cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c51r6n83k
title: MassIVE Reanalysis RMSV000000355.7750 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, MS4A10 [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/c51r6n842
title: MassIVE Reanalysis RMSV000000355.7958 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, C3orf46 [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/c51r6n85j
title: MassIVE Reanalysis RMSV000000355.8136 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TRPV3 [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/c51r6n861
title: MassIVE Reanalysis RMSV000000355.8345 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ART1 [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/c51r6n87h
title: MassIVE Reanalysis RMSV000000355.8524 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, MS4A6E [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/c51r6n880
title: MassIVE Reanalysis RMSV000000355.8732 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PITRM1 [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/c51r6n89g
title: MassIVE Reanalysis RMSV000000678.8 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000083043 CPTAC, TCGA Cancer Proteome Study of Breast Tissue [Notes: Phosphoproteome, Mixture: 28] [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/c51r6n90k
title: MassIVE Reanalysis RMSV000000544.2 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080738/PXD003559 [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/c51r6n912
title: MassIVE Reanalysis RMSV000000575.2 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080225/PXD003408 [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/c51r6n92j
title: MassIVE Reanalysis RMSV000000680.19 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000086768 CPTAC Breast Cancer Confirmatory Study [Notes: Proteome, Mixture: 6] [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/c51r6n931
title: MassIVE Reanalysis RMSV000000370.36 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000082644 Proteomics, post-translational modifications, and integrative analyses reveal heterogeneity of molecular mechanisms within medulloblastoma subgroups [Mixture: Fractionated_Phosphoproteome_Plex03] [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/c51r6n94h
title: MassIVE Reanalysis RMSV000000446.20 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080839/PXD004981 [5 out of 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/c51r6n950
title: MassIVE Reanalysis RMSV000000355.8907 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, LAT [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/c51v5bj0n
title: MassIVE MSV000089533 - MRG proteins are shared by multiple protein complexes with distinct functions.
title: - Human TINTIN complex is composed of BRD8/MRGBP/MRG15 or MRGX and a new subunit EP400NL. - Purification of endogenous EP400NL. - Human TINTIN regulated gene expression. - W172A Y235A MRG15 disturbs PALB2 interactions. - W78A F105A MRGBP inhibits the interaction with MRG15.
DOI: 10.25345/c51v5bj14
title: MassIVE MSV000089741 - Cordinated transcriptional and catabolic programs support iron dependent adaptation to RAS-MAPK pathway inhibition in pancreatic cancer_2
title: Whole cell proteomics of human pancreatic ductal adenocarcinoma cells - KP4 - treated for 48hrs with DMSO or 100nM Trametinib. Cell pellets were collected from n=3 biological replicates per condition. The samples were labeled with TMT reagents and combined together, fractionated into 96 fractions, and then pooled back into 24 fractions. 12 of the fractions were run and correspond to the 12 uploaded files.
DOI: 10.25345/c51v5bj2m
title: MassIVE MSV000089918 - Identification of novel kinases of Tau using fluorescence complementation mass spectrometry (FCMS)
title: Hyperphosphorylation of the microtubule-associated protein Tau is a major hallmark of Alzheimer's disease (AD) and other tauopathies. Understanding the protein kinases that phosphorylate Tau is critical for the development of new drugs that target Tau phosphorylation. At present, the repertoire of the Tau kinases remains incomplete, and methods to uncover novel upstream protein kinases are still limited. Here, we apply our newly developed proteomic strategy, fluorescence complementation mass spectrometry (FCMS), to identify novel kinase candidates of Tau. By constructing Tau- and kinase-fluorescent fragment library, we detected 59 Tau-associated kinases, including 23 known kinases of Tau and 36 novel candidate kinases. In the validation phase using in vitro phosphorylation, four kinase candidates, OXSR1, DAPK2, CSK, and ZAP70, displayed the ability to phosphorylate Tau. Furthermore, co-expression of these four kinases along with Tau increased the phosphorylation of Tau in human neuroglioma H4 cells. Taken together, we demonstrate the proteomic strategy to systematically identify potential kinases that can phosphorylate Tau in cells. Our discovery of new candidate kinases of Tau can present new opportunities for developing AD therapeutic strategies.
DOI: 10.25345/c51v5bj33
title: MassIVE MSV000090127 - Active forgetting requires Sickie function in a dedicated dopamine circuit in Drosophila
title: Forgetting is an essential component of the brain memory management system, providing a balance to memory formation processes by removing unused or unwanted memories, or by suppressing their expression. However, the molecular, cellular and circuit mechanisms underlying forgetting are poorly understood. Here we show that the memory suppressor gene, sickie, functions in a single dopamine neuron (DAn) by supporting the process of active forgetting in Drosophila. RNAi knockdown (KD) of sickie impairs forgetting by reducing the Ca2+ influx and DA release from the DAn that promotes forgetting. Co-immunoprecipitation/mass spectrometry analyses identified cytoskeletal and presynaptic active zone (AZ) proteins as candidates that physically interact with Sickie, and a focused RNAi screen of the candidates showed that Bruchpilot (Brp), a presynaptic AZ protein that regulates calcium channel clustering and neurotransmitter release, impairs active forgetting like sickie KD. In addition, overexpression of brp rescued the impaired forgetting of sickie KD, providing evidence that they function in the same process. Moreover, we show that sickie KD in the DAn reduces the abundance and size of AZ markers but increases their number, suggesting that Sickie controls DAn activity for forgetting by modulating the presynaptic AZ structure. Our results identify a new molecular and circuit mechanism for normal levels of active forgetting and reveal a surprising role of Sickie in maintaining presynaptic AZ structure for neurotransmitter release.
DOI: 10.25345/c51v5bj4k
title: MassIVE Reanalysis RMSV000000668.241 - CCMS ProteoCarta MS-GF+ reanalysis of Mus musculus from Mass spectrometry-based draft of the mouse proteome (Male_Olfactory_bulb_phosphoproteome) [launched by 148d2da0ae3046aeb7af52e0653a7b24]
title: CCMS ProteoCarta database search (MSGF+) reanalysis of Mus musculus (Male_Olfactory_bulb_phosphoproteome) (MSV000089856/PXD030983).
DOI: 10.25345/c51v5bj52
title: MassIVE MSV000090351 - Viscum album mother tinctures metabolome
title: Samples: The plants were harvested from 5 different host threes: Abies alba, Malus domestica, Pinis sylvestris, Quercus sp., Ulmus carpinifolia. Samples were harvested in summer and winter seasons.V. album MT was prepared from fresh plant material according to previous methodology described by our group (Anvisa, 2011; Holandino et al., 2020). The fresh material was fragmented into parts smaller than 5 cm and submitted to an ethanolic maceration process for 21 days at room temperature shaking twice a day. The final alcoholic content ranged from 40 to 50% v/v. The mother tinctures were coded according to the respective host tree and the harvest season, as following: Viscum album subsp. abietis from Abies alba in summer (A-17) or winter (A-18), Viscum album subsp. album from Malus domestica in summer (M-17) or winter (M-18), Viscum album subsp. album from Quercus sp. in summer (Q-17) or winter (Q-18), Viscum album subsp. album from Ulmus carpinifolia in summer (U-17) or winter (U-18), Viscum album subsp. austriacum from Pinus sylvestris in summer (P-17) or winter (P-18). 2) Viscum album mother tinctures analysis by liquid chromatography coupled to high-resolution mass spectrometry: Initially, 1.0 g of mother tincture was weighed and transferred to a 5 mL volumetric flask where a solution 9:1 acetonitrile/water with 0.1% v/v formic acid was added. After homogenization, the solution was centrifuged at 7,056 g for 15 minutes and then 200 microliters of each supernatant were removed for analysis in a DionexUltiMate 3000 liquid Chromatography coupled to a hybrid Quadrupole-Orbitrap high-resolution mass spectrometer (Thermo Q-Exactive Plus) equipped with an electrospray ionization source (ESI). Pooled quality control samples (QC) containing 10 microliters of each MT were also prepared. Chromatography separation was performed in a reversed-phase column (Hypersil Gold C18, 100 mm x 2.1 mm x 3.0 micrometers; Thermo Fisher Scientific). Water with 0.1% v/v of formic acid (A) and acetonitrile with 0.1% v/v of formic acid (B) were used as the mobile phases in an elution gradient of: (i) 0-1 min, 10% B; (ii) 1-16 min, 10-95% B; iii) 16-18 min, 95% B; (iv) 18-18.1 min, 95-10% B; (v) 18.1-22 min 10% B. The flow rate was 0.350 microliters/min and the injection volume 5 microliters. Mass spectra were acquired simultaneously in negative and positive ionization modes in the m/z range of 100-1000 at a resolution of 35k (FWHM) followed by sequential mass spectrometry (MS/MS) experiments ddMS2 top 3 (where the 3 most intense ions of each scan were fragmented automatically). The mass spectrometry conditions were the following: spray voltage 3.9 kV for ESI (+) or 3.6kV for ESI (-), ion transfer capillary 300 C, sheath, and auxiliary gases 45 and 15 arbitrary units, respectively. Data were analyzed by the Xcalibur 2.0.7 program (Thermo Scientific, Bremen, Germany) (Holandino et al., 2020).
DOI: 10.25345/c51v5bj6j
title: MassIVE MSV000090735 - Lin_HipBST_antitoxin_P88_LUMOS
title: This dataset consists of 1 raw MS file acquired on a Thermo Scientific Orbitrap Fusion mass spectrometer operated in Data Dependent Acquisition mode. Samples were generated by Jordan Lin. Sample processing, mass spectrometry acquisition and data analysis was performed by Kento Abe. The files are associated with a manuscript submitted for publication by Jordan Lin et al. The main goal of this paper was to characterize a tripartite toxin-antitoxin system in Legionella pneumophila that is highly conserved within the Legionella genus. Alex Ensminger is the corresponding author of the manuscript (alex.ensminger@utoronto.ca); Anne-Claude Gingras should be contacted for questions on this dataset (gingras@lunenfeld.ca). This submission is associated with 6 Supplementary Files (in addition to this README file). Metadata describes the composition of this dataset. Peptides lists all peptide identification evidence. ProteinGroups lists all protein identification evidence. Phospho_STY_Sites lists all phosphorylated peptide identification evidence. Evidence lists all LC-MS features identified by tandem MS. Parameters lists MaxQuant run parameters.
DOI: 10.25345/c51v5bj71
title: MassIVE Reanalysis RMSV000000384.24 - Semi-supervised learning for sensitive open modification spectral library searching
title: This is the reanalysis results of ANN-SoLo + Rescoring as an integrated module. ANN-SoLo spectral library search engine is a tool for efficient open modification searching. ANN-SoLo uses a cascade search strategy to optimally identify both unmodified and modified peptides: in the first stage a standard search is performed to identify unmodified peptides, after which the remaining unidentified spectra are submitted to second stage during which an open search is performed to additionally identify modified peptides. We have augmented thisapproach by natively integrating PSMrescoring into ANN-SoLo using the mokapot Python framework for semi-supervised learning for peptide detection. The repository includes all the search results of analyzing this phosphoproteomics dataset by running the software against MassIVE-KB peptide library (version 2018/06/15). Without rescoring results are located in the Supplementary files.
DOI: 10.25345/c51v5bj8h
title: MassIVE Reanalysis RMSV000000354.6041 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, LZTFL1 [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/c51v5bj90
title: MassIVE Reanalysis RMSV000000354.6248 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PMPCA [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/c51v5bk03
title: MassIVE Reanalysis RMSV000000354.6633 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ANXA9 [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/c51v5bk1k
title: MassIVE Reanalysis RMSV000000354.7020 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CDK5 [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/c51v5bk22
title: MassIVE Reanalysis RMSV000000354.7406 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, MCART1 [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.