cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6073/pasta/58dfdebfd1b6440510def2394ab92c53
title: Forest Inventory of a Northern Hardwood Forest: Bird Area, 1991 - present, Hubbard Brook Experimental Forest

description: The forest inventory surveys in the bird area were initiated in 1981
 and transects were made permanent in 1991 by Tom Siccama who created
 and designed this tree survey. The inventory is representative of
 approximately 2.5 km2 of mid elevation northern hardwood forest. The
 data set is particularly geared toward producing accurate mortality
 and recruitment estimates. It consists of a total inventory of all
 trees greater than or equal to 10 cm dbh within each of four 10 m wide
 belt transects. The parallel transects are placed approximately 200 m
 apart and 290° bearing in an east-west direction for 2200 to 2900 m.
 In 1991, each live stem greater than or equal to 10 cm dbh was tagged
 with a unique number. Tree vigor is assessed every two years and
 diameter is remeasured every ten years. Every two years, new tags are
 placed on stems that have grown into the 10 cm diameter class. A
 survey of smaller trees (greater than or equal to 2 to less than 10 cm
 dbh) was first taken in 1991 and is resurveyed every ten years. This
 dataset includes 1991 and subsequent samplings. Data from an earlier
 sampling in 1981 can be found in:

 
 Sherry, T., D. Holmes, and T. Siccama. 2019. Forest Inventory of a
 Northern Hardwood Forest: Bird Area at the Hubbard Brook Experimental
 Forest, 1981 ver 7. Environmental Data Initiative.
 https://doi.org/10.6073/pasta/206b98f6553f1ff95cf584dd2185554e
 (Accessed 2021-09-16).

 
 These data were gathered as part of the Hubbard Brook Ecosystem Study
 (HBES). The HBES is a collaborative effort at the Hubbard Brook
 Experimental Forest, which is operated and maintained by the USDA
 Forest Service, Northern Research Station.

 
 These data have been used in the following publication:

 
 Siccama, T.G., Fahey, T.J., Johnson, C.E., Sherry, T.W., Denny, E.G.,
 Girdler, E.B., Likens, G.E., and Schwarz, P.A. 2007. Population and
 biomass dynamics of trees in a northern hardwood forest at Hubbard
 Brook. Can. J. For. Res. 37(4): 737–749. doi:10.1139/X06-261.
DOI: 10.6084/m9.figshare.24081663.v1
title: Novel taxonomic and functional diversity of eight bacteria from the upper digestive tract of chicken.

description: Supplementary Material for 'Novel taxonomic and functional diversity of eight bacteria from the upper digestive tract of chicken', as described in International Journal of Systematic and Evolutionary Microbiology.
DOI: 10.6084/m9.figshare.24081663
title: Novel taxonomic and functional diversity of eight bacteria from the upper digestive tract of chicken.

description: Supplementary Material for 'Novel taxonomic and functional diversity of eight bacteria from the upper digestive tract of chicken', as described in International Journal of Systematic and Evolutionary Microbiology.
DOI: 10.57745/zmf2ko
title: Replication data.rar

description: :unav
DOI: 10.25345/c5v698m3k
title: MassIVE Reanalysis RMSV000000355.7349 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CCHCR1 [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/c5v698m42
title: MassIVE Reanalysis RMSV000000355.7735 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CCL16 [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/c5v698m5j
title: MassIVE Reanalysis RMSV000000355.8122 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PPP1R14D [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/c5v698m61
title: MassIVE Reanalysis RMSV000000355.8332 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ATP1A4 [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/c5v698m7h
title: MassIVE Reanalysis RMSV000000355.8508 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, VPS25 [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/c5v698m80
title: MassIVE Reanalysis RMSV000000355.8717 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TMED8 [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/c5v698m9g
title: MassIVE Reanalysis RMSV000000679.8 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000086793 CPTAC LUAD Discovery Study [Notes: Phosphoproteome, Mixture: 11] [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/c5v698n0k
title: MassIVE Reanalysis RMSV000000451.12 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000083957 Enrichment strategy for searching missing protein, low molecular weight proteins, glycine SDS-PAGE [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/c5v698n12
title: MassIVE Reanalysis RMSV000000681.44 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000084248 Proteogenomics Connects Somatic Mutations to Signalling in Breast Cancer [Notes: Phosphoproteome, Mixture: TCGA_A2-A0YF_BH-A0DD_BH-A0E9_117C_P_BI_20131104_H-PM] [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/c5v698n2j
title: MassIVE Reanalysis RMSV000000676.63 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000081739 Pharmacoproteomic characterisation of human colon and rectal cancer - CPTAC Full Proteomes [Cohort: NA, BioReplicate: Sample_3J] [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/c5v698n31
title: MassIVE Reanalysis RMSV000000679.38 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000086793 CPTAC LUAD Discovery Study [Notes: Phosphoproteome, Mixture: 1] [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/c5v698n4h
title: MassIVE Reanalysis RMSV000000404.15 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080772/PXD003514 [8 out of 8] [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/c5v698n50
title: MassIVE Reanalysis RMSV000000362.182 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000081607 Confetti, Chymotrypsin-Trypsin 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/c5v698n6g
title: MassIVE Reanalysis RMSV000000355.8891 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, KCNIP1 [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/c5v97zw1r
title: MassIVE MSV000089511 - GNPS- Primary metabolome of corn roots exposed to drought and ambient soil moisture treatments, as affected by cross-inoculation of rhizobiota from a congeneric species
title: Primary metabolome of corn roots exposed to drought and ambient soil moisture treatments, as affected by cross-inoculation of rhizobiota from a congeneric species
DOI: 10.25345/c5v97zw27
title: MassIVE MSV000089727 - GC-MS Epipedobates-Skin-Crude metanol 2005
title: Specimens collected between June-August 2005. In the localities of E. Tricolor: Palo Seco Moraspungo E. Darwinwallacei: Mindo E. Boulengeri: Bourbon Emeralds E. anrhonyi: Santa Isabel-Azuay
DOI: 10.25345/c5v97zw3q
title: MassIVE MSV000089904 - GNPS Aspergillus oryzae RIB40 in different media
title: Aspergillus oryzae RIB40 grown in YPD, AF6 and EG:JM media
DOI: 10.25345/c5v97zw46
title: MassIVE MSV000090113 - LC-MSMS of plasma DeoxyCeramide (m18:1/24:0)
title: Characterization of human plasma deoxyceramide m18:1/24:0 associated with type two diabetes in the Jackson Heart Study cohort.
DOI: 10.25345/c5v97zw5p
title: MassIVE Reanalysis RMSV000000668.223 - CCMS ProteoCarta Maestro reanalysis of Mus musculus from Mass spectrometry-based draft of the mouse proteome (Male_Spinal_cord_proteome) [launched by fb749713ee06486fa322870abe44395d]
title: CCMS ProteoCarta open modification search for modified peptide variants (Maestro) reanalysis of Mus musculus (Male_Spinal_cord_proteome) (MSV000089856/PXD030983).
DOI: 10.25345/c5v97zw65
title: MassIVE MSV000090337 - Profiling The Molecular Mechanisms Of A Low Cost Extracellular Matrix Derived Hydrogel Treatment For Idiopathic Pulmonary Fibrosis Models _Proteomics
title: Proteomics analysis of bleomycin-exposed rat lungs treated with different concentrations of decellularized porcine lung extracellular matrix-derived hydrogel 7 days later. Each sample corresponded to one animal lung. Samples labeled T1, T2, and T3 were the control (Fibrosis) group that received 0 mg/mL of ECM-derived hydrogel. Samples labeled T4, T5, and T6 were the (Tratamento 1) group that received 1 mg/mL of the ECM-derived hydrogel treatment. Samples labeled T7, T8, and T9 were the (Tratamento 2) group that received 2 mg/mL of the ECM-derived hydrogel treatment.
DOI: 10.25345/c5v97zw84
title: MassIVE MSV000090927 - LC-MS/MS of Lrrc6 knock out mouse testis
title: LRRC6 has been reported as an assembly factor for dynein arms in the cytoplasm of motile ciliated cells, and when mutated, dynein arm components were located in cytoplasm. Previously, in the absence of LRRC6 in multi-ciliated cells, parts of ODA and IDA components were not present in cilium. We made Lrrc6 knock out mice, and prepared the most motile cilia-abundant tissue, testis, to identify whether the overall protein expresseion pattern is changed without LRRC6. 5 wild type and 6 Lrrc6 KO mice testis were homogenized by 8M urea, reduced by tris (2-carboxyethyl) phosphine hydrochloride (TCEP), and alkylated by iodoacetamide (IAA). The proteins were centrifuged at 21,000 x g to remove pellets. After the buffer of the supernatants were exchanged, concentration was quantified by measuring the absorbance at 205nm by the NanoDropTM 2000c spectrophotometer (Thermo Fisher Scientific) and adjusted to 2.2mg/mL. The protein samples were digested with trypsin at 37 degrees Celsius overnight using 1:50 trypsin. The tryptic peptide samples were labeled with TMT11 with TMT/protein ratio (w/w) of 1:1 for 30 minutes and equal amount of each labeled samples were pooled. The pooled peptide samples of 11-plex were fractionated by a basic RPLC and 50cm C18 capillary column. The peptides were eluted in a 52-minute gradient, and 42 fractions were collected every min and concatenated to 10 fractions. Peptides were detected using Orbitrap Fusion Lumos. The raw-files were imported to IP2 pipeline, which searched MS data against the UniProt Mus musculus database downloaded from the European Bioinformatics Institute website (https://www.uniprot.org/proteomes/UP000000589) and filtered MS data with the default parameters (Codrea and Nahnsen, 2016).
DOI: 10.25345/c5v97zw9m
title: MassIVE Reanalysis RMSV000000354.6027 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, SUCLA2 [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/c5v97zx0q
title: MassIVE Reanalysis RMSV000000354.6233 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, MGRN1 [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/c5v97zx16
title: MassIVE Reanalysis RMSV000000354.6411 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TRPV5 [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/c5v97zx2p
title: MassIVE Reanalysis RMSV000000354.6620 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, RBFA [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/c5v97zx35
title: MassIVE Reanalysis RMSV000000354.7006 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, NUDT6 [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/c5v97zx4n
title: MassIVE Reanalysis RMSV000000354.7390 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, P4HA3 [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/c5v97zx54
title: MassIVE Reanalysis RMSV000000354.7776 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, LFNG [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.