cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5gm81z40
title: MassIVE Reanalysis RMSV000000679.46 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000086793 CPTAC LUAD Discovery Study [Notes: Phosphoproteome, Mixture: 17] [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/c5gm81z5g
title: MassIVE Reanalysis RMSV000000676.91 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000081739 Pharmacoproteomic characterisation of human colon and rectal cancer - CPTAC Full Proteomes [Cohort: CMS1, BioReplicate: Sample_1F] [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/c5gq6r61n
title: MassIVE MSV000089784 - Mouse lung lipidomics response to a wild type infectious clone of H7N9 Influenza virus and mutants
title: Lipidomics data from mouse lung; Treated with wild-type and mutant H7N9 and mockulum; Time points 1, 2, 4 & 7 days; 5 biological replicates
DOI: 10.25345/c5gq6r624
title: MassIVE MSV000090170 - Cell surface makeup of NECTIN1-deficient and proficient human melanoma cells in response to serum withdrawal
title: Cell-surface proteins were purified from A375 human melanoma cells expressing a control shRNA (n=3) or an shRNA against NECTIN1 (n=3) and cultured in the absence of serum.
DOI: 10.25345/c5gq6r63m
title: MassIVE Reanalysis RMSV000000668.279 - CCMS ProteoCarta Maestro reanalysis of Mus musculus from Mass spectrometry-based draft of the mouse proteome (Male_Large_intestine_phosphoproteome) [launched by fb749713ee06486fa322870abe44395d]
title: CCMS ProteoCarta open modification search for modified peptide variants (Maestro) reanalysis of Mus musculus (Male_Large_intestine_phosphoproteome) (MSV000089856/PXD030983).
DOI: 10.25345/c5gq6r643
title: MassIVE MSV000090394 - GNPS - MTBLS874: Marine Biodiscovery Ireland 2017 Samples / BDV10008 Suberites ficus
title: The outcomes of this project are to identify bioactive marine natural products from Irish marine life. This specific dataset contains LC-MS/MS spectra from tissue of the marine sponge Suberites ficus. Files are part of the Metabolights dataset MTBLS874.
DOI: 10.25345/c5gq6r65k
title: MassIVE MSV000090600 - A ubiquitination cascade regulating the integrated stress response and survival in carcinomas
title: Cervia LD, Shibue T, Borah AA, Gaeta B, He L, Leung L, Li N, Moyer S, Shim B, Dumont N, Gonzalez A, Bick N, Kazachkova M, Dempster JM, Krill-Burger JM, Piccioni F, Udeshi ND, Olive ME, Carr SA, Root DE, McFarland JM, Vazquez F, Hahn WC. 2022. Systematic identification of signaling pathways required for the fitness of cancer cells will facilitate the development of new cancer therapies. We used gene essentiality measurements in 726 cancer cell lines to identify selective co-essentiality modules and found a ubiquitination cascade composed of UBA6, BIRC6, KCMF1 and UBR4, which encode an E1, E2 and two heterodimeric E3 subunits, respectively, as required for the survival of a subset of epithelial tumors. Suppressing BIRC6 in cell lines dependent on this ubiquitin ligase complex led to a substantial reduction in cell fitness in vitro and potent tumor regression in vivo. Mechanistically, BIRC6 suppression resulted in selective activation of the integrated stress response (ISR) signaling by upregulation of the heme-regulated inhibitor (HRI), a direct ubiquitination target of the UBA6/BIRC6/KCMF1/UBR4 complex. These observations highlight a ubiquitin ligase complex regulating ISR and identify this complex as a potential therapeutic target for a subset of epithelial cancers. Systematic identification of signaling pathways required for the fitness of cancer cells will facilitate the development of new cancer therapies. We used gene essentiality measurements in 726 cancer cell lines to identify selective co-essentiality modules and found a ubiquitination cascade composed of UBA6, BIRC6, KCMF1 and UBR4, which encode an E1, E2 and two heterodimeric E3 subunits, respectively, as required for the survival of a subset of epithelial tumors. Suppressing BIRC6 in cell lines dependent on this ubiquitin ligase complex led to a substantial reduction in cell fitness in vitro and potent tumor regression in vivo. Mechanistically, BIRC6 suppression resulted in selective activation of the integrated stress response (ISR) signaling by upregulation of the heme-regulated inhibitor (HRI), a direct ubiquitination target of the UBA6/BIRC6/KCMF1/UBR4 complex. These observations highlight a ubiquitin ligase complex regulating ISR and identify this complex as a potential therapeutic target for a subset of epithelial cancers.
DOI: 10.25345/c5gq6r662
title: MassIVE MSV000090777 - Data-Independent Acquisitions Uncover Kidney Proteome Remodeling during Ischemic Reperfusion Kidney Injury using a Fast-scanning ZenoTOF 7600
title: Acute kidney injury (AKI) manifests as a major health concern particularly for the elderly and understanding related proteome changes is critical for prevention and development of novel therapeutics to recover kidney function, and to mitigate the susceptibility for recurrent AKI, or development of chronic kidney disease. In this study, mouse kidneys were subjected to ischemia-reperfusion injury while the contralateral kidneys remained uninjured to assess changes in the kidney proteome. A fast-scanning ZenoTOF 7600 mass spectrometer was used for comprehensive data-independent acquisition (DIA) for protein identification and quantification. Short microflow gradients, and the generation of a deep kidney-specific spectral library allowed for comprehensive and high-throughput assays. Upon AKI the kidney proteome was completely remodeled, and over half of the 3,945 quantified protein groups changed significantly. Downregulated proteins in the injured kidney were involved in energy production, including numerous peroxisomal matrix proteins, many related to lipid metabolism, such as ACOX1, CAT, EHHADH, ACOT4, ACOT8, and Scp2. Injured mice exhibited severely declined health. The comprehensive and sensitive kidney-specific DIA assays, highlighted in this work, feature high-throughput analytical capabilities to achieve deep coverage of the kidney proteome, and will serve as useful tool for the development of novel therapeutics aimed at remediating kidney function.
DOI: 10.25345/c5gq6r67j
title: MassIVE Reanalysis RMSV000000354.5906 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PSKH2 [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/c5gq6r681
title: MassIVE Reanalysis RMSV000000354.6290 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, SUCLG1 [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/c5gq6r69h
title: MassIVE Reanalysis RMSV000000354.6678 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ASB2 [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/c5gq6r70m
title: MassIVE Reanalysis RMSV000000354.7063 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, NUDT12 [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/c5gq6r713
title: MassIVE MSV000090951 - Identification of Nrg1 enhancer binding proteins
title: Hyperglycemia is a risk factor for breast cancer-related morbidity and mortality. Hyperglycemia induces Neuregulin 1 (Nrg1) overexpression in breast cancer, which subsequently promotes tumor progression. However, molecular mechanisms underlying hyperglycemia-induced Nrg1 overexpression remain poorly understood. Here, We used DNA-protein pull-down using Nrg1 enhancer sequence as bait followed by LC/MS and identified RBPJ as a key component of the Nrg1 enhanceosome. We show that hyperglycemia causes active histone modifications at the Nrg1 enhancer, forming enhanceosome complexes where RBPJ, P300, and SETD1A are recruited to upregulate Nrg1 expression.
DOI: 10.25345/c5gq6r72k
title: MassIVE Reanalysis RMSV000000354.7446 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, AFF4 [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/c5gq6r732
title: MassIVE Reanalysis RMSV000000354.7656 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, OVOL1 [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/c5gq6r74j
title: MassIVE Reanalysis RMSV000000354.8043 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, BTRC [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/c5gq6r751
title: MassIVE Reanalysis RMSV000000354.8430 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ATPBD4 [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/c5gq6r76h
title: MassIVE Reanalysis RMSV000000354.8817 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, BRCA1 [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/c5gq6r770
title: MassIVE Reanalysis RMSV000000354.9207 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ARRB2 [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/c5gq6r78g
title: MassIVE Reanalysis RMSV000000354.9416 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, KLK3 [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/c5gq6r79z
title: MassIVE Reanalysis RMSV000000354.9592 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, RP2 [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/c5gq6r802
title: MassIVE Reanalysis RMSV000000354.9798 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, MOS [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/c5gq6r81j
title: MassIVE Reanalysis RMSV000000354.10183 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TFR2 [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/c5gq6r821
title: MassIVE Reanalysis RMSV000000354.10575 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, SYT17 [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/c5gq6r83h
title: MassIVE Reanalysis RMSV000000354.10957 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, SSX3 [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/c5gq6r840
title: MassIVE Reanalysis RMSV000000354.11344 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ASB6 [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/c5gq6r85g
title: MassIVE Reanalysis RMSV000000354.11549 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, INTS10 [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/c5gq6r86z
title: MassIVE Reanalysis RMSV000000354.11722 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PRPF3 [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/c5gq6r87f
title: MassIVE Reanalysis RMSV000000355.4661 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, FAM173B [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.