cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5x05xm6x
title: MassIVE Reanalysis RMSV000000355.6971 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, INSIG2 [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/c5x05xm7d
title: MassIVE Reanalysis RMSV000000355.7364 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, SPIN4 [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/c5x05xm8w
title: MassIVE Reanalysis RMSV000000355.7573 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, MTRF1 [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/c5x05xm9c
title: MassIVE Reanalysis RMSV000000355.7749 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, C16orf3 [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/c5x05xn0g
title: MassIVE Reanalysis RMSV000000355.7959 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, RFPL1 [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/c5x05xn1z
title: MassIVE Reanalysis RMSV000000355.8138 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, OR2T2 [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/c5x05xn2f
title: MassIVE Reanalysis RMSV000000355.8346 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PYCRL [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/c5x05xn3x
title: MassIVE Reanalysis RMSV000000355.8733 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TCF20 [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/c5x05xn4d
title: MassIVE Reanalysis RMSV000000677.7 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000081738 Pharmacoproteomic characterisation of human colon and rectal cancer - CRC65 Full Proteomes [Cohort: P013132] [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/c5x05xn5w
title: MassIVE Reanalysis RMSV000000398.26 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000086899 SubCellBarcode Scalable proteome-wide mapping of protein localization and relocalization [BioReplicate: Subcell_MVYB_HCC827_gef_QE1_20160607_TMT10_IPG3-10_7of15ul] [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/c5x05xn6c
title: MassIVE Reanalysis RMSV000000419.11 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080857/PXD002977 [2 out of 7] [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/c5x05xn7v
title: MassIVE Reanalysis RMSV000000512.7 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080829/PXD004163 [1 out of 5] [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/c5x05xn8b
title: MassIVE Reanalysis RMSV000000586.78 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000079526/PXD000865 [38 out of 46], Placenta [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: 10.6084/m9.figshare.21839448
title: Origin and diversification of pheretimoid megascolecid earthworms in the Japanese Archipelago as revealed by mitogenomic phylogenetics

description: The data deposited are sequence files, parition files, and tree files used in our phylogenetic study of pheretimoid megascolecid earthworms (<em>Amynthas</em> group) in the Japanese Archipelago. In addition, photographs of earthworm specimens used in the study are deposited. <br> File name and #file type <br> 1. Assembled mitogenome sequences of 197 specimens from Japan mitogenome_assembled_197taxa.fasta #fasta file <br> 2. Aligned sequences of 15 mitochondrial genes for 221 taxa (mitogenome data) mitogenome_221taxa.fasta #fasta file mitogenome_partition #partition file mitogenome_221taxa.treefile.tre #tree file <br> 3. Aligned sequences of nuclear ribosomal DNA sequences of 197 specimens from Japan (18S-28S data) 18S28S_197taxa.fasta #fasta file 18S28S_partition #partition file 18S28S_197taxa.treefile.tre #tree file <br> 4. Concatenated sequences of mitogenome and 18S-28S mtnu_197taxa.fasta #fasta file mtnu_partition #partition file mtnu_197taxa.tre #tree file <br> 5. Aligned data of mitochondrial COI gene sequenes of 319 taxa COI_319taxa.fasta #fasta file COI_319taxa_iqtree.tre #tree file mitogenome_guide_tree.nwk #tree file <br> 6. Aligned sequences of 15 mitochondrial genes for 184 selected taxa used in the divergence time estimation mitogenome_184taxa.fasta #fasta file mitogenome_partition #partition file mitogenome_184taxa_iqtree.tre #tree file mt184taxa_clocked_tree.tre #tree file <br> 7. Aligned sequences of mitochondrial 16S rDNA and nuclear 28S rDNA genes used for the divergence time estimation in Magascolecidae Megascolecidae_16S-28S_v2R.phy #sequence file in phylip format Megascolecidae_16S-28S_v2Rpartition #partition file Megascolecidae_16S-28S_v2R_iqtree.tre #tree file Megascolecidae_16S-28S_clocked_tree.tre #tree file <br> 8. 8. Photographs of the whole body and body parts for the specimens of Amynthas used in the study List_of_photographs.xlsx #Excel file phogographs.zip #compressed JPG files <br>
DOI: 10.6084/m9.figshare.21839448.v1
title: Origin and diversification of pheretimoid megascolecid earthworms in the Japanese Archipelago as revealed by mitogenomic phylogenetics

description: The data deposited are sequence files, parition files, and tree files used in our phylogenetic study of pheretimoid megascolecid earthworms (<em>Amynthas</em> group) in the Japanese Archipelago. In addition, photographs of earthworm specimens used in the study are deposited. <br> File name and #file type <br> 1. Assembled mitogenome sequences of 197 specimens from Japan mitogenome_assembled_197taxa.fasta #fasta file <br> 2. Aligned sequences of 15 mitochondrial genes for 221 taxa (mitogenome data) mitogenome_221taxa.fasta #fasta file mitogenome_partition #partition file mitogenome_221taxa.treefile.tre #tree file <br> 3. Aligned sequences of nuclear ribosomal DNA sequences of 197 specimens from Japan (18S-28S data) 18S28S_197taxa.fasta #fasta file 18S28S_partition #partition file 18S28S_197taxa.treefile.tre #tree file <br> 4. Concatenated sequences of mitogenome and 18S-28S mtnu_197taxa.fasta #fasta file mtnu_partition #partition file mtnu_197taxa.tre #tree file <br> 5. Aligned data of mitochondrial COI gene sequenes of 319 taxa COI_319taxa.fasta #fasta file COI_319taxa_iqtree.tre #tree file mitogenome_guide_tree.nwk #tree file <br> 6. Aligned sequences of 15 mitochondrial genes for 184 selected taxa used in the divergence time estimation mitogenome_184taxa.fasta #fasta file mitogenome_partition #partition file mitogenome_184taxa_iqtree.tre #tree file mt184taxa_clocked_tree.tre #tree file <br> 7. Aligned sequences of mitochondrial 16S rDNA and nuclear 28S rDNA genes used for the divergence time estimation in Magascolecidae Megascolecidae_16S-28S_v2R.phy #sequence file in phylip format Megascolecidae_16S-28S_v2Rpartition #partition file Megascolecidae_16S-28S_v2R_iqtree.tre #tree file Megascolecidae_16S-28S_clocked_tree.tre #tree file <br> 8. 8. Photographs of the whole body and body parts for the specimens of Amynthas used in the study List_of_photographs.xlsx #Excel file phogographs.zip #compressed JPG files <br>
DOI: 10.25345/c5x05xn9t
title: MassIVE Reanalysis RMSV000000675.178 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000090571 Chemical phosphoproteomics reveals kinase network topologies associated to genotypes and phenotypes of cancer cells [Cohort: HL60_TBCA] [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/c5x05xp0x
title: MassIVE Reanalysis RMSV000000355.8905 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, FAM103A1 [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/c5x34mw5z
title: MassIVE MSV000089534 - 20220524_ChemProp2_Xenobiotic Metabolism_Experiment 2
title: Chemical Proportionality Experiment of B.subtilis and E.coli added with pooled antibiotics (Sulfamethoxazole, sulfadimethoxine, cyproconazole and asulam) to look for potential biotransformation.
DOI: 10.25345/c5x34mw6f
title: MassIVE MSV000089742 - GNPS - 95 actinobacteria strains in ISP-2 liquid media
title: Culture extracts of 95 Streptomyces strains cultured in ISP-2 media. Extracts from supernatant of liquid media (~1.6 mL broth supernatant) were obtained using Oasis HLB SPE and eluted with 80% Acetonitrile. Untargeted LC-MS/MS was acquired in positive ion mode.
DOI: 10.25345/c5x34mw7x
title: MassIVE MSV000090128 - GNPS - NT LC-MS/MS of Mauricio's Hamburger Biotransformations
title: Mauricio's Hamburger Biotransform from gut microbiome via NT LC-MS/MS Mauricio's Hamburger Biotransform from gut microbiome via NT LC-MS/MS
DOI: 10.25345/c5x34mw8d
title: MassIVE Reanalysis RMSV000000668.239 - CCMS ProteoCarta Maestro reanalysis of Mus musculus from Mass spectrometry-based draft of the mouse proteome (Male_Urinary_bladder_proteome) [launched by fb749713ee06486fa322870abe44395d]
title: CCMS ProteoCarta open modification search for modified peptide variants (Maestro) reanalysis of Mus musculus (Male_Urinary_bladder_proteome) (MSV000089856/PXD030983).
DOI: 10.25345/c5x34mw9w
title: MassIVE MSV000090352 - GNPS_Q0302_20220920_Molecular networking parameters
title: Further to these mechanistic insights, the bioengineering potential of an AdoMet proteusin epimerase was explored to introduce stability-promoting d-amino acid residues into a variety of peptides. Leader-independent substrates are so far limited to peptides related to the native precursor core.
DOI: 10.25345/c5x34mx00
title: MassIVE MSV000090558 - Specific-pathogen-free, Germ-free, and monocolonized mouse methanol extracts
title: q exactive hf, 28 min method, comparison between SPF, GF, and monocolonized mice methanol extraction, comparison between ctrl and fiber diet mice methanol extraction
DOI: 10.25345/c5x34mx1g
title: MassIVE Reanalysis RMSV000000357.2 - MSstatsShiny input for MSstatsPTM workflow analysis
title: MSstatsShiny input for dataset 2 of the MSstatsShiny manuscript.
DOI: 10.25345/c5x34mx2z
title: MassIVE MSV000090941 - Pyruvate Kinase M (PKM) binds ribosomes in a poly-ADP ribosylation dependent manner to induce translational stalling
title: In light of the numerous studies identifying post-transcriptional regulators on the surface of the endoplasmic reticulum (ER), we asked whether there are factors that regulate compartment specific mRNA translation in human cells. Using a proteomic survey of spatially regulated polysome interacting proteins, we identified the glycolytic enzyme Pyruvate Kinase M (PKM) as a cytosolic polysome interactor and investigated how it influences mRNA translation. We discovered that the PKM polysome interaction is directly regulated by ADP levels providing a link between carbohydrate metabolism and mRNA translation. By performing enhanced crosslinking immunoprecipitation sequencing we found that PKM crosslinks to mRNA sequences that are immediately downstream of regions that encode lysine and glutamate enriched tracts. Using ribosome footprint protection sequencing, we found that PKM binding to ribosomes causes translational stalling near these lysine and glutamate encoding sequences. Lastly, we observed that PKM recruitment to polysomes is dependent on poly ADP ribosylation activity (PARylation)and may depend on cotranslational PARylation of lysine and glutamate residues of nascent polypeptide chains. Overall, our study uncovers a novel role for PKM in posttranscriptional gene regulation, linking cellular metabolism and mRNA translation.
DOI: 10.25345/c5x34mx3f
title: MassIVE Reanalysis RMSV000000354.6247 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TMEM128 [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/c5x34mx4x
title: MassIVE Reanalysis RMSV000000354.6636 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, RNF166 [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/c5x34mx5d
title: MassIVE Reanalysis RMSV000000354.7022 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CFL1 [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/c5x34mx6w
title: MassIVE Reanalysis RMSV000000354.7405 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, VIT [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/c5x34mx7c
title: MassIVE Reanalysis RMSV000000354.7614 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TREX1 [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.