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MetabolomicsUntargeted In Silico Compound Classification - A Novel Metabolomics Method to Assess the Chemodiversity in Bryophytes

In plant ecology, biochemical analyses of bryophytes and vascular plants are often conducted on dried herbarium specimen as species typically grow in distant and inaccessible locations. Here, we present an automated in silico compound classification framework to annotate metabolites using an unta...

2026-01-30 | MTBLS851 | MetaboLights
ModelsConradie2010_RPControl_CellCycle
This model is from the article: Restriction point control of the mammalian cell cycle via the cyclin E/Cdk2:p27 complex. Conradie R, Bruggeman FJ, Ciliberto A, Csikász-Nagy A, Novák B, Westerhoff HV, Snoep JL FEBS J.2010 Jan; 277(2): 357-67 20015233, ...
2024-09-02 | BIOMD0000000265 | BioModels
ProteomicsTowards a universal sample preparation method for denaturing top-down proteomics of complex proteomes
A universal and standardized sample preparation method becomes vital for denaturing top-down proteomics (dTDP) to advance the scale and accuracy of proteoform delineation in complex biological systems. It needs to have high protein recovery, minimum bias, good reproducibility, and compatibility with...
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2020-05-22 | PXD018248 | Pride
Histone Ptms Membrane ultrafiltration Chloroform-methanol precipitation Membrane proteins Sp3 Denaturing top-down proteomics Cze-ms/ms Sds Sample preparation 
ProteomicsTop Down Histone H4 - SUM159 Butyrate
Proteins physiologically exist and function as ‘proteoforms’ that arise from one gene but acquire additional function by further variation such as post-translational modification (PTM). When multiple PTMs coexist on single protein molecules top down proteomics becomes the only feasible method; howev...
ORGANISM(S): Homo sapiens (Human) 
2019-11-22 | PXD013766 | Pride
Top-down Histone h4 
ProteomicsTop-down detection of oxidative protein footprinting by Collision-Induced Dissociation, Electron-Transfer Dissociation and Electron-Capture Dissociation
Fast photochemical oxidation of proteins (FPOP) footprinting is a structural mass spectrometry method that maps proteins by fast and irreversible chemical reactions. The position of oxidative modification reflects solvent accessibility and site reactivity and thus provides information about protein ...
ORGANISM(S): Bos taurus (Bovine) Equus caballus (Horse) 
2023-07-20 | PXD031926 | Pride
Electron-transfer dissociation Fast photochemical oxidation of proteins Top-down Collision-induced dissociation Mass spectrometry. Electron-capture dissociation 
ProteomicsNovel Proteome Extraction Method Illustrate a Conserved Immunological Signature of MSI-H Colorectal Tumors
Direct comparison of conventional Vs. TOP proteome extraction, and effcts of fixation-time
ORGANISM(S): Homo sapiens (Human) 
2020-07-10 | PXD019254 | Pride
Top method Formalin Fixation time 
ProteomicsIntegrated Protein Precipitation–SPE Workflow for Deep Top-Down Proteomic Analysis of Human Serum
Top-down proteomics of human serum is hindered by extreme dynamic range and cumbersome prefractionation. Here we establish a fully solution-based protein precipitation–solid-phase extraction (PP–SPE) workflow for deep, low-molecular-weight-biased proteoform profiling. Using systematically optimized ...
ORGANISM(S): Homo Sapiens 
2026-05-23 | PXD073228 |
ProteomicsUniversal Solid-Phase Protein Preparation (USP3) for bottom-up and top-down proteomics
Selecting a sample preparation strategy for mass spectrometry-based proteomics is critical to the success of quantitative workflows. Here we present a universal, solid-phase protein preparation (USP3) method which is rapid, robust and scalable, facilitating high-throughput protein sample preparation...
ORGANISM(S): Homo sapiens (Human) 
2019-06-05 | PXD011169 | Pride
Top-down proteomics Universal solid-phase protein preparation Bottom-up proteomics Intact mass spectrometry 
ProteomicsEnhancing Top-Down Proteomics Data Analysis by Combining Deconvolution Results through a Machine Learning Strategy
Top-down mass spectrometry (MS) is a powerful tool for identification and comprehensive characterization of proteoforms arising from alternative splicing, sequence variation, and post-translational modifications. While the technique is powerful, it suffered from the complex dataset generated from to...
ORGANISM(S): Macaca mulatta (Rhesus macaque) 
2020-05-06 | PXD018043 | Pride
Top-down spectra deconvolution 
ProteomicsCapillary zone electrophoresis-tandem mass spectrometry for top-down proteomics of mouse brain integral membrane proteins
Mass spectrometry (MS)-based top-down characterization of integral membrane proteins (IMPs) is crucial for understanding their functions in biological processes. However, it is technically challenging due to their low solubility in typical MS-compatible buffers. In this work, for the first time, we ...
ORGANISM(S): Mus musculus (Mouse) 
2023-12-07 | PXD042298 | Pride
Top-down proteomics  integral membrane protein  proteoform  capillary zone electrophoresis-mass spectrometry  mouse brain 
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