cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5st7f493
title: MassIVE Reanalysis RMSV000000355.6461 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, APOOL [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.
DOI: 10.5063/f11834xd
title: TBEP Up in the Air and Down in the Water_Nitrogen Data, Tampa Bay Watershed Florida 2021 to 2022

description: Data is being collected on nitrogen forms and concentrations in atmospheric wet deposition, stormwater runoff and throughfall from the urban tree canopy. Sampling sites are Pinellas and Hillsborough Counties Florida. Data includes nitrate stable isotope analysis of wet deposition and stormwater, as well as cell count data from a bioassay of wet deposition, stormwater, and throughfall with Karenia brevis.
DOI: 10.25345/c5st7f506
title: MassIVE Reanalysis RMSV000000355.6848 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CALM1 [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.
DOI: 10.25345/c5st7f51p
title: MassIVE Reanalysis RMSV000000355.7057 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, OR14I1 [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.
DOI: 10.5063/f11j986p
title: Biological soil crusts and plant-plant interactions in a sagebrush steppe community

description: Biological soil crusts, which cover the soil over extensive portions of the arid and semi-arid regions of Earth, can have both strong positive and negative effects on vascular plants, and thus can organize plant community structure. Our understanding of these effects has generally been extrapolated from the direct effects of biological soil crusts on one or more plant species, and usually on short term germination and early establishment. However, if biocrusts provide an “organizing principle” in arid systems, the effects of crusts on communities might be expressed as “chains” or “cascades” in which the effects of crusts on plants extend to how they influence interactions among crust-affected plant species. In field measurements, at the scale of patches (generally &gt; 10 m diameter) the dominant shrub, Artemisia tridentata, was positively associated with biocrusts and negatively associated with bunchgrass species. At the scale of individual shrubs and the open matrix among shrubs, biocrusts and bunchgrasses were negatively associated with Artemisia. In the greenhouse, biocrusts fixed large amounts of nitrogen over a ranges of moisture and temperature levels, and had positive effects on germination and establishment. In two-year field experiments, biocrusts increased the growth of Festuca and the photosynthetic rates of Artemisia. In a second element of an apparent cascade, Festuca planted under Artemisia canopies were over twice as large as those planted in open sites or in Artemisia removal treatments. Biological soil crusts can facilitate vascular plants over a long time frame and contribute to a facilitation chain in which biocrusts facilitate Artemisia shrubs and Festuca, and Artemisia facilitates Festuca, appears to exclude other bunchgrass species, and at large scales may create patchy habitat that increases biocrust cover in relatively grass-free spaces among shrubs.
DOI: 10.25345/c5st7f525
title: MassIVE Reanalysis RMSV000000355.7240 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, FAM92B [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.
DOI: 10.25345/c5st7f53n
title: MassIVE Reanalysis RMSV000000355.7451 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, KEL [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.
DOI: 10.25345/c5st7f544
title: MassIVE Reanalysis RMSV000000355.7627 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PLEKHA2 [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.
DOI: 10.5063/f11v5cd6
title: The effect of shrubs on animals in Panoche Southern California

description: The following data was collected in Panoche hills in Southern California during the summer of 2019. 7 cameras were deployed facing shrub and open microsites and were rotated once. The cameras remained deployed for a total of 14 days.
DOI: 10.25345/c5st7f55m
title: MassIVE Reanalysis RMSV000000355.7836 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ZBTB47 [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.
DOI: 10.25345/c5st7f563
title: MassIVE Reanalysis RMSV000000355.8223 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, SCN1B [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.
DOI: 10.5063/f1222s75
title: Geolocations of all Larrea tridentata shrubs at key ecological areas within the Mojave Desert

description: The geolocation of all Larrea tridentata shrubs within the Mojave Desert. All shrubs have been geolocated via the Google earth satellite.
DOI: 10.25345/c5st7f57k
title: MassIVE Reanalysis RMSV000000355.8611 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, GAGE8 [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.
DOI: 10.5063/f12j699m
title: Zooplankton survey of Oneida Lake, New York, 1964 to present

description: This dataset contains information on the crutacean zooplankton in Oneida Lake and is part of the collection "Cornell Oneida Lake Data". The Cornell Biological Field Station (CBFS) serves as a primary field site for aquatic research at Cornell University (more information can be found at http://www.cbfs.dnr.cornell.edu) and is part of the Department of Natural Resources, College of Agriculture and Life Sciences, Cornell University. The centerpiece of the station's research program is a 60-year database on the food web of Oneida Lake, New York, that has been collected with support from the Cornell University Brown Endowment and from the New York State Department of Environmental Conservation. The data are collected by personnel from the Cornell Biological Field Station and include limnology, benthos, zooplankton, phytoplankton, and fish survey data, primarily from Oneida Lake and spanning 1957 to the present. This data package contains biomass, density, and average size data for zooplankton collected at six sites on Oneida Lake, NY from 1964 to present. The data package also contains a location table with latitude and longitude of each sampling site as well as a table containing common name, scientific name, taxonomic data, and taxonomic serial number (ITIS) for each of the taxon used in the primary tables.
DOI: 10.25345/c5st7f582
title: MassIVE Reanalysis RMSV000000362.102 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000081607 Confetti, LysC CID [launched by 31fc25a7c92347c2b9f58f8f26be259f]
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/c5st7f59j
title: MassIVE Reanalysis RMSV000000413.15 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000088236 Spatially and cell-type resolved quantitative proteomic atlas of healthy human skin [Subject: Inner_dermis] [launched by 31fc25a7c92347c2b9f58f8f26be259f]
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/f12r3q48
title: Data used for article "Historical use of coastal wetlands by small-scale fisheries in the Northern Gulf of California" Morzaria et al.

description: We used wetland resource users’ Local Ecological Knowledge to document historical patterns of commercial species abundance, areas of fishing importance, trophic level, and species richness and composition in coastal wetlands in the Northern Gulf of California, Mexico. We also reconstructed the environmental history of coastal wetlands in this region from bibliographic sources and photographic records, to document impacts that could have affected coastal fisheries. We found a consistent downward trend in target species abundance; the decrease was perceived as more pronounced by fishers that began fishing in or prior to the 1950’s, pointing to shifting baselines, and the failure of resource users to recognize environmental change and accept degraded states as normal. Areas of fishing importance within coastal wetlands also decreased over time. The trophic level of catch showed no distinct pattern across wetland sites or time. Perceived species richness and composition increased with wetland size. Our analysis of the small-scale use of coastal wetlands in the Northern Gulf is relevant to food security and can provide insight into how local populations adapt to depleted coastal food webs. This data set includes raw interview data from resource users and experts, areas of fishing importance, participatory drawings, photographic and map collections, and a bibliographic database.
DOI: 10.25345/c5st7f60n
title: MassIVE Reanalysis RMSV000000429.16 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080869/PXD005296 [11 out of 12] [launched by 31fc25a7c92347c2b9f58f8f26be259f]
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/c5st7f614
title: MassIVE Reanalysis RMSV000000383.14 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080854/PXD003811 [4 out of 10] [launched by 31fc25a7c92347c2b9f58f8f26be259f]
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/f12v2djk
title: Avian biodiversity data from Global Biodiversity Information Facility for the Central Desert Ecological Sites of California

description: Bird observations at different spatial scales at several sites and regions across deserts in California. All data pulled from GBIF.
DOI: 10.25345/c5st7f62m
title: MassIVE Reanalysis RMSV000000477.5 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080831/PXD004915 [3 out of 4] [launched by 31fc25a7c92347c2b9f58f8f26be259f]
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/f1319tbj
title: A set of Keyhole Markup Language polygons to describe site-level ecoregional differences in the plants and animals of Central California Deserts.

description: A set of Keyhole Markup Language (KML) polygons were generated to describe site-level ecological differences in plant and animal communities within California Deserts. All polygons were acquired and generated with Google Earth satellite.
DOI: 10.25345/c5st7f633
title: MassIVE Reanalysis RMSV000000362.166 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000081607 Confetti, LysC-Chymotrypsin HCD [launched by 31fc25a7c92347c2b9f58f8f26be259f]
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/c5st7f64k
title: MassIVE Reanalysis RMSV000000501.7 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080774/PXD001333 [4 out of 4] [launched by 31fc25a7c92347c2b9f58f8f26be259f]
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/f13f4n24
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/c5st7f652
title: MassIVE MSV000091215 - Plant Project Run for Archaeology
title: This was a run of 280+ plant samples collected from New Mexico, Mexico, and Southern Belize.
DOI: 10.25345/c5sx64d9m
title: MassIVE MSV000089620 - Critical Assessment of Metaproteome Investigation (CAMPI): a Multi-Lab Comparison of Established Workflows
title: Metaproteomics, the study of the collective proteome within a microbial ecosystem, has substantially grown over the past few years. This growth comes from the increased awareness that it can powerfully supplement metagenomics and metatranscriptomics analyses. Although metaproteomics is more challenging than single-species proteomics, its added value has already been demonstrated in various biosystems, such as gut microbiomes or biogas plants. Because of the many challenges, a variety of metaproteomics workflows have been developed, yet it remains unclear what the impact of the choice of workflow is on the obtained results. Therefore, we set out to compare several well-established workflows in the first community-driven, multi-lab comparison in metaproteomics: the critical assessment of metaproteome investigation (CAMPI) study. In this benchmarking study, we evaluated the influence of different workflows on sample preparation, mass spectrometry acquisition, and bioinformatic analysis on two samples: a simplified, lab-assembled human intestinal sample and a complex human fecal sample. We find that the same overall biological meaning can be inferred from the metaproteome data, regardless of the chosen workflow. Indeed, taxonomic and functional annotations were very similar across all sample-specific data sets. Moreover, this outcome was consistent regardless of whether protein groups or peptides, or differences at the spectrum or peptide level were used to infer these annotations. Where differences were observed, those originated primarily from different wet-lab methods rather than from different bioinformatic pipelines. The CAMPI study thus provides a solid foundation for benchmarking metaproteomics workflows, and will therefore be a key reference for future method improvement.
DOI: 10.5063/f13j3bdj
title: Zooplankton in offshore Lake Ontario during intensive sampling year 2013

description: Intensive sampling of the offshore waters of Lake Ontario occurs on a five-year cycle as part of the Cooperative Science and Monitoring Initiative (CSMI). This datapackage includes zooplankton data collected in Lake Ontario by various research groups (USGS, OMNRF, DFO Canada, EPA, NYSDEC, USFWS, Cornell) during the CSMI year of 2013 . Research cruises were conducted from April through early November This datapackage includes zooplankton average size (mm), density (#/m3) and biomass (ug dry weight/m3) by species for each site and depth interval sampled. It also includes calculations based on area afor the combined depth stratified tows to get a whole water column estimate and for the tows covering the top 100 m or the whole water column. Other trophic indicators measured during CSMI years include nutrients (total phosphorus, dissolved silica), water clarity (secchi depth), dissolved oxygen, chlorophyll a, and an assessment of phytoplankton, the microbial food web, mysids, and the benthic community. Some rotifer data are also available. These additional data sets are not included in this datapackage. Mysids are available in the datapackage Holda et al. (2017).
DOI: 10.25345/c5sx64f0q
title: MassIVE MSV000090005 - GNPS - Komagataella_phaffii_metabolites_BEH_Amide_10mM_HCOONH4_17min
title: LC-MS/MS metabolomics data of Komagataella phaffii recorded on a Q Exactive HF in positive and negative ion mode. ACQUITY UPLC BEH Amide column 2.1 x 150 mm, 1.7 uM (Waters Corp., Milford, MA) column A: 100% H2O, 10 mM HCOONH4, 0.125% formic acid B: 95% ACN, 5% H2O, 10 mM HCOONH4, 0.125% formic acid.
DOI: 10.5063/f13r0r93
title: Geolocations of all Larrea tridentata shrubs at key ecological areas within the Mojave Desert

description: The geolocation of all Larrea tridentata shrubs within the Mojave Desert. All shrubs have been geolocated via the Google earth satellite.