cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5tb0z03f
title: MassIVE MSV000090121 - Mass spectrometry analysis 2022-08-07
title: The proteins were digested with trypsin using in-house packed glass fiber filters following a suspension trapping (STrap) protocol, or in-gel digested following a conventional protocol and desalted using C18-based StageTips (CDS Analytical LLC, Oxford, PA). 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; 10 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 (-50, -65 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 identification and quantitation were performed using the Proteome Discoverer software (version 2.5, Thermo Scientific) with most of the default parameters. An Arabidopsis thaliana database; 40,668 sequences) was used for the protein identification. Other parameters include: 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.
DOI: 10.5063/f1z899v7
title: A set of Keyhole Markup Language polygons to describe regional-level ecological differences in plants and animals of Central California Deserts

description: A set of Keyhole Markup Language (KML) polygons were generated to describe regional-level ecological differences in plant and animal communities within California Deserts. All polygons were acquired and generated with Google Earth satellite.
DOI: 10.25345/c5tb0z04x
title: MassIVE Reanalysis RMSV000000668.226 - CCMS ProteoCarta Maestro reanalysis of Mus musculus from Mass spectrometry-based draft of the mouse proteome (Male_Spleen_proteome) [launched by fb749713ee06486fa322870abe44395d]
title: CCMS ProteoCarta open modification search for modified peptide variants (Maestro) reanalysis of Mus musculus (Male_Spleen_proteome) (MSV000089856/PXD030983).
DOI: 10.5063/f1zp44kt
title: GBIF data for all herptile species within Central California Deserts, USA.

description: The purpose of this dataset is to evaluate herptile species' biodiversity in California's southwest desert. Species data was downloaded from the Global Diversity Information Facility (GBIF).GBIF.org (21 September 2022) GBIF Occurrence Download https://doi.org/10.15468/dl.5jhd82
DOI: 10.25345/c5tb0z05d
title: MassIVE MSV000090345 - HIV-1 Transcription Inhibitor 1E7-03 Decreases Nucleophosmin (NPM1) Phosphorylation
title: CEM T cells were treated with an HIV-1 transcription inhibitor, 1E7-03, that binds to the non-catalytic RVxF accommodating site of protein phosphatase 1 (PP1) and inhibits HIV-1 replication. LC-MS analysis was condcuted for label-free quantitative proteome and phosphoproteome analyses of non-infected and HIV-1 infected CEM T cells that were untreated or treated with 1E7-03.
DOI: 10.25345/c5tb0z06w
title: MassIVE MSV000090551 - Astrocytes regulate brain fatty acid uptake and food intake via cluster of differentiation (CD)36 in diet-induced obesity
title: Upon high-fat diet (HFD) feeding, exaggerated amounts of saturated fatty acids (FAs) flush the brain and induce a state of lipotoxicity, promoting overfeeding and obesity development. Astrocytes actively regulate brain glucose uptake and recently emerged as critical players in the homeostatic regulation as well as in the pathophysiology of systemic energy homeostasis. Here, we demonstrate an increased expression of the FA receptor and transporter cluster of differentiation (CD)36 in glial fibrillary acidic protein (GFAP)-expressing hypothalamic astrocytes upon HFD-induced obesity in mice. Genetically modified mouse models, bioluminescence uptake detection of labeled FAs into the brain and brain metabolomics revealed that postnatal CD36 ablation in GFAP-expressing astrocytes in adult mice prevents from increased central FA uptake and FA synthesis in diet-inducd obese mice. Depletion of CD36 in primary hypothalamic astrocytes in vitro impaired lipid accumulation and mitochondrial oxydative phosphorylation (OXPHOS). This led to an induction of the integrated stress response with enhanced expression of growth differentiation factor 15 (GDF-15), especially in the presence of the saturated FA palmitate. Astrocyte-specific CD36 ablation resulted in protection from diet-induced obesity via reduced food intake and a food preference for low-calorie chow diet over high-calorie high-fat diet exclusively in obese mice, all mediated via increased hindbrain GDF15 signaling. Collectively, these experiments revealed that astrocytes actively regulate brain FA uptake via CD36 and that ablation of astrocyte CD36 signaling induces an adaptive stress response resulting in a protection from diet-induced obesity via increased central GDF-15 signaling.
DOI: 10.5063/f1zs2txv
title: Water Quality in Offshore Lake Ontario during Intensive Sampling Years 2003 and 2008: Results from the LOLA (Lake Ontario Lower foodweb Assessment) program.

description: Intensive sampling of the offshore waters of Lake Ontario occurs on a five-year cycle. The 2003 and 2008 binational sampling program is known as the Lake Ontario Lower foodweb Assessment (LOLA). Research cruises were conducted in spring (April), summer (July or August) and fall (September) along several north-south transects. Trophic indicators in this data package include nutrients (total phosphorus (TP), soluble reactive phosphorus (SRP), dissolved silicate(Si02), and total dissolved inorganic nitrogen(nitrate and nitrite), water clarity (Secchi depth), and chlorophyll a. Other measurements measured include density and biomass of zooplankton, assessment of phytoplankton and the microbial food web, benthic community assessment, and water column profiles (temperature, fluorescence, turbidity, and oxygen).
DOI: 10.25345/c5tb0z07c
title: MassIVE MSV000090729 - Native MS of Daptomycin in Nanodiscs
title: Native MS data examining incorporation of daptomycin into intact nanodiscs at different concentrations and with different lipids
DOI: 10.25345/c5tb0z08v
title: MassIVE MSV000090935 - Identification of direct substrates of recombinant ZAKbeta in mouse skeletal muscle extracts
title: ZAK (also known as MRK or MLTK) is a MAP3 kinase and diverse roles have been assigned to the two ZAK isoforms ZAK(alpha) and ZAK(beta) from various experimental models. ZAK(beta) has been shown to respond to mechanical perturbation of cytoskeletal stress fibres as well as repeated contractions of Tibialis anterior muscle, leading to the activation of p38. This phosphoproteomics study identifies direct targets of ZAKbeta kinase activity in mouse skeletal muscle. Muscle extracts were first treated with FSBA to irreversibly inhibit all endogenous kinases and then recombinant active ZAK(beta) was added to the treated group while the control group remained untreated. Enriched S/T phosphopeptides were then analysed by LC/MS and a list of 114 S/T phosphopeptides from 49 individual proteins obtained
DOI: 10.25345/c5tb0z09b
title: MassIVE Reanalysis RMSV000000354.6240 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, DHRS13 [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/c5tb0z10f
title: MassIVE Reanalysis RMSV000000354.6627 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TNFRSF9 [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/c5tb0z11x
title: MassIVE Reanalysis RMSV000000354.7014 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CBR1 [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/c5tb0z12d
title: MassIVE Reanalysis RMSV000000354.7398 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, MCM3 [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/c5tb0z13w
title: MassIVE Reanalysis RMSV000000354.7607 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CYP4B1 [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/c5tb0z14c
title: MassIVE Reanalysis RMSV000000354.7784 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, SNX15 [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/c5tb0z15v
title: MassIVE Reanalysis RMSV000000354.7995 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CDC20B [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/c5tb0z16b
title: MassIVE Reanalysis RMSV000000354.8380 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PPM1A [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/c5tb0z17t
title: MassIVE Reanalysis RMSV000000354.8767 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, WWTR1 [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/c5tb0z189
title: MassIVE Reanalysis RMSV000000354.9157 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, DPH3 [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/c5tb0z19s
title: MassIVE Reanalysis RMSV000000354.9543 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, IP6K2 [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/c5tb0z20w
title: MassIVE Reanalysis RMSV000000354.9749 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, IP6K3 [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/c5tb0z21c
title: MassIVE Reanalysis RMSV000000354.9927 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CTSZ [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/c5tb0z22v
title: MassIVE Reanalysis RMSV000000354.10136 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, MED21 [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/c5tb0z23b
title: MassIVE Reanalysis RMSV000000354.10523 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PARN [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/c5tb0z24t
title: MassIVE Reanalysis RMSV000000354.10908 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, DNASE1L1 [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/c5tb0z259
title: MassIVE Reanalysis RMSV000000354.11295 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, KLKB1 [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/c5tb0z26s
title: MassIVE Reanalysis RMSV000000354.11502 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TGFBI [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/c5tb0z278
title: MassIVE Reanalysis RMSV000000354.11676 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ALKBH2 [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/c5tb0z28r
title: MassIVE Reanalysis RMSV000000355.4612 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TRIM45 [launched by dab8bba1f45f4e4082f7fa74fbbf30fb]
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.