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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 
ProteomicsStradard protein and yeast top-down data
We developed a novel dissociation strategy in the data acquisition process, the Mesh strategy to dissociate multiple charge states of one proteoform with stepped HCD (high collision energy dissociation). We proved that the ‘Mesh’ strategy could generate fragments with improved sequence coverage and...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2022-06-09 | PXD022941 | Pride
Stepped hcd Instrument control Real-time Mesh Top-down 
ProteomicsIn silico Orbitrap top-down proteomics datasets generated using FTMS simulator (Spectroswiss)
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 genera...
ORGANISM(S): Homo sapiens (Human) 
2026-03-09 | PXD063573 | Pride
Ftms simulator In silico Human proteins Deconvolution Top-down proteomics Orbitrap 
ProteomicsInsilico TOF top-down proteomics datasets generated using FTMS simulator (Spectroswiss)
This dataset consists of in silico generated TOF top-down proteomics spectra created using the FTMS simulator software (Spectroswiss). The simulated datasets are designed to evaluate FDR estimation in spectral deconvolution. Protein sequences were used to generate MS datasets with varying resolution...
ORGANISM(S): Homo sapiens (Human) 
2026-03-09 | PXD063631 | Pride
Ftms simulator In silico Human proteins Deconvolution Top-down proteomics Orbitrap 
ProteomicsQuantifying Positional Isomers (QPI) by top-down mass spectrometry
Proteomics has exposed a plethora of post-translational modifications, but demonstrating functional relevance requires new approaches. Top-down proteomics can characterize co-occurring modifications in terms of localization, abundance and hierarchy. Here, we present a top-down MS analysis workflow f...
ORGANISM(S): Homo sapiens (Human) 
2021-03-18 | PXD012084 | Pride
Top-down mass spectrometry Positional isomers Quantitation Phosphorylation 
ProteomicsBenchmarking multiple fragmentation methods on an Orbitrap Fusion for top-down phospho-proteoform characterization
Top-down analysis of intact proteins by mass spectrometry provides an ideal platform for comprehensive proteoform characterization, in particular, for the identification and localization of post-translational modifications (PTM) co-occurring on a protein. One of the main bottlenecks in top-down prot...
ORGANISM(S): Homo sapiens (Human) 
2015-07-16 | PXD001845 | Pride
Fragmentation Bora Ethcd Top down proteomics Phosphorylation Proteoform Orbitrap fusion 
ProteomicsTop-Down proteomics of unfractionated Bovine heart mitochondria
Top-Down proteomics pilot experiment of unfractionated Bovine Heart Mitochondria (BHM) using ultra high resolution Q-ToF tandem mass spectrometry (maXis 4G ETD, Bruker Daltonics).
ORGANISM(S): Bos taurus (Bovine) 
2018-04-05 | PXD005350 | Pride
Bovine Mitochondrion Protein Intact Top-down proteomics 
ProteomicsMASH Explorer: A Universal Software Environment for Top-Down Proteomics
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 forma...
ORGANISM(S): Homo sapiens (Human) 
2021-09-09 | PXD020615 | Pride
Top-down proteomics  data analysis software  proteoform characterization  intact protein analysis 
ProteomicsCapillary zone electrophoresis-tandem mass spectrometry with activated ion electron transfer dissociation for large-scale top-down proteomics
Capillary zone electrophoresis (CZE)-tandem mass spectrometry (MS/MS) has been recognized as an efficient approach for top-down proteomics recently for its high-capacity separation and highly sensitive detection of proteoforms. However, the commonly used collision-based dissociation methods often ca...
ORGANISM(S): Escherichia coli 
2019-06-11 | PXD012247 | Pride
Top-down proteomics E. coli Cze-ms Ai-etd 
ProteomicsThe Isotopic Depletion Increases the Spatial Resolution of FPOP Top-Down Analysis.
Protein radical labeling offers an alternative analytical method for probing protein structure or protein interaction with other bio-molecules. Since the Fast Photochemical Oxidation of Proteins has already shown its essential role in studying biomolecular as-semblies and it was successfully adopted...
ORGANISM(S): Homo sapiens (Human) 
2024-01-26 | PXD044447 | Pride
Protein isotope depletion Ire Fast photochemical oxidation of proteins Mass spectrometry Insulin response element Top-down Foxo4 Electron-capture dissociation Multicasi. 
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