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257 results for “Proteomic analysis”
Data from: Dual-compartmental transcriptomic + proteomic analysis of a marine endosymbiosis exposed to environmental change
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Data from: Pangenome and immuno-proteomics analysis of Acinetobacter baumannii strains revealed the core peptide vaccine targets
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Data from: Analysis of the cerebrospinal fluid proteome in Alzheimer's disease
Alzheimer's disease is a neurodegenerative disorder accounting for more than 50% of cases of dementia. Diagnosis of Alzheimer's disease relies on cognitive tests and analysis of amyloid beta, protein tau, and hyperphosphorylated tau in cerebrospinal fluid. Although these markers provide relatively high sensitivity and specificity for early disease detection, they are not suitable for monitor of disease progression. In the present study, we used label-free shotgun mass spectrometry to analyse the cerebrospinal fluid proteome of Alzheimer's disease patients and non-demented controls to identify potential biomarkers for Alzheimer's disease. We processed the data using five programs (DecyderMS, Maxquant, OpenMS, PEAKS, and Sieve) and compared their results by means of reproducibility and peptide identification, including three different normalization methods. After depletion of high abundant proteins we found that Alzheimer's disease patients had lower fraction of low-abundance proteins in cerebrospinal fluid compared to healthy controls (p<0.05). Consequently, global normalization was found to be less accurate compared to using spiked-in chicken ovalbumin for normalization. In addition, we determined that Sieve and OpenMS resulted in the highest reproducibility and PEAKS was the programs with the highest identification performance. Finally, we successfully verified significantly lower levels (p<0.05) of eight proteins (A2GL, APOM, C1QB, C1QC, C1S, FBLN3, PTPRZ, and SEZ6) in Alzheimer's disease compared to controls using an antibody-based detection method. These proteins are involved in different biological roles spanning from cell adhesion and migration, to regulation of the synapse and the immune system.
Data from: Meta-analysis of Arabidopsis thaliana phospho-proteomics data reveals compartmentalization of phosphorylation motifs
Protein (de)phosphorylation plays an important role in plants. To provide a robust foundation for subcellular phosphorylation signaling network analysis and kinase-substrate relationships, we performed a meta-analysis of 27 published and unpublished in-house mass spectrometry–based phospho-proteome data sets for Arabidopsis thaliana covering a range of processes, (non)photosynthetic tissue types, and cell cultures. This resulted in an assembly of 60,366 phospho-peptides matching to 8141 nonredundant proteins. Filtering the data for quality and consistency generated a set of medium and a set of high confidence phospho-proteins and their assigned phospho-sites. The relation between single and multiphosphorylated peptides is discussed. The distribution of p-proteins across cellular functions and subcellular compartments was determined and showed overrepresentation of protein kinases. Extensive differences in frequency of pY were found between individual studies due to proteomics and mass spectrometry workflows. Interestingly, pY was underrepresented in peroxisomes but overrepresented in mitochondria. Using motif-finding algorithms motif-x and MMFPh at high stringency, we identified compartmentalization of phosphorylation motifs likely reflecting localized kinase activity. The filtering of the data assembly improved signal/noise ratio for such motifs. Identified motifs were linked to kinases through (bioinformatic) enrichment analysis. This study also provides insight into the challenges/pitfalls of using large-scale phospho-proteomic data sets to nonexperts.
Data from: iTRAQ-based quantitative proteomic analysis on S100 calcium binding protein A2 in metastasis of laryngeal cancer
Laryngeal cancer is the most frequent neoplasm in the head and neck region, with the vast majority of tumors originating from squamous cells. The survival rate of patients with laryngeal cancer has not improved substantially over the past 25 years. To acquire further knowledge regarding the molecules responsible for laryngeal cancer oncogenesis and, in turn, to improve target therapy,iTRAQ and mass spectrometry analysis were utilized to detect differences in protein expression from 15 paired laryngeal cancer and adjacent non-cancerous tissue samples. Using mass spectrometry analysis, the expression levels of 100 proteins in laryngeal cancer samples were distinct from the non-tumor, non-cancerous samples. Further validation of the differentially expressed proteins S100A2, KRT16, FGB and HSPB1 were carried out using quantitative real-time RT-PCR, immunoblot and immunohistochemistry. Functional analysis of one of the highly expressed proteins, S100 calcium binding protein A2 (S100A2), was performed using RNA interference. As a consequence, attenuated S100A2 expression enhanced the ability of HEp-2 cell lines to migrate and invade in vitro. Our investigation complements the current understanding of laryngeal cancer progression. Furthermore, this study supports the concept that enhanced expression of S100A2 may be a promising strategy in developing novel cancer therapeutic drugs.
Data from: Association of extracellular dNTP utilization with a GmPAP1-like protein in cell wall proteomic analysis of soybean roots
Plant root cell walls are dynamic systems that serve as the first plant compartment responsive to soil conditions, such as phosphorus (P) deficiency. To date, evidence for the regulation of root cell wall proteins by P deficiency remains sparse. In order to facilitate understanding of roles played by soybean (Glycine max) root cell wall proteins (CWPs) in adaptation to P deficiency, iTRAQ proteomic analysis was conducted. A total of 53 CWPs with differential accumulation in response to P deficiency were identified. Subsequent qRT-PCR analysis correlated the accumulation of 21 of 27 up-regulated proteins, and 8 of 26 down-regulated proteins with corresponding gene expression patterns in response to P deficiency. One up-regulated CWP, the purple acid phosphatase 1-like (GmPAP1-like), was functionally characterized. Bean (Phaseolus vulgaris) transgenic hairy roots overexpressing GmPAP1-like displayed increased root associated acid phosphatase activity. Plus, relative growth and P content were significantly enhanced in GmPAP1-like overexpression lines compared to control lines when dNTP was applied as the sole external P source. Taken together, it suggests that modulation of cell wall proteins possibly regulates complex root system changes in response to P deficiency, and that the cell wall localized GmPAP1-like protein is involved in extracellular dNTP utilization in soybean.
Guo et al., Table S20 - Global analysis of the heparin-enriched plasma proteome captures matrisome-associated proteins in Alzheimer's disease
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Proteomic analysis
<p>Proteomic analysis of lyophilized extracellular vesicles and skeletal muscles.</p>
Expression proteomics and histone analysis reveals extensive chromatin network changes and a role for histone tail trimming during cellular differentiation
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Code to reproduce the data analysis performed in the study "EXCRETE workflow enables deep proteomics of the microbial extracellular environment"
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Data accompanying "Standardised workflow for mass spectrometry-based single-cell proteomics data analysis using the scp package"
<p>Data and scripts accompanying the paper <em>Standardised workflow for mass spectrometry-based single-cell proteomics data analysis using scp</em>.</p> <ul> <li>d.zip contains raw MS data from samples run on timsTOF SCP.</li> <li>raw.zip contains raw MS data from samples run on orbitrap mass spectrometers (Orbitrap Fusion Lumos Tribrid and Exploris 240).</li> <li>mzML.zip contains raw MS data in mzML format from all samples.</li> <li>sage.zip contains output results from the sage software (results.sage.tsv and quant.tsv) as well as configuration files (results.json) for both orbitrap (cbio) and timsTOF (giga) data.</li> <li>sample_annotation.zip contains csv files with samples annotation for each acquisition batch and used to build the colData.</li> <li>example_subset.zip contains csv files for short example datasets displayed in the paper.</li> <li>scp.rds file contains the initial QFeatures object of the full dataset with 56 PSM sets corresponding to the 56 MS runs.</li> <li>build_QF_dataset.Rmd file is the script used to build the scp.rds file described above from sage outputs and sample annotation.</li> </ul> <p>These file descriptions are also available in the README.txt file.</p>
Exploring Minor Proteins and Peptides in Human Milk: a Proteomic Analysis Across Lactation Stages
ClinicalTrials.gov study NCT06787963. IPD Sharing: NO. Countries: 1. Publications: 0.
Proteomic Analysis of Mononuclear Cells After a High-Fat, High-Carbohydrate Meal With or Without Orange Juice
ClinicalTrials.gov study NCT02587507. IPD Sharing: Not stated. Countries: 0. Publications: 3.
Identification of Gestational Diabetes Mellitus Related Urinary Biomarkers Along Pregnancy (From Early Pregnancy to Postpartum) by Using Proteomics and Metabolomics Analysis
ClinicalTrials.gov study NCT03246295. IPD Sharing: Not stated. Countries: 0. Publications: 3.
Data from: A proteomic strategy for global analysis of plant protein complexes
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Data from: A quantitative proteomic analysis of cofilin phosphorylation in myeloid cells and its modulation using the LIM kinase inhibitor Pyr1
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Data from: Quantitative proteomic analysis reveals posttranslational responses to aneuploidy in yeast
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Data from: Association of extracellular dNTP utilization with a GmPAP1-like protein in cell wall proteomic analysis of soybean roots
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Data from: iTRAQ-based quantitative proteomic analysis on S100 calcium binding protein A2 in metastasis of laryngeal cancer
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Data from: Analysis of the cerebrospinal fluid proteome in Alzheimer's disease
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ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.