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ProteomicsTop-Down proteomics and Bottom-Up terminomics for the Detection of Protein Termini in C. elegans
Here we investigate how top-down proteomics (TDP) can be of value for the detection of protein termini. Either GELFrEE or solid-phase enrichment was conducted for pre-fraction. To verify the detected N-termini HUNTER (High-efficiency Undecanal-based N Termini EnRichment) was employed. Reductive dime...
ORGANISM(S): Caenorhabditis elegans 
2022-09-26 | PXD033668 | Pride
Orbitrap q exactive plus Gelfree Mspathfinder Top-down proteomic C. elegans Orbitrap fusion lumos Informed proteomics Bottom-up proteomics Prosight 
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 
ProteomicsPredicting electrophoretic mobility of proteoforms for large-scale top-down proteomics
Large-scale top-down proteomics characterizes proteoforms in cells globally with high confidence and high throughput using reversed-phase liquid chromatography (RPLC)-tandem mass spectrometry (MS/MS) or capillary zone electrophoresis (CZE)-MS/MS. The false discovery rate (FDR) from the target-decoy ...
ORGANISM(S): Escherichia coli 
2020-02-17 | PXD017265 | Pride
Top-down proteomics Electrophoretic mobility Cze-ms Proteoform 
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 
ProteomicsRevealing Corynebacterium glutamicum proteoforms through top-down proteomics
Corynebacterium glutamicum is a bacterium widely employed in the industrial production of amino acids as well as a broad range of other biotechnological products. The present study describes the characterization of C. glutamicum proteoforms, and their post-translational modifications (PTMs) employin...
ORGANISM(S): Corynebacterium glutamicum ATCC 13032 
2022-12-10 | PXD038038 | Pride
Top-down proteomics Corynebacterium glutamicum Proteoforms 
ProteomicsTDFragMapper: Evaluating experimental parameters for confident intact protein characterization in top-down proteomics
New software-tool allowing an easy visualization of fragment ions and thus a rapid evaluation of key experimental parameters on the sequence coverage obtained for the MS/MS analysis of intact proteins. Our tool can deal with multiple fragmentation methods. We demonstrate that TDFragMapper can rapidl...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) Streptococcus dysgalactiae Escherichia coli 
2021-12-30 | PXD024643 | Pride
Visualization tool Top-down proteomics Lc-ms/ms 
ProteomicsSarcomeric Proteoform Landscape in Ischemic Cardiomyopathy Defined by Top-down Proteomics
In ischemic cardiomyopathy (ICM), left ventricular systolic dysfunction leads to reduced blood flow and oxygen supply to the heart. Alterations in sarcomeric protein function and expression play prominent roles in the onset and progression of cardiomyopathies; however, the molecular mechanisms under...
ORGANISM(S): Homo sapiens (Human) 
2023-02-20 | PXD038066 | Pride
Ischemic cardiomyopathy Top-down proteomics Sarcomere Z-disk proteins Myofilament proteins Quantitative proteomics Human heart proteomics 
ProteomicsProtamine characterization by top-down proteomics: Boosting proteoform identification with DBSCAN
Protamines replace histones as the main nuclear protein in sperm cells having a crucial role in compacting the paternal genome. Human spermatozoa contain the protamine 1 (P1) and the family of protamine 2 (P2) proteins. Alterations in protamine PTMs or on the P1/P2 ratio could be associated with mal...
ORGANISM(S): Homo sapiens (Human) 
2021-05-13 | PXD024405 | Pride
Male infertility  sperm  protamine  lc-ms/ms  top down proteomics  proteoform  post-translational modifications  bioinformatics  dbscan. 
ProteomicsOptimization of a Top-Down Proteomics Platform for Closely-Related Pathogenic Bacteria Discrimination
The current technique used for microbial identification in hospitals is MALDI-TOF MS. However, it suffers from important limitations, in particular for closely-related species or when the database used for the identification lacks the appropriate reference. In this work, we set up a high throughput ...
ORGANISM(S): Shigella flexneri Salmonella enterica subsp. enterica serovar Muenchen Salmonella enterica subsp. enterica serovar Enteritidis Salmonella enterica subsp. enterica serovar Typhimurium Escherichia coli O26:H11 Shigella sonnei Escherichia coli O157:H7 Salmonella enterica subsp. enterica serovar Newport Escherichia coli 
2020-09-24 | PXD019247 | Pride
Mass spectrometry Optimization Top-down proteomics Bacteria 
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 
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