MASH Native Demo Data for Users
Ontology highlight
ABSTRACT:
INSTRUMENT(S): maXis II, solariX
ORGANISM(S): Bos Taurus (ncbitaxon:9913) Sus Scrofa (ncbitaxon:9823) Homo Sapiens (ncbitaxon:9606)
SUBMITTER: 
Ying Ge
PROVIDER: MSV000091693 | MassIVE | Wed Apr 12 11:23:00 BST 2023
REPOSITORIES: MassIVE
Similar Datasets
Project description:This dataset consists of in silico generated Orbitrap top-down proteomics spectra created using the FTMS simulator software (Spectroswiss). The simulated datasets are designed to evaluate false discovery rate (FDR) estimation in spectral deconvolution workflows. Protein sequences were used to generate MS spectra with varying resolution, noise, and charge characteristics. The dataset includes deconvolved TSV files and corresponding mzML spectra for each simulated run.
2026-03-09 | PXD063573 | Pride
Project description:Cowpea (Vigna unguiculata) is an important protein source in Sub-Saharan Africa. Optimizing resilience and productivity through genetic engineering in cowpea has been slow due in part to a lack of defined species-specific regulatory elements and difficulty testing gene function within the native system. In many plant species, Agrobacterium-mediated transient gene expression is widely used to validate constructs before investing in transgenic lines, but its implementation in legumes has been challenging. In this study, we optimized an in planta agroinfiltration assay in trifoliate cowpea leaves using a betalain reporter. To demonstrate the “intact plant” aspect of this system, we used this assay to characterize drought-inducible promoters by challenging cowpea plants with drought stress. Subsequently, to identify and broaden the pool of native promoters known in cowpea, we developed a user-friendly web application, CowPEAsy, allowing users to interrogate gene expression from our canopy-level, developmental-series RNA-Seq dataset. Finally, using CowPEAsy, we identified six promoters that showed constitutive expression across all conditions and verified these promoters with our transient system. This work provides an in vivo platform for preliminary validation of regulatory elements in cowpea and other legumes and enhances current genetic resources by identifying a suite of physiologically relevant promoters of varying strengths.
2025-02-13 | GSE280644 | GEO
Project description:Knowledge of differential gene expression between pulp and odontoblasts might give insight to the regulation of these spatially related but functionally diverse cells. Our aim was large-scale analysis of expression profiles of native human pulp tissue and odontoblasts, and search for genes expressed only in odontoblasts. Keywords: comparative expression analysis
2007-08-08 | GSE8694 | GEO
Project description:Knowledge of differential gene expression between pulp and odontoblasts might give insight to the regulation of these spatially related but functionally diverse cells. Our aim was large-scale analysis of expression profiles of native human pulp tissue and odontoblasts, and search for genes expressed only in odontoblasts. Experiment Overall Design: Microarray using Affymetrix HGU133A (for pulp) and HGU133plus 2.0 array (for odontoblasts) was performed to pooled pulp and odontoblasts of native human third molars. Microarray analysisâ repeatability was estimated by comparing our pulp sample with expression profiles of two pulp samples downloaded from the GEO-database. The genes expressed only in our pulp sample or in odontoblasts were divided into categories, and the expression of selected odontoblast-specific genes of extracellular matrix (ECM) organization and biogenesis category was confirmed with RT-PCR and Western blot.
2008-06-16 | E-GEOD-8694 | biostudies-arrayexpress
Project description:MASH Explorer, a universal, comprehensive, and user-friendly software environment for top-down proteomics. MASH Explorer integrates multiple spectral deconvolution and database searching algorithms into a single, universal platform which can process top-down proteomics data from various vendor formats, for the first time. It addresses the urgent need in the rapidly growing top-down proteomics community and is freely available to all users worldwide. With the critical need and tremendous support from the community, we envision this MASH Explorer software package will play an integral role in advancing top-down proteomics to realize its full potential for biomedical research.
2021-09-09 | PXD020615 | Pride
Project description:Accurately measuring protein complex dynamics (i.e., composition and/or abundance changes) in cells is vital for advancing fundamental and translational research. In this work, we present a pilot study establishing capillary zone electrophoresis (CZE)-mass spectrometry (MS) based quantitative native proteomics to determine significant changes in protein complex abundance during the transition from logarithmic to stationary phase growth in Escherichia coli. The approach integrates (1) efficient and fast native-state CZE-MS to obtain the mass and signal intensity of protein complexes for label-free quantification, (2) in-source collision-induced dissociation, enabling informative fragmentation that reveals oligomeric states, and (3) denatured top-down proteomics for the identification of proteoforms, which form the protein complexes. We revealed differentially expressed protein complexes during the growth of Escherichia coli. For example, the glutamate decarboxylase beta hexamer (~317 kDa) exhibits a significantly higher abundance at the stationary phase, which aligns with its biological function. This work represents the first quantitative native proteomics study using online native CZE-MS.
2025-12-08 | PXD068962 | Pride
Project description:I. Exp Design 1. Type of experiment: Comparison of native versus cultured RPE cells 2. Experimental factors: Native RPE versus ARPE-19 cells grown on different matrices 3. How many hybridizations in exp: 21 4. If a common reference used for all the hybs: no 5. Quality control steps: three independent arrays for each condition 6. Description: The expression profile of ARPE-19 cells grown on different matrices were compared to morphologically normal native macular RPE cells that were laser capture microdissected from 3 donors. II. Samples used, extract prep, and labeling 1. Biosource: Human donor globes from NDRI (63, 71, 74 years old) and ARPE-19 cells. 2. Manipulations: Human donor globes were cryopreserved, and morphologically normal RPE cells from the macula were laser capture micodissected. ARPE-19 cells were grown on different matrices (plastic, Matrigel, collagen I, collagen IV, laminin, and fibronectin). 3. Extract preparation: Total RNA from cells were extracted with the RNeasy kit (Qiagen) using the manufacturerâs instructions. 4. Labeling protocol: Total RNA from cells was reverse transcribed with 33P-dCTP and 33P-dATP, and second strand cDNA was labeled with 33P-dCTP and 33P-dATP. 5. No external controls were added. III. Hybridization procedures and parameters 1. Sample, array type, batch and serial # used 2. Hybridization protocol: Hybridization was carried out using the manufacturerâs recommendations. Arrays were prehybridized with Microhyb solution containing denatured Cot-1 DNA and poly dA at 42oC for two hours. Hybridization was carried out at 42oC overnight using a hybridization oven set at 8-10 rpm. Arrays were washed twice at 50oC for 20 minutes using 2x SSC, 1%SDS and once at room temperature for 15 minutes using 0.5x SSC, 1%SDS. IV. Measurement data and specifications of data processing 1,2. Arrays were exposed to a phosphorimaging screen for 3 days and scanned at 50 mm resolution with a BioRad FX Pro-Plus phosphorimager. TIFF images from the phosphorimager were exported into ResGen Pathways 3 software for analysis. 3. Data processing: A gene was expressed if its background subtracted intensity was greater than 1.4 fold background. The data were normalized using a simple global scaling procedure, and Cluster/Treeview and Statistical Analysis of Microarrays (SAM version 1.12) programs were used for analysis.
2010-06-05 | E-GEOD-741 | biostudies-arrayexpress
Project description:Description I. Exp Design 1. Type of experiment: Comparison of native versus cultured RPE cells 2. Experimental factors: Native RPE versus ARPE-19 cells grown in different culture conditions 3. How many hybridizations in exp: 20 4. If a common reference used for all the hybs: no 5. Quality control steps: three independent arrays for each condition, and five different donor globes for native RPE 6. Description: The expression profile of ARPE-19 cells grown under different culture conditions were compared to morphologically normal native macular RPE cells that were laser capture microdissected from 5 donors. II. Samples used, extract prep, and labeling 1. Biosource: Human donor globes from NDRI and Sierra Eye and Tissue Bank, and ARPE-19 cells. 2. Manipulations: Human donor globes were cryopreserved, and morphologically normal RPE cells from the macula were laser capture micodissected. ARPE-19 cells were grown on different matrices (subconfluent culture density in presence of serum, confluent culture density in presence of serum, confluent culture density with serum withdrawn medium, differentiated (grown for 2.5 months) in serum, and differentiated (grown for 2.5 months) and then serum withdrawn medium). 3. Extract preparation: Total RNA from cells were extracted with the RNeasy kit (Qiagen) using the manufacturer's instructions. 4. Labeling protocol: Total RNA from cells was reverse transcribed with 33P-dCTP and 33P-dATP, and second strand cDNA was labeled with 33P-dCTP and 33P-dATP. 5. No external controls were added. III. Hybridization procedures and parameters 1. Sample, array type, batch and serial # used 2. Hybridization protocol: Hybridization was carried out using the manufacturer's recommendations. Arrays were prehybridized with Microhyb solution containing denatured Cot-1 DNA and poly dA at 42oC for two hours. Hybridization was carried out at 42oC overnight using a hybridization oven set at 8-10 rpm. Arrays were washed twice at 50oC for 20 minutes using 2x SSC, 1%SDS and once at room temperature for 15 minutes using 0.5x SSC, 1%SDS. IV. Measurement data and specifications of data processing 1,2. Arrays were exposed to a phosphorimaging screen for 3 days and scanned at 50 mm resolution with a BioRad FX Pro-Plus phosphorimager. TIFF images from the phosphorimager were exported into ResGen Pathways 3 software for analysis. 3. Data processing: A gene was expressed if its background subtracted intensity was greater than 1.4 fold background. The data were normalized using a simple global scaling procedure, and Cluster/Treeview and Statistical Analysis of Microarrays (SAM version 1.12) programs were used for analysis.
2010-06-05 | E-GEOD-1836 | biostudies-arrayexpress
Project description:To understand widespread differences in the DNA methylation patterns of Conyza canadensis leaf samples from its native and non-native ranges. Using Whole Genome Bisulfite Sequencing, we found average read coverages in high mapped reads across native and non-native samples of Conyza canadensis. Using R bioconductor package, we found enrichment score of methylated sites in both native and non-native samples. while analyzing CG, CHG and CHH methylation, we found relatively low CG and CHG methylation across transcriptional units in natives over non-natives. However, differentially methylated regions were found to be 53% hypomethylated and 41% hypermethylated in non-natives on genic regions.
2024-09-30 | GSE240046 | GEO