cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5xk84z7c
title: MassIVE Reanalysis RMSV000000355.7628 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, DPY19L2P1 [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/c5xk84z8v
title: MassIVE Reanalysis RMSV000000355.7835 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, GJB6 [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/c5xk84z9b
title: MassIVE Reanalysis RMSV000000355.8013 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, OR1M1 [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/c5xk8500v
title: MassIVE Reanalysis RMSV000000355.8221 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ODF3 [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/c5xk8501b
title: MassIVE Reanalysis RMSV000000355.8609 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, RABL5 [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/c5xk8502t
title: MassIVE Reanalysis RMSV000000586.49 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000079526/PXD000865 [2 out of 46], Testis [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/c5xk85039
title: MassIVE Reanalysis RMSV000000444.18 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080868/PXD003523 [2 out of 14] [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/c5xk8504s
title: MassIVE Reanalysis RMSV000000402.9 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080825/PXD002612 [3 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/c5xk85058
title: MassIVE Reanalysis RMSV000000626.6 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000086369 The exploration of Missing Proteins by a combination approach to enrich the low abundance membrane proteins from several cancer cell lines [Subject: HeLa] [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/c5xk8506r
title: MassIVE Reanalysis RMSV000000371.2 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080714/PXD001798 [1 out of 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/c5xk85077
title: MassIVE Reanalysis RMSV000000473.30 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000079830/PXD000815 [11 out of 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/c5xk8508q
title: MassIVE Reanalysis RMSV000000366.110 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000086387 A Quantitative Proteome Map of the Human Body, TMT10 MS3 [Mixture: 39] [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/c5xk85096
title: MassIVE MSV000091214 - Octanedioic-acid supplementation protects from acute kidney injury via stimulation of renal peroxisomal activity over mitochondrial
title: Lysine succinylation is a posttranslational modification associated with the control of several diseases, including acute kidney injury (AKI). Hypersuccinylation favors peroxisomal fatty acid oxidation (FAO) instead of mitochondrial. In addition, the medium-chain fatty acids (MCFAs) dodecanedioic acid (DC12) and octanedioic acid (DC8), upon FAO, generate succinyl-CoA, resulting in hypersuccinylation. To test the protective roles of MCFAs during AKI, mice were fed with control, 10% DC12, or 10% DC8 diet, then, subjected to either ischemic-AKI , or cisplatin-AKI models. Supplementation was provided until sacrifice. Biochemical, histologic, genetic, and proteomic analysis were performed, the latter involving a lysine-succinylome-based analysis. Both DC8 and DC12 prevented the rise of AKI markers in mice that underwent renal injury. However, DC8 was even more protective against AKI than DC12. Finally, succinylome analysis evidenced that the kidneys of DC8-fed mice showed an extensive succinylation of peroxisomal activity-related proteins, and a decline in mitochondrial FAO, in comparison to control-fed mice. DC8 supplementation drives renal protein hypersuccinylation, promoting a shift from mitochondrial to peroxisomal FAO, and protecting against AKI. DC8 is convenient, inexpensive, easily administered, and efficient. We believe this study could be translated in the future to clinical settings, which would highly benefit patients at high risk of AKI.
DOI: 10.25345/c5xp6v730
title: MassIVE MSV000089619 - SRC inhibition enables formation of a growth suppressive MAGI1-PP2A complex in isocitrate dehydrogenase mutant cholangiocarcinoma
title: The dataset comprises proteome mapping and phosphoproteome mapping of IDH1m ICC cells SNU-1079 and RBE with SRC WT or SRC T341I mutation and IDH1 WT lines HuCCT1 and CCLP1 were treated with Dasatinib (20nM) or vehicle for 1 hour. Quantitative proteomics was performed using TMT- labeling and the SPS-powered MS3. Phosphopeptides were enriched with titanium dioxide and phosphotyrosine antibody-conjugated beads. Proteome mapping: Two TMT sets were analyzed: Set 1: Kugel_proteomics_set_1_fraction_1.raw to Kugel_proteomics_set_1_fraction_12.raw: TMT labeling: HUCCT1 Dasatinib 20mM (128n), CCLP1 DMSO (128c), SNU1079 Dasatinib 20mM 1 (129n), SNU1079 SRCT341I DMSO 1 (129c), SNU1079 DMSO 1 (130n), SNU1079 SRCT341I Dasatinib 20mM 1 (130c), bridge (131). Set 1: Kugel_proteomics_set_2_fraction_1.raw to Kugel_proteomics_set_2_fraction_12.raw: TMT labeling: HUCCT1 DMSO (128n), CCLP1 Dasatinib 20mM (128c), SNU1079 SRCT341I DMSO 2 (129n), SNU1079 Dasatinib 20mM 2 (129c), SNU1079 SRCT341I Dasatinib 20mM 2 (130n), SNU1079 DMSO 2 (130c), bridge (131). Phosphoproteome mapping: Two experiments were performed: Experiment 1 (one TMT set): Kugel_phosphoproteomics_set_1_fraction_1.raw to Kugel_phosphoproteomics_set_1_fraction_12 and Kugel_phosphoproteomics_set_1_pY. TMT labeling: SNU1079 SRCT341I DMSO (126), SNU1079 SRCT341I Dasatinib (127n), SNU1079 DMSO (127c), SNU1079 Dasatinib (128n). Experiment 2 (one TMT sets): Kugel_phosphoproteomics_set_2_1 to Kugel_phosphoproteomics_set_2_24 and Kugel_phosphoproteomics_set_2_pY. TMT labeling: RBE DMSO (127n), RBE Dasatinib (127c), RBE SRCT341I DMSO (128n), RBE SRCT341I Dasatinib (128c), HuCCT1 DMSO (129n), HuCCT1 Dasatinib (129c), CCLP1 DMSO (130n), CCLP1 Dasatinib (130c).
DOI: 10.25345/c5xp6v74g
title: MassIVE MSV000090004 - GNPS - Komagataella_phaffii_metabolites_BEH_Amide_10mM_HCOONH4_15min
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 100 mm, 1.7 uM (Waters Corp., Milford, MA) column A: 100% H2O, 10 mM HCOONH4, 0.1% formic acid B: 80% ACN, 20% H2O, 10 mM HCOONH4, 0.1% formic acid.
DOI: 10.25345/c5xp6v75z
title: MassIVE Reanalysis RMSV000000668.115 - CCMS ProteoCarta Maestro reanalysis of Mus musculus from Mass spectrometry-based draft of the mouse proteome (Cell_line_9580) [launched by fb749713ee06486fa322870abe44395d]
title: CCMS ProteoCarta open modification search for modified peptide variants (Maestro) reanalysis of Mus musculus (Cell_line_9580) (MSV000089856/PXD030983).
DOI: 10.25345/c5xp6v76f
title: MassIVE Reanalysis RMSV000000666.39 - CCMS ProteoCarta Maestro reanalysis of Zea mays from Growth heterosis in maize is associated with expression heterosis of chloroplast ribosomes (Mixture MatureLeafBlade) [launched by 25d00eb062cf42859106267f298c2eec]
title: CCMS ProteoCarta open modification search for modified peptide variants (Maestro) reanalysis of Zea mays (Mixture MatureLeafBlade) from MSV000085916.
DOI: 10.25345/c5xp6v77x
title: MassIVE MSV000090436 - Matrix stiffness regulates the protein profile of extracellular vesicles of pancreatic cancer cells 30-09-2022
title: The fibrotic stroma characterizing pancreatic ductal adenocarcinoma (PDAC) derives from a progressive rigidification of PDAC tissue, which induces epithelial mesenchymal transition and promotes metastatic dissemination. The aim of this study was to investigate the influence of matrix stiffness on PDAC progression analysing the proteome of PDAC-derived extracellular vesicles (EVs). PDAC derived cell lines (mPDAC and KPC) were grown on synthetic supports with a stiffness of 3 and 12 kPa and the protein expression levels in cell-derived EVs were analyzed by a quantitative MSE label-free mass spectrometry approach. Our analysis figured out 15 differentially expressed proteins (DEPs) in mPDAC-EVs and 20 DEPs in KPC-EVs in response to matrix rigidification. Up-regulated proteins participate to the processes of matrix remodeling, cell adhesion, migration and metabolism. A multimodal network analysis revealed that the majority of DEPs are strongly related to pancreatic cancer. Interestingly, among the DEPs, 11 related genes (ACTB/ANXA7/C3/IGSF8/LAMC1/LGALS3/PCD6IP/SFN/TPM3/VARS/YWHAZ) for mPDAC-EVs and 9 genes (ACTB/ALDH2/GAPDH/HNRNPA2B/ITGA2/NEXN/PKM/RPN1/S100A6) for KPC-EVs were significantly overexpressed in tumor-derived tissues according to gene expression profiling interaction analysis (GEPIA). In particular, investigating the potential clinical relevance of these data, the cluster of ITGA2, GAPDH and PKM genes displayed an adverse effect (p &lt; 0.05) on the disease-free survival of PDAC patients.
DOI: 10.25345/c5xp6v78d
title: MassIVE MSV000090612 - Anticancer compounds from Annona muricata target protein glycosylation processes in lung cancer cells_glycoproteomics
title: Treatment of A549 lung cancer cells with novel cytotoxic compounds isolated from Annona muricata. Mass spectrometry data was obtained for proteomics and glycoproteomics.
DOI: 10.25345/c5xp6v79w
title: MassIVE MSV000090820 - GNPS - ONR plasma - sleep disruption study
title: Data were acquired using a C18 column (RP) in positive ionization mode.
DOI: 10.25345/c5xp6v800
title: MassIVE Reanalysis RMSV000000354.6127 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, FANK1 [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/c5xp6v81g
title: MassIVE Reanalysis RMSV000000354.6511 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TLE3 [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/c5xp6v82z
title: MassIVE Reanalysis RMSV000000354.6900 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, UBE2M [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/c5xp6v83f
title: MassIVE Reanalysis RMSV000000354.7280 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, EEF1G [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/c5xp6v84x
title: MassIVE Reanalysis RMSV000000354.7490 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, C22orf31 [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/c5xp6v85d
title: MassIVE Reanalysis RMSV000000354.7669 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, VIPR2 [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/c5xp6v86w
title: MassIVE Reanalysis RMSV000000354.7877 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, FHL3 [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/c5xp6v87c
title: MassIVE Reanalysis RMSV000000354.8263 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, HK1 [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/c5xp6v88v
title: MassIVE Reanalysis RMSV000000354.8650 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, SLC38A6 [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.