants cause an autosomal dominant EHMT2-related Kleefstra syndrome-Histone modifications mass spect"},{"lang":"en-US","title":"Histone modifications quantified by mass spectrometry dataset used in: De novo EHMT2 variants cause an autosomal dominant EHMT2-related Kleefstra syndrome via loss of G9a methyltransferase activity. A. Hnizda, B. Martinez-Delgado et al.","titleType":"Subtitle"}],"publisher":"MassIVE","container":{},"publicationYear":2026,"subjects":[],"contributors":[],"dates":[{"date":"2026","dateType":"Issued"}],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Mass Spectrometry","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[],"descriptions":[],"geoLocations":[],"fundingReferences":[],"url":"https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?accession=MSV000102033","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2026-06-03T20:23:36Z","registered":"2026-06-03T20:23:37Z","published":null,"updated":"2026-06-03T20:23:37Z"},"relationships":{"client":{"data":{"id":"cdl.ucsd","type":"clients"}}}},{"id":"10.25345/c5kw57z3j","type":"dois","attributes":{"doi":"10.25345/c5kw57z3j","identifiers":[],"creators":[{"name":"Neeloffer Mookherjee","affiliation":["University of Manitoba"],"nameIdentifiers":[]}],"titles":[{"lang":"en-US","title":"MassIVE MSV000102032 - Biological Sex Modifies Plasma Proteome Response to Traffic-Related Air Pollution"},{"lang":"en-US","title":"Air pollution is a major contributor to disease-related mortality globally. It is increasingly appreciated that environmental factors can influence sex-related differences in disease etiology and prevalence. Although air pollution has a significant impact on human health and disease, sex-related differences in molecular responses to air pollution is not well understood. As detrimental effects of inhaled toxicants extend beyond the lungs and can alter protein levels in circulation, the objective of this study was to characterize sex-related differences in the plasma proteome following exposure to diesel exhaust (DE) as a proxy for air pollution. Healthy, adult males and females (N=5 each) were exposed to filtered air (FA) and a range of controlled DE concentrations (20, 50, and 150 ug PM2.5/m^3), randomized across four visits with a 4-week washout period between each exposure. Plasma collected 24 hours after each exposure was analyzed using tandem mass tag (TMT)-labeled LC-MS/MS. Sex-disaggregated data analysis revealed significant changes in plasma protein abundance in both males and females, across all DE concentrations compared to FA, with males eliciting a more extensive response than females. A linear mixed model analysis with sex:exposure interaction terms revealed 91 proteins with significant interaction effects, of which 57 proteins showed sex-stratified response to DE; 38 significantly altered in males, 14 in females, and 5 in both sexes. These results demonstrate that biological sex is a significant effect modifier of DE-mediated alteration of the plasma proteome and provides a strong rationale for integrating sex to elucidate the impact of air pollution on health.","titleType":"Subtitle"}],"publisher":"MassIVE","container":{},"publicationYear":2026,"subjects":[],"contributors":[],"dates":[{"date":"2026","dateType":"Issued"}],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Mass Spectrometry","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[],"descriptions":[],"geoLocations":[],"fundingReferences":[],"url":"https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?accession=MSV000102032","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2026-06-03T19:02:44Z","registered":"2026-06-03T19:02:45Z","published":null,"updated":"2026-06-03T19:02:45Z"},"relationships":{"client":{"data":{"id":"cdl.ucsd","type":"clients"}}}},{"id":"10.25345/c5qn5zr8s","type":"dois","attributes":{"doi":"10.25345/c5qn5zr8s","identifiers":[],"creators":[{"name":"Couradeau, Estelle","nameType":"Personal","givenName":"Estelle","familyName":"Couradeau","affiliation":["The Pennsylvania State University"],"nameIdentifiers":[]}],"titles":[{"lang":"en-US","title":"MassIVE MSV000102031 - GNPS- soil untargeted GCMS metabolomics data from three ecosites in Chingaza Paramo Colombia"},{"lang":"en-US","title":"This dataset contains untargeted metabolomics data from soil samples collected across three ecosites defined by plant assemblages in the paramo ecosystem of Laguna Seca, Chingaza, Colombia (Espeletia, Chusquea, Peatland), with three plots and three replicates per ecosite (27 samples total). Metabolite extraction was performed using cold methanol with vortex and ultrasonic-assisted extraction, followed by a two-step derivatization: methoximation with O-methoxyamine in pyridine and silylation with BSTFA/TMCS, with methyl heptadecanoate-D33 added as an internal standard. Quality control samples were prepared by pooling equal volumes of all extracts. MS data acquisition was carried out on an Agilent GC/Q-TOF 7250 mass spectrometer with electron ionization (EI) at 70 eV, with chromatographic separation achieved using an Agilent J\u0026amp;W HP-5MS column (30 m X 0.25 mm, 0.25 um) with helium as carrier gas and a temperature ramp from 60C to 325C. Detection was performed over a mass range of 50-600 m/z at 5 spectra/s.","titleType":"Subtitle"}],"publisher":"MassIVE","container":{},"publicationYear":2026,"subjects":[],"contributors":[],"dates":[{"date":"2026","dateType":"Issued"}],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Mass Spectrometry","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[],"descriptions":[],"geoLocations":[],"fundingReferences":[],"url":"https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?accession=MSV000102031","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2026-06-03T13:31:38Z","registered":"2026-06-03T13:31:38Z","published":null,"updated":"2026-06-03T13:31:38Z"},"relationships":{"client":{"data":{"id":"cdl.ucsd","type":"clients"}}}},{"id":"10.25345/c5vd6pk12","type":"dois","attributes":{"doi":"10.25345/c5vd6pk12","identifiers":[],"creators":[{"name":"Ludovico, Ivo Diaz","nameType":"Personal","givenName":"Ivo Diaz","familyName":"Ludovico","affiliation":["UNLP"],"nameIdentifiers":[]}],"titles":[{"lang":"en-US","title":"MassIVE MSV000102030 - Proteomic Profiling of THP-1-Derived Human Macrophages Exposed to Lipid-Free Apolipoprotein A-I (APOA1)"},{"lang":"en-US","title":"This dataset contains LC-MS/MS proteomic data from PMA-differentiated THP-1 human macrophages exposed to recombinant lipid-free APOA1, APOA1 p.K131del (K107del), or PBS control. The analysis was performed to characterize proteomic remodeling induced by lipid-free APOA1 and its naturally occurring amyloidogenic variant. Raw files, mzML files, sample annotations, and protein and peptide identification results are included.","titleType":"Subtitle"}],"publisher":"MassIVE","container":{},"publicationYear":2026,"subjects":[],"contributors":[],"dates":[{"date":"2026","dateType":"Issued"}],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Mass Spectrometry","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[],"descriptions":[],"geoLocations":[],"fundingReferences":[],"url":"https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?accession=MSV000102030","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2026-06-03T12:21:03Z","registered":"2026-06-03T12:21:04Z","published":null,"updated":"2026-06-03T12:21:04Z"},"relationships":{"client":{"data":{"id":"cdl.ucsd","type":"clients"}}}},{"id":"10.25345/c5057d65z","type":"dois","attributes":{"doi":"10.25345/c5057d65z","identifiers":[],"creators":[{"name":"Landeta-Salgado, Catalina","nameType":"Personal","givenName":"Catalina","familyName":"Landeta-Salgado","affiliation":["Universidad de Chile"],"nameIdentifiers":[]}],"titles":[{"lang":"en-US","title":"MassIVE MSV000102029 - Metabolomic Profiling and Bioactivity Evaluation of Fermented and Non-Fermented Ulva and Durvillaea spp."},{"lang":"en-US","title":"Metabolomic profiling comparing fermented and non-fermented seaweeds.","titleType":"Subtitle"}],"publisher":"MassIVE","container":{},"publicationYear":2026,"subjects":[],"contributors":[],"dates":[{"date":"2026","dateType":"Issued"}],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Mass Spectrometry","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[],"descriptions":[],"geoLocations":[],"fundingReferences":[],"url":"https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?accession=MSV000102029","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2026-06-03T11:53:07Z","registered":"2026-06-03T11:53:08Z","published":null,"updated":"2026-06-03T11:53:08Z"},"relationships":{"client":{"data":{"id":"cdl.ucsd","type":"clients"}}}},{"id":"10.25345/c53t9dm62","type":"dois","attributes":{"doi":"10.25345/c53t9dm62","identifiers":[],"creators":[{"name":"McNutt, Patrick","nameType":"Personal","givenName":"Patrick","familyName":"McNutt","affiliation":["Wake Forest School of Medicine"],"nameIdentifiers":[]}],"titles":[{"lang":"en-US","title":"MassIVE MSV000102028 - Proteomic characterization of ocular tear fluid reveals preclinical biomarkers of sulfur mustard toxicity"},{"lang":"en-US","title":"Sulfur mustard (SM) vapor causes ocular injury after a 6-24 h latent period, when molecular damage has occurred, but clinical signs are not yet apparent. Characterizing ocular responses during this early phase is important for understanding SM pathogenesis, identifying molecular readouts of injury progression, and developing biomarkers of exposure. Tear fluid is well-suited for this purpose because it can be collected noninvasively and reflects responses from injured ocular tissues. We tested whether temporal changes in the tear fluid proteome reflect cellular and molecular responses to corneal SM exposure. Rabbits were exposed to SM vapor using a corneal vapor cap, and tear fluid was collected at baseline, 4 h, 1 d, and 5 d, corresponding to the latent period, acute lesion, and early recovery. A large proteomic response was detected at 4 h, before clinical signs emerged, involving extracellular injury signaling, epithelial injury, and innate immune activation. By 1 d, the tear fluid proteome transitioned to inflammatory cell activation with metabolic, redox, and proteostasis stress. By 5 d, the response was reduced but retained a residual signature of immune, epithelial, and stress responses. This temporal progression is consistent with the molecular mechanisms of SM toxicity and provides insight into acute ocular vesicant injury. These findings establish tear fluid as a noninvasive molecular reporter of ocular SM injury progression. They also reveal a molecular signature of vesicant exposure, which emerges prior to clinical signs, and provide foundational data for developing tear-based biomarkers of chemical exposure, injury assessment, and therapeutic testing.","titleType":"Subtitle"}],"publisher":"MassIVE","container":{},"publicationYear":2026,"subjects":[],"contributors":[],"dates":[{"date":"2026","dateType":"Issued"}],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Mass Spectrometry","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[],"descriptions":[],"geoLocations":[],"fundingReferences":[],"url":"https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?accession=MSV000102028","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2026-06-03T11:21:59Z","registered":"2026-06-03T11:22:00Z","published":null,"updated":"2026-06-03T11:22:00Z"},"relationships":{"client":{"data":{"id":"cdl.ucsd","type":"clients"}}}},{"id":"10.25345/c57m04d98","type":"dois","attributes":{"doi":"10.25345/c57m04d98","identifiers":[],"creators":[{"name":"Carpentieri, Andrea","nameType":"Personal","givenName":"Andrea","familyName":"Carpentieri","affiliation":["Universita degli studi di Napoli Federico II, Dipartimento di scienze chimiche"],"nameIdentifiers":[]}],"titles":[{"lang":"en-US","title":"MassIVE MSV000102027 - Multi-level evidence of early polyethylene biodeterioration by Pseudomonas aeruginosa: from surface oxidation to metabolic and proteomic adaptation"},{"lang":"en-US","title":"Polyethylene (PE) is a synthetic polymer with a wide range of applications. Due to its recalcitrant nature, it is highly resistant to degradation and deterioration, leading to its accumulation in the environment. To facilitate polyethylene biodegradation, it is crucial to identify microorganisms that can enhance PE's hydrophilicity and/or shorten its polymeric chains through oxidation. In this study, we report the isolation of a novel strain of Pseudomonas aeruginosa from plastic debris. Growth analyses demonstrated that the bacterium prolongs its stationary phase in the presence of LDPE, indicating a potential use of LDPE-derived compounds as an auxiliary carbon source. FTIR analysis revealed reduced intensity of LDPE CH stretching bands, consistent with early oxidative modifications, while FESEM imaging showed surface erosions and grooves exclusively on LDPE exposed to the bacterium. Bacterial metabolic profile suggests that cultural conditions in presence of LDPE represent the optimal or preferred growth state of P. aeruginosa, the metabolomics data suggest that polyethylene is not a neutral substrate for P. aeruginosa but rather induces physiological changes that promote cellular survival and adaptation. GC-MS analysis detected low-molecular-weight compounds compatible with LDPE degradation products. Moreover, the culture supernatant displayed oxidative activities and six proteins were uniquely expressed upon LDPE exposure, suggesting the activation of LDPE-responsive pathways. In presence of LDPE, the bacterium synthesizes proteins that likely support plastic degradation.","titleType":"Subtitle"}],"publisher":"MassIVE","container":{},"publicationYear":2026,"subjects":[],"contributors":[],"dates":[{"date":"2026","dateType":"Issued"}],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Mass Spectrometry","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[],"descriptions":[],"geoLocations":[],"fundingReferences":[],"url":"https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?accession=MSV000102027","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2026-06-03T10:58:33Z","registered":"2026-06-03T10:58:34Z","published":null,"updated":"2026-06-03T10:58:34Z"},"relationships":{"client":{"data":{"id":"cdl.ucsd","type":"clients"}}}},{"id":"10.25345/c5cc0v744","type":"dois","attributes":{"doi":"10.25345/c5cc0v744","identifiers":[],"creators":[{"name":"Varjosalo, Markku","nameType":"Personal","givenName":"Markku","familyName":"Varjosalo","affiliation":["University of Helsinki"],"nameIdentifiers":[]}],"titles":[{"lang":"en-US","title":"MassIVE MSV000102026 - Multi-layered regulatory networks driving human neuronal differentiation"},{"lang":"en-US","title":"To investigate regulatory changes during neuronal differentiation, we conducted an integrative, multi-omics analysis of LUHMES cells collected at Day 1, Day 3, and Day 6 of differentiation. We combined enhancer-promoter interaction mapping using NET-CAGE and Hi-Cap with transcriptomics, total proteomics, and phosphoproteomics to characterize coordinated changes in chromatin interactions, gene expression, protein abundance, and phosphorylation dynamics.","titleType":"Subtitle"}],"publisher":"MassIVE","container":{},"publicationYear":2026,"subjects":[],"contributors":[],"dates":[{"date":"2026","dateType":"Issued"}],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Mass Spectrometry","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[],"descriptions":[],"geoLocations":[],"fundingReferences":[],"url":"https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?accession=MSV000102026","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2026-06-03T08:48:09Z","registered":"2026-06-03T08:48:10Z","published":null,"updated":"2026-06-03T08:48:10Z"},"relationships":{"client":{"data":{"id":"cdl.ucsd","type":"clients"}}}},{"id":"10.25345/c5h41k19r","type":"dois","attributes":{"doi":"10.25345/c5h41k19r","identifiers":[],"creators":[{"name":"He, Ding","nameType":"Personal","givenName":"Ding","familyName":"He","affiliation":["The Hong Kong University of Science and Technology"],"nameIdentifiers":[]}],"titles":[{"lang":"en-US","title":"MassIVE MSV000102025 - The data for the manuscript titled \"Isomeric Diversity of Dissolved Organic Matter Increases from Estuarine to Marine environments\""},{"lang":"en-US","title":"The data is for the review of the manuscript titled \"Isomeric Diversity of Dissolved Organic Matter Increases from Estuarine to Marine environments\" submitted to Nature Communications.","titleType":"Subtitle"}],"publisher":"MassIVE","container":{},"publicationYear":2026,"subjects":[],"contributors":[],"dates":[{"date":"2026","dateType":"Issued"}],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Mass Spectrometry","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[],"descriptions":[],"geoLocations":[],"fundingReferences":[],"url":"https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?accession=MSV000102025","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2026-06-03T06:40:50Z","registered":"2026-06-03T06:40:51Z","published":null,"updated":"2026-06-03T06:40:51Z"},"relationships":{"client":{"data":{"id":"cdl.ucsd","type":"clients"}}}},{"id":"10.25345/c5mw28v3s","type":"dois","attributes":{"doi":"10.25345/c5mw28v3s","identifiers":[],"creators":[{"name":"Dr. Nevan J. Krogan","affiliation":["Department of Cellular and Molecular Pharmacology, University of California San Francisco, USA"],"nameIdentifiers":[]}],"titles":[{"lang":"en-US","title":"MassIVE MSV000102024 - TEST9b Interrogating VACV and MPXV Host Interactomes reveals several novel pro-viral strategies"},{"lang":"en-US","title":"Poxviruses like Vaccinia (VACV) and Monkeypox (MPXV) have been central to immunization history and can trigger severe outbreaks. Despite extensive research, many poxvirus gene functions remain unclear, with numerous redundant protein roles yet to be described. To systematically dissect poxvirus-host interactions and uncover new viral functions, we applied a global, multi-omics approach combining affinity purification-mass spectrometry (AP-MS), structural modeling, and viral genetics. Mapping the full VACV proteome (n=210) and divergent MPXV proteins (n=57), we identified 2,292 VACV-human and 854 MPXV-human protein-protein interactions (PPIs), the majority of which are novel.","titleType":"Subtitle"}],"publisher":"MassIVE","container":{},"publicationYear":2026,"subjects":[],"contributors":[],"dates":[{"date":"2026","dateType":"Issued"}],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Mass Spectrometry","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[],"descriptions":[],"geoLocations":[],"fundingReferences":[],"url":"https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?accession=MSV000102024","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2026-06-03T06:14:05Z","registered":"2026-06-03T06:14:06Z","published":null,"updated":"2026-06-03T06:14:06Z"},"relationships":{"client":{"data":{"id":"cdl.ucsd","type":"clients"}}}},{"id":"10.25345/c5rn30n6f","type":"dois","attributes":{"doi":"10.25345/c5rn30n6f","identifiers":[],"creators":[{"name":"Strenkert, Daniela","nameType":"Personal","givenName":"Daniela","familyName":"Strenkert","affiliation":["Michigan State University"],"nameIdentifiers":[]}],"titles":[{"lang":"en-US","title":"MassIVE MSV000102023 - Chlamydomonas reinhardtii proteome on wildtype and fdx5 mutants grown in Cu replete, deficient and dark hypoxia"},{"lang":"en-US","title":"Proteomic data were obtained from Chlamydomonas reinhardtii wild-type cells and fdx5 mutants grown photoheterotrophically in TAP medium under three conditions: with copper supplementation (Cu-replete), without copper supplementation (Cu-deficient), or in the dark without oxygen for 48 hours (dark hypoxia). Following growth of three biological replicates per condition, samples were digested with trypsin and analyzed by LC-MS/MS. Data was searched with MS-GF+ using PNNL's Data Management System (DMS) processing pipeline.","titleType":"Subtitle"}],"publisher":"MassIVE","container":{},"publicationYear":2026,"subjects":[],"contributors":[],"dates":[{"date":"2026","dateType":"Issued"}],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Mass Spectrometry","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[],"descriptions":[],"geoLocations":[],"fundingReferences":[],"url":"https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?accession=MSV000102023","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2026-06-03T06:13:06Z","registered":"2026-06-03T06:13:07Z","published":null,"updated":"2026-06-03T06:13:07Z"},"relationships":{"client":{"data":{"id":"cdl.ucsd","type":"clients"}}}},{"id":"10.25345/c5wd3qf9q","type":"dois","attributes":{"doi":"10.25345/c5wd3qf9q","identifiers":[],"creators":[{"name":"Conlon, Frank","nameType":"Personal","givenName":"Frank","familyName":"Conlon","affiliation":["McAllister Heart Institute, UNC-Chapel Hill"],"nameIdentifiers":[]}],"titles":[{"lang":"en-US","title":"MassIVE MSV000102022 - Xenopus tropicalis heart proteome submission"},{"lang":"en-US","title":"Sex differences in the mammalian heart are well-documented. Females exhibit smaller absolute heart mass, longer rate-corrected QT intervals, distinct repolarization kinetics, and different trajectories of hypertrophy, fibrosis, and heart failure with preserved ejection fraction, while males show earlier and more frequent ischemic disease (Regitz-Zagrosek and Kararigas, 2017; Arnold and Disteche, 2018). An outstanding phylogenetic question is, do cardiac sex differences track the origin of the XY system, the origin of viviparity, both, or neither? Here we examine cardiac sex differences in Xenopus tropicalis, an amphibian diverged from mammals by approximately 350 million years (Hellsten et al., 2010). X. tropicalis is oviparous and lacks a placenta. It therefore provides a pre-mammalian baseline against which the cardiac phenotype of a placental mammal can be contrasted. Here we show that 99.6% of human X-linked genes derive from two X. tropicalis autosomes, a two-autosome ancestry conserved across five placental mammals but absent in chicken. On this pre-XY coordinate system we identify 64 candidate sex-biased cardiac proteins and 19 sex-biased transcripts. Gene set enrichment identifies the complement and coagulation module as coordinately female-biased. Eleven candidate proteins overlap the mouse cardiac sex-biased proteome. A cardiac sex-bias program therefore exists outside the therian XY system and placental gestation. Functional categorization of the sex-biased transcripts by pathway over-representation identifies translational, metabolic, and signaling axes that are distinct from the female-biased complement and coagulation signature dominating the sex-biased cardiac proteome. Cross-species comparison against the GTEx human heart sex-DE catalogue demonstrates that the pre-mammalian cardiac sex-biased transcriptional program is essentially lineage-specific at the gene-symbol level, while the sex-biased proteomic program preserves pathway-level information across 350 million years of divergence, establishing that the conserved component of cardiac sex-bias resides primarily at the protein layer.","titleType":"Subtitle"}],"publisher":"MassIVE","container":{},"publicationYear":2026,"subjects":[],"contributors":[],"dates":[{"date":"2026","dateType":"Issued"}],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Mass Spectrometry","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[],"descriptions":[],"geoLocations":[],"fundingReferences":[],"url":"https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?accession=MSV000102022","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2026-06-03T04:21:26Z","registered":"2026-06-03T04:21:27Z","published":null,"updated":"2026-06-03T04:21:27Z"},"relationships":{"client":{"data":{"id":"cdl.ucsd","type":"clients"}}}},{"id":"10.25345/c5125qq3z","type":"dois","attributes":{"doi":"10.25345/c5125qq3z","identifiers":[],"creators":[{"name":"Metz, Thomas O.","nameType":"Personal","givenName":"Thomas O.","familyName":"Metz","affiliation":["Pacific Northwest National Laboratory"],"nameIdentifiers":[]}],"titles":[{"lang":"en-US","title":"MassIVE MSV000102021 - Ion Mobility-mass spectrometry Dashboard (IMDash): an automated, multi-platform computational pipeline to support production of robust and large-scale experimental collision cross-section libraries, MetaSci datasets"},{"lang":"en-US","title":"Samples were analyzed on an Agilent 6560 Ion Mobility Quadrupole Time of Flight (QTOF) MS system by direct infusion with ESI in both positive and negative ionization mode with multiple IMS field strengths. Raw data was processed to extract CCS values using the IMDash tool.","titleType":"Subtitle"}],"publisher":"MassIVE","container":{},"publicationYear":2026,"subjects":[],"contributors":[],"dates":[{"date":"2026","dateType":"Issued"}],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Mass Spectrometry","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[],"descriptions":[],"geoLocations":[],"fundingReferences":[],"url":"https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?accession=MSV000102021","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2026-06-03T00:30:37Z","registered":"2026-06-03T00:30:38Z","published":null,"updated":"2026-06-03T00:30:38Z"},"relationships":{"client":{"data":{"id":"cdl.ucsd","type":"clients"}}}},{"id":"10.25345/c54t6fh69","type":"dois","attributes":{"doi":"10.25345/c54t6fh69","identifiers":[],"creators":[{"name":"Waldbauer, Jacob","nameType":"Personal","givenName":"Jacob","familyName":"Waldbauer","affiliation":["University of Chicago"],"nameIdentifiers":[]}],"titles":[{"lang":"en-US","title":"MassIVE MSV000102020 - P. putida KT2440 and S12 on ferulate/vanillate/4=hydroxybenzoate"},{"lang":"en-US","title":"Quantitative expression proteomics analyses of Pseudomonas putida strains KT2440 and S12 grown on lignin-related aromatics, including ferulate, vanillate and 4-hydroxybenzoate. Quantitation by diDO-IPTL (Waldbauer et al. (2017) Anal Chem).","titleType":"Subtitle"}],"publisher":"MassIVE","container":{},"publicationYear":2026,"subjects":[],"contributors":[],"dates":[{"date":"2026","dateType":"Issued"}],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Mass Spectrometry","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[],"descriptions":[],"geoLocations":[],"fundingReferences":[],"url":"https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?accession=MSV000102020","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2026-06-02T19:14:07Z","registered":"2026-06-02T19:14:08Z","published":null,"updated":"2026-06-02T19:14:08Z"},"relationships":{"client":{"data":{"id":"cdl.ucsd","type":"clients"}}}},{"id":"10.25345/c58k75b02","type":"dois","attributes":{"doi":"10.25345/c58k75b02","identifiers":[],"creators":[{"name":"Srivastava, Sanjeeva","nameType":"Personal","givenName":"Sanjeeva","familyName":"Srivastava","affiliation":["Indian Institute of Technology Bombay"],"nameIdentifiers":[]}],"titles":[{"lang":"en-US","title":"MassIVE MSV000102019 - Plasma Proteomic Signatures Distinguish Treatment Resolution and Recurrence in Tuberculosis Patients"},{"lang":"en-US","title":"Tuberculosis (TB) recurrence following treatment remains poorly understood at the host biological level. Using untargeted mass spectrometry-based plasma proteomics, we conducted the first systematic longitudinal investigation of paired pre- and post-treatment plasma proteomes in culture-confirmed TB recurrence and sustained cure patients within the RePORT India cohort. Recurrence-trajectory patients harboured a distinct immunothrombotic and metabolic signature at diagnosis, characterised by broad complement-coagulation activation and Warburg-like metabolic reprogramming of host immune cells. While sustained cure patients engaged coordinated regulatory rebalancing of these pathways during treatment, recurrence-trajectory patients conspicuously failed to mount this counter-regulatory response. Cortisol-binding globulin and prolactin-induced protein emerged as persistent discriminators across both timepoints, reflecting an unresolved inflammatory state that survives standard therapy. These findings identify host immunothrombotic dysregulation and failed regulatory resolution as potential determinants of recurrence risk, and highlight important proteins for risk stratification in TB-endemic populations.","titleType":"Subtitle"}],"publisher":"MassIVE","container":{},"publicationYear":2026,"subjects":[],"contributors":[],"dates":[{"date":"2026","dateType":"Issued"}],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Mass Spectrometry","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[],"descriptions":[],"geoLocations":[],"fundingReferences":[],"url":"https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?accession=MSV000102019","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2026-06-02T16:09:01Z","registered":"2026-06-02T16:09:02Z","published":null,"updated":"2026-06-02T16:09:02Z"},"relationships":{"client":{"data":{"id":"cdl.ucsd","type":"clients"}}}},{"id":"10.25345/c5db7w46s","type":"dois","attributes":{"doi":"10.25345/c5db7w46s","identifiers":[],"creators":[{"name":"Droit, Arnaud","nameType":"Personal","givenName":"Arnaud","familyName":"Droit","affiliation":["CHU de Quebec Universite Laval"],"nameIdentifiers":[]}],"titles":[{"lang":"en-US","title":"MassIVE MSV000102018 - PeptiDIA: A Machine Learning Framework for Enhanced Peptide Identification in Fast-Gradient Data-Independent Acquisition Proteomics"},{"lang":"en-US","title":"This dataset comprises data independent acquisition (DIA) mass spectrometry runs of six tissue types from two species: human (artery, heart, adipose tissue) and mouse (colon, liver, ileum). Each biological sample was analyzed on a Thermo Orbitrap Exploris 480 coupled to an Evosep One LC system under two chromatographic regimes: a fast gradient (300 samples per day, 4.8 min) and a long gradient (30 samples per day, 48 min), yielding 112 raw files in total. Raw files were converted to mzML with ThermoRawFileParser and searched with DIA-NN v2.0 in library free mode (deep learning spectral prediction) against the UniProt human (UP000005640) and mouse (UP000000589) reference proteomes, with trypsin digestion (1 missed cleavage), N terminal methionine excision, and carbamidomethylation of cysteine as a fixed modification. The paired fast and long gradient design underpins PeptiDIA, machine learning framework that recovers additional peptide identifications from fast gradient DIA data using matched long gradient identifications as reference labels.","titleType":"Subtitle"}],"publisher":"MassIVE","container":{},"publicationYear":2026,"subjects":[],"contributors":[],"dates":[{"date":"2026","dateType":"Issued"}],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Mass Spectrometry","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[],"descriptions":[],"geoLocations":[],"fundingReferences":[],"url":"https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?accession=MSV000102018","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2026-06-02T15:27:56Z","registered":"2026-06-02T15:27:57Z","published":null,"updated":"2026-06-02T15:27:57Z"},"relationships":{"client":{"data":{"id":"cdl.ucsd","type":"clients"}}}},{"id":"10.25345/c5j38kz04","type":"dois","attributes":{"doi":"10.25345/c5j38kz04","identifiers":[],"creators":[{"name":"Cheng, Steven Le Hung","nameType":"Personal","givenName":"Steven Le Hung","familyName":"Cheng","affiliation":["Max Planck for Plant Breeding"],"nameIdentifiers":[]}],"titles":[{"lang":"en-US","title":"MassIVE MSV000102017 - Engineering of a plant ribosylated nucleotide immune second messenger"},{"lang":"en-US","title":"Pure 100 microM pRib-AMP or Thio-pRib-AMP added to plant lysates derived from Arabidopsis leaves. The quantity of pRib-AMP and Thio-pRib-AMP were measured at 0, 0.5, 1, 2, 4 and 24 hrs and compared to pure respective chemical standards. Supplementary files: Level 1 Identification.","titleType":"Subtitle"}],"publisher":"MassIVE","container":{},"publicationYear":2026,"subjects":[],"contributors":[],"dates":[{"date":"2026","dateType":"Issued"}],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Mass Spectrometry","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[],"descriptions":[],"geoLocations":[],"fundingReferences":[],"url":"https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?accession=MSV000102017","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2026-06-02T11:04:52Z","registered":"2026-06-02T11:04:54Z","published":null,"updated":"2026-06-02T11:04:54Z"},"relationships":{"client":{"data":{"id":"cdl.ucsd","type":"clients"}}}},{"id":"10.25345/c5nv99r20","type":"dois","attributes":{"doi":"10.25345/c5nv99r20","identifiers":[],"creators":[{"name":"Eubel, Holger","nameType":"Personal","givenName":"Holger","familyName":"Eubel","affiliation":["Leibniz University Hannover, Department of Plant Proteomics"],"nameIdentifiers":[]}],"titles":[{"lang":"en-US","title":"MassIVE MSV000102016 - TCA cycle plasticity buffers the knock-down of 2-oxoglutarate dehydrogenase to rescue kernel development"},{"lang":"en-US","title":"The tricarboxylic acid (TCA) cycle is a central metabolic hub that connects nitrogen, carbon and energy metabolism in multiple ways. The 2-oxoglutarate dehydrogenase (ODH) enzyme complex is part of the cycle with additional roles in signaling pathways and epigenetics. Maize plants with an endosperm-specific knockdown of ODH were analyzed by magnetic resonance imaging (MRI), respiration assays, oxygen microsensors, electron microscopy, transcriptomics, proteomics and metabolomics to study kernel development. Proteins were extracted from endosperm samples using a single pot solid phase enhanced sample preparation (SP3) workflow with trypsin as a protease. Peptides were desalted on Evotips and separated by an EVOSEP HPLC with the 40 SPD method before being transferred to a timsTOF Pro mass spectrometer operated in a pre-installed data-independent acquisition (DIA) strategy using the parallel accumulation serial fragmentation (PASEF) scan mode.","titleType":"Subtitle"}],"publisher":"MassIVE","container":{},"publicationYear":2026,"subjects":[],"contributors":[],"dates":[{"date":"2026","dateType":"Issued"}],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Mass Spectrometry","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[],"descriptions":[],"geoLocations":[],"fundingReferences":[],"url":"https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?accession=MSV000102016","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2026-06-02T10:17:32Z","registered":"2026-06-02T10:17:33Z","published":null,"updated":"2026-06-02T10:17:33Z"},"relationships":{"client":{"data":{"id":"cdl.ucsd","type":"clients"}}}},{"id":"10.25345/c5sn01j56","type":"dois","attributes":{"doi":"10.25345/c5sn01j56","identifiers":[],"creators":[{"name":", Gertjan","nameType":"Personal","givenName":"Gertjan","familyName":"","affiliation":["laboratory for Mass Spectrometry of Biomolecules, University of Amsterdam"],"nameIdentifiers":[]}],"titles":[{"lang":"en-US","title":"MassIVE MSV000102015 - Unravelling metabolic drivers, cross feeding networks, and temporal dynamics induced by prebiotics supplementation in the infant gut microbiome."},{"lang":"en-US","title":"Gut microbial communities have a significant regulatory impact on intestinal physiology, such as gut motility and barrier function. The microbial effect on gut motility is often evoked by bioactive molecules from various sources, including digested carbohydrates, fibers or proteins. In turn, gut transit time (directly linked to motility) is a key modulator of host microbiota interactions. Dysmotility (abnormal gut movement) is often linked to disease states like diarrhea or constipation and similarly, has also been associated with e.g. colics in infants. Newborn babies are colonized during and directly after normal vaginal delivery by the bacteria of the mother, and by handling of parents and nurses and during breastfeeding with skin bacteria. The microbiota of young babies is developing rapidly and will change during feeding with formula milk and later during introduction of solid food. Some children may develop colics, while causes are still unclear, though it is sought to originate from immature intestines, leading to abdominal pain and cramps. Due to a lack of good medication for abnormal gut function in infants, prebiotic might provide a good alternative. Prebiotics are compounds, generally complex carbohydrates such as fiber, indigestible by the host but metabolisable by the micobiota. The microbial fermentation end products and changed microbiota composition are thought to have beneficial effects on the host. We thus aim at performing culturing, metagenomics as well as using an in-house intestinal organ culture system to uncover such mechanisms. Metabolomic analysis will be used to uncover potential cross feeding products between the members in the microbial community, as well as molecules (resulting from secondary metabolism) which might have an effect on gut motility by correlating with the obtained motility data.","titleType":"Subtitle"}],"publisher":"MassIVE","container":{},"publicationYear":2026,"subjects":[],"contributors":[],"dates":[{"date":"2026","dateType":"Issued"}],"language":"en","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Mass Spectrometry","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":[],"version":null,"rightsList":[],"descriptions":[],"geoLocations":[],"fundingReferences":[],"url":"https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?accession=MSV000102015","contentUrl":null,"metadataVersion":0,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2026-06-02T08:49:14Z","registered":"2026-06-02T08:49:15Z","published":null,"updated":"2026-06-02T08:49:15Z"},"relationships":{"client":{"data":{"id":"cdl.ucsd","type":"clients"}}}},{"id":"10.25345/c5x921z73","type":"dois","attributes":{"doi":"10.25345/c5x921z73","identifiers":[],"creators":[{"name":"Greening, David","nameType":"Personal","givenName":"David","familyName":"Greening","affiliation":["Baker Heart \u0026 Diabetes Institute"],"nameIdentifiers":[]}],"titles":[{"lang":"en-US","title":"MassIVE MSV000102014 - Plasma extracellular vesicles in hypoxia-ischemia mediated preterm brain injury"},{"lang":"en-US","title":"Fetal brain extracellular vesicles (EVs) enter the peripheral blood and carry protein cargo reflective of the healthy or injured fetal brain. To determine whether the protein cargo of circulating EVs are useful biomarkers of hypoxia-ischemia-mediated preterm brain injury, fetal sheep plasma collected six hours after acute hypoxia induced by umbilical cord occlusion (or sham occlusion) underwent EV isolation, and DIA-based quantitative proteomics to identify EV-associated protein network, and enabling diagnostic accuracy (AUC+0.90) of hypoxia-mediated preterm brain injury. 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