cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5sx64f16
title: MassIVE Reanalysis RMSV000000668.116 - CCMS ProteoCarta Maestro reanalysis of Mus musculus from Mass spectrometry-based draft of the mouse proteome (Cell_line_9591) [launched by fb749713ee06486fa322870abe44395d]
title: CCMS ProteoCarta open modification search for modified peptide variants (Maestro) reanalysis of Mus musculus (Cell_line_9591) (MSV000089856/PXD030983).
DOI: 10.25345/c5sx64f2p
title: MassIVE Reanalysis RMSV000000668.313 - CCMS ProteoCarta ModDecode reanalysis of Mus musculus from Mass spectrometry-based draft of the mouse proteome (Cell_line_16990) [launched by ab1ddc566e8244bd975da925e6cb9107]
title: CCMS ProteoCarta peptidoform interpretation (ModDecode) of Maestro open modification search results for Mus musculus (Cell_line_16990) from MSV000089856/PXD030983.
DOI: 10.5063/f13t9fnz
title: Geolocations of all Ephedra californica shrubs at key ecological areas within the San Joaquin Desert.

description: The geolocation of all Ephedra californica shrubs withing key ecological areas within the San Joaquin Desert. All shrubs have been geolocated via the Google earth satellite.
DOI: 10.25345/c5sx64f35
title: MassIVE Reanalysis RMSV000000666.45 - CCMS ProteoCarta ModDecode reanalysis of Zea mays from Growth heterosis in maize is associated with expression heterosis of chloroplast ribosomes (Mixture RIL_RIL16-BioRep12) [launched by 8e5aac31b5c4425187a9a7a77b313058]
title: CCMS ProteoCarta peptidoform interpretation (ModDecode) of Maestro open modification search results for Zea mays (Mixture RIL_RIL16-BioRep12) from MSV000085916.
DOI: 10.25345/c5sx64f4n
title: MassIVE MSV000090437 - Workflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues
title: Abelin JG, Bergstrom EJ, Taylor HB, Rivera KD, Klaeger S, Xu C, Verzani EK, White CJ, WoldemichaelHB, Virshup M, Olive ME, Maynard M, Vartany S, Allen JD, Phulphagar KM, Kane MH, Rachimi S, Mani DR, Gillette MA, Satpathy S, Clauser KR, Udeshi ND, and Carr SA. 2022. Serial multiomic analyses of proteome, phosphoproteome and acetylome provides functional insights into disease pathology and drug effects while conserving precious human material. To date, ubiquitylome and HLA peptidome analyses have required separate samples for parallel processing each using distinct protocols. Here we present MONTE, a highly-sensitive multi-omic native tissue enrichment workflow that enables serial, deepscale analysis of HLA-I and HLA-II immunopeptidome, ubiquitylome, proteome, phosphoproteome and acetylome from the same tissue samples. We demonstrate the capabilities of MONTE in a proof-of-concept study of primary patient lung adenocarcinoma(LUAD) tumors. Depth of coverage and quantitative precision at each of the 'omes is not compromised by serialization, and the addition of HLA immunopeptidomics enables identification of putative immunotherapeutic targets such as cancer/testis antigens and neoantigens. MONTE can provide insights into disease-specific changes in antigen presentation, protein expression, protein degradation, cell signaling, cross-talk and epigenetic pathways involved in disease pathology and treatment.
DOI: 10.5063/f1416vgx
title: Western Indian Ocean coral and fish local normalised species richness data, data collection period 1991 to 2019, depth 1 to 20 meters

description: Coral and fish species richness and environmental stress in ~300 georeferenced coral reef sites to evaluate local scale heterogeneity. Also include 21 specific environmental variables that were evaluated. Local coral and fish taxonomic richness were normalized to cover and biomass to partially account for human disturbances to coral cover and fish biomass. Field study sites were in 4 ecoregions and 8 countries that ranged in latitude from 2.04oS (Kenya) to 26.08oS (Mozambique) and longitudes of 32.96oE (Mozambique) to 57.71oE in (Mauritius)
DOI: 10.25345/c5sx64f54
title: MassIVE MSV000090821 - Deep metaproteome uncovers functional partitions of soil microbiome
title: 2D LC-MS/MS global metaproteomics to study the taxonomy and function partitions of the Kansas prairie soil community.
DOI: 10.5063/f14b2zrb
title: Reduced reflectance and altered color: The potential cost of external particulate matter accumulation on urban Rock Pigeon feathers, Denton, TX, Summer 2020

description: Feather quality in birds is considered an honest signal of individual health as feather appearance and function depend on an individual’s ability to maintain them. In addition to flight and insulation, feathers are essential for social interactions and sexual selection in the form of visual signals. Airborne particulate matter (PM) can accumulate on feather surfaces and alter feather appearance. We quantified PM accumulation on Rock Pigeon (Columba livia) feathers and analyzed the spectral properties of extracted particulates. Feathers were sampled from two pigeon populations, one rural and one urban, in the Dallas-Fort Worth area, with 47% and 93% developed land cover, respectively, within 2 km of the populations. We determined accumulated PM gravimetrically after rinsing feathers and then measured the visible-near-infrared diffuse reflectance and color properties of extracted particulates. The rate of PM accumulation on rural birds was higher than on urban birds. However, feather particulates collected from urban pigeons had significantly lower total reflectance, reflectance in the visible portion of the spectrum, lightness, and hue angle compared to those of rural pigeons. The hue angle of rural feather particulates displayed a negative relationship with PM accumulation while total reflectance, reflectance in the visible range, and lightness of urban feather particulates were negatively related to PM accumulation. Our findings suggest that wild birds could incur an urban pollution penalty as PM accumulation has the potential to alter feather properties. Further research is needed to better understand the influence of external PM accumulation on the physiological and behavioral health of birds.
DOI: 10.25345/c5sx64f6m
title: MassIVE Reanalysis RMSV000000354.6128 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, WNT9B [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/c5sx64f73
title: MassIVE Reanalysis RMSV000000354.6512 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, HSD11B1 [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: 10.5063/f14j0ckc
title: A list of species identified within The Central Drylands of California

description: Extensive longitudinal surveys within region. Plants were censused using transects with quadrants and animals via direct observation or camera traps.
DOI: 10.25345/c5sx64f8k
title: MassIVE Reanalysis RMSV000000354.6899 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, MUM1 [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: 10.5063/f14m930j
title: Host range and severity of major North American tree pests and pathogens

description: The data contains hosts and severity scores of 297 major North American tree pests and pathogens collected from literature. Host range was indexed by taxonomic richness (number of host genera), mean pairwise distance, and standard effect size of the mean pairwise distance. Full details and results of analyses can be found in: Wang, S. S., Gougherty, A. V., and Davies, T. J. (in press). Non-native tree pests have a broader host range than native pests and differentially impact host lineages. Journal of Ecology.
DOI: 10.25345/c5sx64f92
title: MassIVE Reanalysis RMSV000000354.7107 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PTRF [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/c5sx64g05
title: MassIVE Reanalysis RMSV000000354.7282 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, AHSG [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: 10.5063/f14t6gts
title: Geolocations of all Ephedra californica shrubs at key ecological areas within the Mojave Desert.

description: The geolocation of all Ephedra californica shrubs within the Mojave Desert. All shrubs have been geolocated via the Google earth satellite.
DOI: 10.25345/c5sx64g1n
title: MassIVE Reanalysis RMSV000000354.7491 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, KLHDC9 [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/c5sx64g24
title: MassIVE Reanalysis RMSV000000354.7878 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, RIPPLY1 [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: 10.5063/f14x567h
title: The Sacramento-San Joaquin Delta genus and community level classification maps derived from airborne spectroscopy data

description: Since 2004, airborne hyperspectral imagery has been acquired over the Sacramento - San Joaquin Delta in northern California to map submerged and floating invasive species and study how they affect the Delta ecosystem. Acquiring imagery over 2220 square kilometers of the Delta typically required 60-70 flightlines each year, which were then further processed to surface reflectance, georegistered, and prepared for analysis. Further, each flightline was processed using multiple spectral mapping methods such as spectral angle mapper, spectral mixture analysis, spectral indexes, and continuum removal over water and cellulose absorption bands. The outputs of these transformations were used as inputs to a Random Forests classifier. Concurrent with image acquisition, field data (800-2000 points) were collected across the Delta for training and validation of the classification products. The field data were divided into test and training polygons. These polygons were overlaid on the transformed files and pixel data were extracted corresponding to the polygons. The training data were used to train the Random Forests classifier to identify 10 classes (water, submerged aquatic vegetation, emergent marsh, soil, non-photosynthetic vegetation, water hyacinth, water primrose, pennywort, shadow, riparian vegetation). The classifier was validated quantitatively using the test data at both pixel and polygon level using overall accuracy and kappa metrics. The classifier was then applied to all flightlines and class maps were produced. Mosaics of these class maps are published in this dataset.
DOI: 10.25345/c5sx64g3m
title: MassIVE Reanalysis RMSV000000354.8264 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CRISPLD2 [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/c5sx64g43
title: MassIVE Reanalysis RMSV000000354.8651 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, AGXT2L1 [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: 10.5063/f15b00w3
title: Genomic and morphological data from the native lizard Teira dugesii, Madeira island (32.7607° N, 16.9595° W), Portugal, July 2019.

description: This dataset corresponds to Genotyping-by-sequencing (GBS) data, dorsal luminance data and data on head dimensions of the wall lizard Teira dugesii from starkly contrasting shingle beach and inland habitats on the Portuguese island of Madeira. The study used a matched pairs sampling design to examine morphological and genomic divergence between four beach and adjacent (&lt;1 km) inland areas. Beach populations were found to be significantly darker than corresponding inland populations. Geometric morphometric analyses revealed divergence in head morphology: beach lizards have generally wider snouts. GBS analyses allowed rejection of the hypothesis that beach populations form a distinct lineage. Bayesian analyses provide strong support for models that incorporate gene flow, relative to those that do not, replicated at all pairs of matched sites. Madeiran lizards show morphological divergence between habitats in the face of gene flow, revealing how divergence may originate within small islands. A preprint describing the work is deposited here, while a full report on the work will be published in the journal Communications Biology in 2023.
DOI: 10.25345/c5sx64g5k
title: MassIVE Reanalysis RMSV000000354.8859 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CHRM4 [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: 10.5063/f15h7drn
title: Meteorological and thermal structure data at Lake Janauacá from November 2014 to September 2016

description: This dataset contains meteorological data, measured and simulated temperature and buoyancy frequency data that reported in the paper titled 'Hydrodynamic modeling of stratification and mixing in shallow, tropical floodplain lakes' by Zhou et al.. The meteorological data includes time (Time) shortwave radiation (SWin), air temperature (Tair), relative humidity (RH), wind speed (WS), wind direction (WD) and rainfall (Rain) that prepared for the AEM3D and DYRESM simulations during the periods of field campaigns from November 2014 to September 2016 (Met_campaigns) as well as the data for AEM3D simulations with simulation length extended based on the campaign periods (Met_extended.nc). Correspondingly, temperature and buoyancy frequency data have been organized into two files, one for the campaign periods (T_N_campaigns.nc) and the other for the extended periods (T_N_extended.nc). Each temperature and buoyancy frequency data file contains time (Time), depth (depth), temperature (T) and buoyancy frequency (N), with measured data marked with 'measured' and simulated data marked with 'aem3d' or 'dyresm'. These data have been directly used to create Fig. 3, 4, 7, 11 in the paper and Fig. S1, S2, S5, S7, S9, S11 and S14 to S17 in the support information.
DOI: 10.25345/c5sx64g62
title: MassIVE Reanalysis RMSV000000354.9039 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, VSX1 [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/c5sx64g7j
title: MassIVE Reanalysis RMSV000000354.9252 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, NEFL [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: 10.5063/f15m644x
title: The effect of shrub density on animal abundance in Carrizo Plain National Monument

description: The following data was collected during the 2019 field season in the Carrizo Plain National Monument in Southern California, United States. 16 Cameras were deployed at varying shrub densities ranging from no shrub individuals to a high number of individuals (11-12 shrubs). These cameras were deployed in 2 of our major sites. Cameras were not rotated and were deployed for a total of 27 continuous days. All animals in each photo were recorded as well as their behaviour, time of photo, and local density.
DOI: 10.25345/c5sx64g81
title: MassIVE Reanalysis RMSV000000354.9428 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, NOX4 [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: 10.5063/f15t3hz5
title: Global Ocean Health Index 2019 assessment

description: Scores from the 2019 global Ocean Health Index (OHI) assessment and accompanying data and models. The global Ocean Health Index assesses ocean health for 220 coastal countries and territories and has been conducted yearly since 2012. The Index describes how well we are sustainably managing 10 goals which represent the full suite of benefits that people want and need from the ocean. These goals include: artisanal fishing opportunity, biodiversity, carbon storage, clean waters, coastal livelihoods and economies, coastal protection, food provision, natural products, sense of place, and tourism and recreation. Each goal is given a score ranging from 0 to 100, and the full suite of goal scores are then averaged to obtain an overall index score for each region. Please see https://oceanhealthindex.org/ for additional resources and information.OHI prep github: https://github.com/OHI-Science/ohiprep_v2019OHI Global github: https://github.com/OHI-Science/ohi-global/releases/tag/v2019.1