cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c54b2x854
title: MassIVE MSV000089602 - Photoreactivity profiling of cupriachelins from Cupriavidus necator B-4383 under UV sunlight
title: In this experiment we tested the photoreactivity of cupriachelins fraction upon exposure to UV sunlight
DOI: 10.25345/c54b2x86m
title: MassIVE MSV000089810 - Translational profiling identifies sex-specific metabolic and epigenetic reprogramming of microglia in cerebral Ab amyloidosis models with an antibiotic-altered microbiome
title: Microglia are the resident macrophages of CNS that constantly screen the brain and engage in pathological processes by changing their morphology, expressing various antigens, and becoming phagocytic. Our previous studies showed alterations in gut microbiome by antibiotic treatment in APPPS1 21 mice resulted in significant attenuation in amyloidosis and altered microglial phenotype that are specific to male mice. Whether the phenotypical transformation of microglial cells is a neuroprotective response to cellular damage at early stages or principal drivers of disease is an intriguing question. There is a large gap in understanding how the transcriptional profiles relate to functional protein abundances. Here, by generating APPPS1 21 CD11br microglia reporter mice, we investigated the translational state of microglial ribosomes during their phenotypic transition in a sex-specific manner. First, we identify microglial polypeptides that reveal sex-specific oxidative stress due to Ab deposition. Next, we show antibiotic-treatment results in substantial remodeling of epigenetic landscape for metabolic shift to accommodate increased bioenergetic and biosynthetic demands associated with microglial polarization in a sex-specific manner. The male mice showed glycolytic shift for neuroprotective phenotype to promote Ab clearance via phagocytosis. However, the female mice showed loss of energy homeostasis due to persistent mitochondrial dysfunction associated with inflammatory phenotype. This microglial plasticity to support neuroenergetic homeostasis for its function based on sex, paves the way for therapeutic modulation of immunometabolism for neurodegeneration.
DOI: 10.25345/c54b2x873
title: MassIVE MSV000089987 - Wakimoto's Lab. In-House Variovorax Bacterial Strains
title: Metabolite profile of soil-isolated Variovorax in our laboratory
DOI: 10.25345/c54b2x88k
title: MassIVE MSV000090196 - GNPS - MetaData Tool Test Number 14
title: This dataset is created as a test to validate whether the metadata provided is successfully recognised. This dataset is purely a test and should not be considered valid for any scientific experiments. The metadata provided in this dataset was created using a custom-made tool. This dataset tests if the output file will still work when the program has been compiled into an .exe
DOI: 10.25345/c54b2x892
title: MassIVE MSV000090239 - Pulmonary proteomic changes due to particle pollution exposure during pregnancy
title: Pregnant mice at 14-weeks of gestation were challenged with particle pollutants (titanium dioxide, concentrated urban air or diesel exhaust particles) to determine the biological changes these cause to the pulmonary proteome by comparison to healthy lungs. The lung tissue samples were processing following the suspension trapping (STrap) protocol using in-house packed filters (GF/F, Whatman). The peptides were desalted using the spinnable StageTip protocol. The LC-MS/MS analysis was performed using an Orbitrap Eclipse MS (Thermo Scientific) coupled with an Ultimate 3000 nanoLC system and a FAIMS Pro Interface (Thermo Scientific). Peptides were first loaded onto a trap column and then separated by an analytical column (PepMap C18, 3.0 um; 15 cm x 75mm I.D.; Thermo Scientific) at 300 nl/min flow rate using a binary buffer system (buffer A, 0.1% formic acid in water; buffer B, 0.1% formic acid in acetonitrile) with a 165-min gradient (1% to 10% in 8 min; then to 25% buffer B over 117 min; 25% to 32% buffer B in 10 min, then to 95% buffer B over 3 min; back to 1% B in 5 min, and stay equilibration at 1% B for 20 min). Multiple CVs (-45, -60 and -80) were applied for FAIMS separation. For all experiments, the survey scans (MS1) were acquired at a resolution of 60,000 in the Orbitrap. The maximum injection time was set to Auto, and AGC target was set to Standard. Monoisotopic peak selection was set to Peptides, and the charge state filter was set to 2-7. For MS/MS acquisition, precursors were isolated with a width of 1.6 m/z, fragmented with HCD using 30% collision energy with a maximum injection time of 50 ms, and collected in Orbitrap at 15,000 resolution. The dynamic exclusion was set to 30 s, and can be shared across different FAIMS experiments. Protein quantitation was performed using the MaxQuant software (version 1.6.4.5) with most of the default parameters, including trypsin as an enzyme with maximally two missed cleavage sites; acetylation (protein N-terminal and Lys), oxidation (Met), and phosphorylation (Ser, Thr, Tyr) as variable modifications; cysteine carbamidomethylation as a fixed modification; peptide length must be at least 7 amino acids; false discovery rate (FDR) were set at 1% for both protein and peptide identification.
DOI: 10.25345/c54b2x905
title: MassIVE MSV000090420 - GNPS - MTBLS874: Marine Biodiscovery Ireland 2017 Samples / BDV10030 Suberites ficus
title: The outcomes of this project are to identify bioactive marine natural products from Irish marine life. This specific dataset contains LC-MS/MS spectra from tissue of the marine sponge Suberites ficus. Files are part of the Metabolights dataset MTBLS874.
DOI: 10.25345/c54b2x91n
title: MassIVE MSV000090803 - Antibody responses to dietary antigens elicits specific plasma cells in the infant thymus
title: Background. Human infants develop IgG responses to dietary antigens during the first two years of life. Yet, the source of these antibodies is unclear. In previous studies, we reported on the thymus as a unique functional niche for plasma cells (PC) specific to environmental antigens. Here we examined whether PC specific to dietary antigens also accumulate in the infant thymus. Methods. We tested IgG reactivity to 112 food antigens and allergens in the serum of 20 neonates and infants using microarrays. The presence of PC-secreting IgG specific to the most prominent antigens was then assessed among thymocytes in the same cohort. Using a liquid chromatography-mass-spectrometry (LC-MS) proteomics approach, we looked for traces of these antigens in the thymus. Results. Our studies first confirmed that cows milk proteins are prevalent targets of serum IgG in early life. Subjects with the highest serum IgG titers to cows milk proteins also harbored IgG-producing PC specific to the same antigens in the thymic niche. Further, we detected multiple peptide fragments of cows milk antigens in the thymus. Lastly, we verified that both serum IgG and IgG secreted by thymic PC recognized the peptide epitopes found in the thymus. Conclusions. Our studies reveal the presence of antibody-secreting PC specific to common dietary antigens in the infant thymus. The presence of these antigens in the thymus suggested that activation and differentiation of specific PC occurred in this organ. Further studies are warranted to evaluate the possible implication of these cells in tolerance to dietary antigens.
DOI: 10.25345/c54b2x924
title: MassIVE Reanalysis RMSV000000354.5932 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, C17orf82 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c54b2x93m
title: MassIVE Reanalysis RMSV000000354.6110 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, GOLPH3 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c54b2x943
title: MassIVE Reanalysis RMSV000000354.6315 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, WDR1 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c54b2x95k
title: MassIVE Reanalysis RMSV000000354.6704 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TTC23 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c54b2x962
title: MassIVE Reanalysis RMSV000000354.7090 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PRDM5 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c54b2x97j
title: MassIVE Reanalysis RMSV000000354.7473 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TRIM11 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c54b2x981
title: MassIVE Reanalysis RMSV000000354.7860 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, RAB27B [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c54b2x99h
title: MassIVE Reanalysis RMSV000000354.8069 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, DPYS [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c54b2xb0m
title: MassIVE Reanalysis RMSV000000354.8246 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CAMK1 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c54b2xb13
title: MassIVE Reanalysis RMSV000000354.8455 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CDKAL1 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c54b2xb2k
title: MassIVE Reanalysis RMSV000000354.8842 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, NCF2 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c54b2xb32
title: MassIVE Reanalysis RMSV000000354.9233 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ZDHHC7 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c54b2xb4j
title: MassIVE Reanalysis RMSV000000354.9616 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CCDC27 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c54b2xb51
title: MassIVE Reanalysis RMSV000000354.9824 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ZNF317 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c54b2xb6h
title: MassIVE Reanalysis RMSV000000354.10002 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ASF1B [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c54b2xb70
title: MassIVE Reanalysis RMSV000000354.10211 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, GOT1L1 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c54b2xb8g
title: MassIVE Reanalysis RMSV000000354.10389 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PLUNC [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c54b2xb9z
title: MassIVE Reanalysis RMSV000000354.10596 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, MAGEF1 [launched by 89f2bcaf3c714e3788b179581bc93515]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.5281/zenodo.7186194
title: The Young Supernova Experiment Data Release 1 (YSE DR1) Light Curves

description: This is the official Zenodo data release of the Young Supernova Experiment Public Data Release 1 (YSE DR1) light curves associated with the paper, <em>"The Young Supernova Experiment Data Release 1 (YSE DR1): Light Curves and Photometric Classification of 1975 Supernovae</em><em>"</em>.<em> </em>YSE DR1 is comprised of processed multi-color Pan-STARRS1 (PS1)-<em>griz</em> and Zwicky Transient Facility (ZTF)-<em>gr </em>photometry lightcurve files in the SNANA data format of 1975 transients with host galaxy associations, redshifts, spectroscopic/photometric classifications, and additional data products from November 24th, 2019 to December 20, 2021. See Aleo et al. (2022) for details. "yse_dr1_zenodo.tar.gz" -- All lightcurve data with no cut on signal to noise (S/N). "yse_dr1_zenodo_snr_geq_4.tar.gz" -- All lightcurve data with S/N &gt;= 4. This can be used to recreate the analysis in Aleo et al. (2022). "parsnip_results_for_ysedr1_table_A1_full_for_online" -- The full version of Table~C2 in Aleo et al. (2022). The full ParSNIP (tertiary classification) results for YSE DR1. NOTE: An example tutorial on how to download the YSE DR1 data (full sample, spec sample, phot sample), grab metadata, and recreate a plot from the paper can be found on Github.
description: If you have any questions about this data set, please reach out to Patrick D. Aleo at paleo2@illinois.edu.
DOI: 10.5281/zenodo.7186195
title: The Young Supernova Experiment: Public Data Release 1 (YSE DR1) Lightcurves

description: This is the official Zenodo data release of the Young Supernova Experiment Public Data Release 1 (YSE DR1) lightcurves associated with the paper, <em>"The Young Supernova Experiment: Public Data Release 1 (YSE DR1) and First Application to the Photometric Classification of 1500 Supernovae"</em>.<em> </em>YSE DR1 is comprised of processed multi-color Pan-STARRS1 (PS1)-<em>griz</em> and Zwicky Transient Facility (ZTF)-<em>gr </em>photometry lightcurve files in the SNANA data format of 1993 transients with host galaxy associations, redshifts, spectroscopic/photometric classifications, and additional data products from November 24th, 2019 to December 20, 2021. See Aleo et al. (2022) for details. "yse_dr1_zenodo.tar.gz" -- all lightcurve data with no cut on signal to noise (S/N). "yse_dr1_zenodo_snr_geq_4.tar.gz" -- all lightcurve data with S/N &gt;= 4. This can be used to recreate the analysis in Aleo et al. (2022).