cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c5tx35g36
title: MassIVE Reanalysis RMSV000000676.56 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000081739 Pharmacoproteomic characterisation of human colon and rectal cancer - CPTAC Full Proteomes [Cohort: CMS4, BioReplicate: Sample_8B] [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/c5tx35g4p
title: MassIVE Reanalysis RMSV000000512.8 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080829/PXD004163 [4 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/c5tx35g55
title: MassIVE Reanalysis RMSV000000382.90 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080596/PXD004242 [24 out of 51] [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/c5tx35g6n
title: MassIVE Reanalysis RMSV000000681.64 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000084248 Proteogenomics Connects Somatic Mutations to Signalling in Breast Cancer [Notes: Phosphoproteome, Mixture: TCGA_A2-A0EV_AN-A0AM_D8-A142_117C_P_BI_20130724_H-PM] [launched by 31fc25a7c92347c2b9f58f8f26be259f]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5tx35g74
title: MassIVE Reanalysis RMSV000000582.8 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of MSV000080856/PXD002650 [4 out of 4] [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/c5tx35g8m
title: MassIVE Reanalysis RMSV000000355.8931 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, NUDT16 [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/c5v11vq17
title: MassIVE MSV000089581 - Fungi from Brazilian amazon - MMSRG
title: samples of fungus from Brazilian amazon, isolated from different sources and analysis of the metabolomic
DOI: 10.25345/c5v11vq2q
title: MassIVE MSV000089789 - Endophytic Fungus Pure Culture (Costa Rica)
title: extract of pure culture broth, first collection (PI: Giselle Tamayo-Castillo, Priscila Chaverri, Ph.D. candidate Efrain Escudero)
DOI: 10.25345/c5v11vq36
title: MassIVE MSV000089966 - The ribosome inhibitor chloramphenicol induces motility deficits in human spermatozoa: a proteomic approach identifies potentially involved proteins
title: Mature spermatozoa are almost completely devoid of cytoplasm; as such it has long been believed that they do not contain ribosomes and are therefore not capable of synthesising proteins. However, since the 1950s, various studies have shown translational activity within spermatozoa, particularly during their in vitro capacitation. But the type of ribosomes involved (cytoplasmic or mitochondrial) is still debated. Here, we investigate the presence and activity of the two types of ribosomes in mature human spermatozoa. By targeting ribosomal RNAs and proteins, we show that both types of ribosomes are localized in the midpiece as well as in the neck and the base of the head of the spermatozoa. We assessed the impact of cycloheximide (CHX) and chloramphenicol (CP), inhibitors of cytoplasmic and mitochondrial ribosomes, respectively, on different sperm parameters. Neither CHX, nor CP impacted sperm vitality, mitochondrial activity (measured through the ATP content), or capacitation (measured through the content in phosphotyrosines). However, increasing CP concentrations induced a decrease in total and progressive motilities as well as on some kinematic parameters while no effect was observed with CHX. A quantitative proteomic analysis was performed by mass spectrometry in SWATH mode to compare the proteomes of spermatozoa capacitated in the absence or presence of the two ribosome inhibitors. Among the ~ 700 proteins identified in the different tested conditions, 3, 3 and 25 proteins presented a modified abundance in the presence of 1 and 2 mg/ml of CHX, and 1 mg/ml of CP, respectively. The observed abundance variations of some CP-down regulated proteins were validated using Multiple-Reaction Monitoring (MRM). Taken together, our results are in favor of an activity of mitochondrial ribosomes. Their inhibition by CP results in a decrease in the abundance of several proteins, at least FUNDC2 and QRICH2, and consequently induces sperm motility deficits.
DOI: 10.25345/c5v11vq4p
title: MassIVE MSV000090175 - Alternative proteoforms and proteoform-dependent assemblies in humans and plants
title: 2 fractionation experiments of HEK293T (ion exchange chromatography). We used this dataset to search for proteoforms using the algorithm described in the accompanied paper.
DOI: 10.25345/c5v11vq55
title: MassIVE Reanalysis RMSV000000668.276 - CCMS ProteoCarta Maestro reanalysis of Mus musculus from Mass spectrometry-based draft of the mouse proteome (Male_Hippocampus_phosphoproteome) [launched by fb749713ee06486fa322870abe44395d]
title: CCMS ProteoCarta open modification search for modified peptide variants (Maestro) reanalysis of Mus musculus (Male_Hippocampus_phosphoproteome) (MSV000089856/PXD030983).
DOI: 10.25345/c5v11vq6n
title: MassIVE MSV000090399 - GNPS - MTBLS874: Marine Biodiscovery Ireland 2017 Samples / BDV10012 Aslia lefevrei
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 sea cucumber Aslia lefevrii. Files are part of the Metabolights dataset MTBLS874.
DOI: 10.25345/c5v11vq74
title: MassIVE MSV000090782 - Development of combined targeted therapies with BTK inhibitors and dasatinib to treat CNS-infiltrating E2A-PBX1+/preBCR+ ALL
title: The translocation t(1;19), coding for the oncogenic fusion protein E2A (TCF3)-PBX1, is involved in the acute lymphoblastic leukemia (ALL) and is associated with pre-B cell receptor (preBCR+) phenotype. Relapse in E2A-PBX1+ ALL patients occurs frequently in central nervous system (CNS). Therefore, there is a medical need for the identification of CNS active substances for the treatment of E2A-PBX1+/preBCR+ ALL. Using unbiased shRNA library screen approaches, we identified Bruton's tyrosine kinase (BTK) as key gene involved in proliferation and in dasatinib sensitivity of E2A-PBX1+/preBCR+ ALL. BTK-depleted cells by shRNAs and sgRNAs showed decreased proliferation of dasatinib-treated E2A-PBX1+/preBCR+ cells compared with control-transduced cells. Moreover, the combination of dasatinib with BTK inhibitors (BTKi) (ibrutinib, acalabrutinib or zanubrutinib) significantly decreased E2A-PBX1+/preBCR+ human and murine cells proliferation, reduced phosphorylation and total protein levels of PLCG2 and BTK and increased the disease-free survival of mice in secondary transplantation assays, reducing especially CNS-leukemic infiltration. Hence, dasatinib with ibrutinib reduced pPLCG2 and pBTK in primary ALL patient samples, including E2A-PBX1+ ALLs. In summary, genetic depletion and pharmacological inhibition of BTK increase the dasatinib sensitivity in human and mouse E2A-PBX1+/preBCR+ ALL and the combination of dasatinib and BTKi is very effective reducing CNS-infiltration of E2A-PBX1+/preBCR+ ALL cells in vivo.
DOI: 10.25345/c5v11vq8m
title: MassIVE Reanalysis RMSV000000354.5911 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, LGALS9 [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/c5v11vq93
title: MassIVE Reanalysis RMSV000000354.6089 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TLE6 [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/c5v11vr06
title: MassIVE Reanalysis RMSV000000354.6295 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, AP1M2 [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/c5v11vr1p
title: MassIVE Reanalysis RMSV000000354.6473 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CLEC1B [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/c5v11vr25
title: MassIVE Reanalysis RMSV000000354.6682 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CSAG1 [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/c5v11vr3n
title: MassIVE Reanalysis RMSV000000354.7067 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CPLX1 [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/c5v11vr44
title: MassIVE Reanalysis RMSV000000354.7451 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CTRL [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/c5v11vr5m
title: MassIVE Reanalysis RMSV000000354.7839 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, DNAJB4 [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/c5v11vr63
title: MassIVE Reanalysis RMSV000000354.8048 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ANXA11 [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: 10.5281/zenodo.5576099
title: Accelerating DNA-PAINT imaging with a deep neural network

description: (RawFrames_P5-IS_20pM.tif) Raw DNA-PAINT SMLM frames with isolated emitters taken on TOM20 labelled MNTB neuronal rat tissue with P5 imaging strand at 20 pM concentration. (Binned_HighDensity_30kpatches.tif and Binned_HighDensity_30kpatches.csv) Artificially summed high-density emitter patches with the corresponding emitter coordinates used for training the DeepSTORM neural network. (DeepSTORM_model_metadata.mat and DeepSTORM_model_weights_best.hdf5) The trained model metadata and weights used for all predicted images in the study. (Figure 4_Large_super-resolution_image.png) The large super-resolution image in Figure 4 and Figure S4. (High-density-frames_Images 1 - 5 .tif) Five high-emitter density raw frames for alpha-tubulin and TOM20 of 400 frames each. (Ground-truth-rendered_Image 1 - 5.tif) Five ground truth images rendered in Picasso (drift-corrected, linked localisations, pixel size 13.37 nm/pixel) for alpha-tubulin and TOM20. (Low density frames for GT images.zip) Five low-emitter density (0.5 nM) raw frames for alpha-tubulin and TOM20 of 10000 frames each which were used to render ground truth images. (Bassoon_Homer_datasets.zip) Three Bassoon and Homer datasets each with a ground truth image and the corresponding high-density raw frames (5 nM, 800 frames).
DOI: 10.5281/zenodo.5704569
title: Accelerating DNA-PAINT imaging with a deep neural network

description: (RawFrames_P5-IS_20pM.tif) Raw DNA-PAINT SMLM frames with isolated emitters taken on TOM20 labelled MNTB neuronal rat tissue with P5 imaging strand at 20 pM concentration. (Binned_HighDensity_30kpatches.tif and Binned_HighDensity_30kpatches.csv) Artificially binned high-density emitter patches with the corresponding emitter coordinates used for training the DeepSTORM neural network. (DeepSTORM_model_metadata.mat and DeepSTORM_model_weights_best.hdf5) The trained model metadata and weights (Figure 4_Large_super-resolution_image.png) The large super-resolution image in Figure 4 and Figure S4
DOI: 10.5281/zenodo.5773037
title: Accelerating DNA-PAINT imaging with a deep neural network

description: (RawFrames_P5-IS_20pM.tif) Raw DNA-PAINT SMLM frames with isolated emitters taken on TOM20 labelled MNTB neuronal rat tissue with P5 imaging strand at 20 pM concentration. (Binned_HighDensity_30kpatches.tif and Binned_HighDensity_30kpatches.csv) Artificially summed high-density emitter patches with the corresponding emitter coordinates used for training the DeepSTORM neural network. (DeepSTORM_model_metadata.mat and DeepSTORM_model_weights_best.hdf5) The trained model metadata and weights used for all predicted images in the study. (Figure 4_Large_super-resolution_image.png) The large super-resolution image in Figure 4 and Figure S4. (High-density-frames_Images 1 - 5 .tif) Five high-density emitter raw frames for alpha-tubulin and TOM20 of 400 frames each.
DOI: 10.5281/zenodo.6940110
title: Accelerating DNA-PAINT imaging with a deep neural network

description: (RawFrames_P5-IS_20pM.tif) Raw DNA-PAINT SMLM frames with isolated emitters taken on TOM20 labelled MNTB neuronal rat tissue with P5 imaging strand at 20 pM concentration. (Binned_HighDensity_30kpatches.tif and Binned_HighDensity_30kpatches.csv) Artificially summed high-density emitter patches with the corresponding emitter coordinates used for training the DeepSTORM neural network. (DeepSTORM_model_metadata.mat and DeepSTORM_model_weights_best.hdf5) The trained model metadata and weights used for all predicted images in the study. (Figure 4_Large_super-resolution_image.png) The large super-resolution image in Figure 4 and Figure S4. (High-density-frames_Images 1 - 5 .tif) Five high-emitter density raw frames for alpha-tubulin and TOM20 of 400 frames each. (Ground-truth-rendered_Image 1 - 5.tif) Five ground truth images rendered in Picasso (drift-corrected, linked localisations, pixel size 13.37 nm/pixel) for alpha-tubulin and TOM20. (Low-density-frames_Image 1-4_0.5nM.tif) Three or four low-emitter density (0.5 nM) raw frames for alpha-tubulin and TOM20 of 10000 frames each which was used to render ground truth images.
DOI: 10.5281/zenodo.6966132
title: Accelerating DNA-PAINT imaging with a deep neural network

description: (RawFrames_P5-IS_20pM.tif) Raw DNA-PAINT SMLM frames with isolated emitters taken on TOM20 labelled MNTB neuronal rat tissue with P5 imaging strand at 20 pM concentration. (Binned_HighDensity_30kpatches.tif and Binned_HighDensity_30kpatches.csv) Artificially summed high-density emitter patches with the corresponding emitter coordinates used for training the DeepSTORM neural network. (DeepSTORM_model_metadata.mat and DeepSTORM_model_weights_best.hdf5) The trained model metadata and weights used for all predicted images in the study. (Figure 4_Large_super-resolution_image.png) The large super-resolution image in Figure 4 and Figure S4. (High-density-frames_Images 1 - 5 .tif) Five high-emitter density raw frames for alpha-tubulin and TOM20 of 400 frames each. (Ground-truth-rendered_Image 1 - 5.tif) Five ground truth images rendered in Picasso (drift-corrected, linked localisations, pixel size 13.37 nm/pixel) for alpha-tubulin and TOM20. (Low density frames for GT images.zip) Five low-emitter density (0.5 nM) raw frames for alpha-tubulin and TOM20 of 10000 frames each which were used to render ground truth images. (Bassoon_Homer_datasets.zip) Three Bassoon and Homer datasets each with a ground truth image and the corresponding high-density raw frames (5 nM, 800 frames).
DOI: 10.25345/c5v11vr7k
title: MassIVE Reanalysis RMSV000000354.8226 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PRG2 [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.