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ProteomicsSequence Coverage Visualizer: A web application for protein sequence coverage 3D visualization
Protein structure is connected with its function and interaction and plays an extremely important role in protein characterization. As one of the most important analytical methods for protein characterization, Proteomics is widely used to determine protein composition, quantitation, interaction, and...
ORGANISM(S): Homo sapiens (Human) 
2022-12-14 | PXD032786 | Pride
Proteomics Protein sequence coverage 3d structure Visualization 
ProteomicsSequence coverage by multiple reads in shotgun proteomics to validate single amino acid variants
Mass spectrometry-based shotgun proteomics is currently based on assigning matches between mass-spectra of protein fragments resulting from protease digestion and amino acid sequences predicted from nucleic acid sequences. At the same time, the method lacks reliability in identification of every sin...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2021-12-07 | MSV000088536 | MassIVE
TranscriptomicsStructural annotation of equine protein-coding genes determined by mRNA sequencing
The horse, like a majority of animal species, has a limited amount of species-specific expressed sequence data available in public databases. As a result, structural models for a majority of genes defined in the equine genome are predictions based on ab initio sequence analysis or the projection of...
ORGANISM(S): Equus caballus 
2010-11-10 | E-GEOD-21925 | biostudies-arrayexpress
TranscriptomicsU87MG Decoded: The Genomic Sequence of a Cytogenetically Aberrant Human Cancer Cell Line
U87MG is a commonly studied grade IV glioma cell line that has been analyzed in at least 1,700 publications over four decades. In order to comprehensively characterize the genome of this cell line and to serve as a model of broad cancer genome sequencing, we have generated greater than 30x genomic s...
ORGANISM(S): Homo sapiens 
2010-01-24 | E-GEOD-19986 | biostudies-arrayexpress
ProteomicsAccurate Taxonomic Annotation from Metagenomic Data for Deep Metaproteomic Coverage of Microbiota
We developed an accurate taxonomic annotation strategy from metagenomic data for deep metaproteomic coverage, and also compared the performance of the state-of-the-art LC-MS/MS techniques using a simulated microbial community with 12 species. In addition, we also achieved deep proteome coverage of h...
ORGANISM(S): Enterococcus Faecalis Escherichia Coli Atcc 25922 Pseudomonas Aeruginosa Klebsiella Pneumoniae Homo Sapiens Enterococcus Casseliflavus Morganella Morganii Lactobacillus Acidophilus Clostridium Butyricum Citrobacter Freundii Complex Enterobacter Asburiae Klebsiella Aerogenes Bacteroides Fragilis 
PXD034815 |
ProteomicsData-independent acquisition protease-multiplexing enables increased proteome sequence coverage across multiple fragmentation modes
The use of multiple proteases has been shown to increase protein sequence coverage in proteomics experiments, but due to the additional sample preparation and analysis time required, it has not been widely adapted in routine proteomic workflows. While data-independent acquisition (DIA) has been prim...
ORGANISM(S): Homo sapiens (Human) 
2022-03-18 | PXD027242 | Pride
Dia Gluc Multiplexing Aspn 
GenomicsMapping meiotic crossovers in Arabidopsis using low-coverage whole-genome sequencing
Whole-genome DNA libraries were prepared from a population of just under 100 Col/Ler F1 backcrossed to Col. Low-coverage whole-genome sequencing was used to map meiotic crossovers in this population following the protocol described in Rowan et al., 2015, doi: 10.1534/g3.114.016501.
ORGANISM(S): Arabidopsis thaliana 
2015-10-15 | E-MTAB-3926 | biostudies-arrayexpress
ProteomicsDeep Coverage and Extended Sequence Reads Obtained with a Single Archaeal Protease Expedite de novo Protein Sequencing by Mass Spectrometry
Label-free protein sequencing is critically enabled by bottom-up, mass spectrometry-based proteomics workflows. Applications such as antibody sequencing or antigen discovery require de novo reconstruction of peptide and protein sequences. While trypsin has long served as the gold-standard protease i...
ORGANISM(S): Homo sapiens (Human) 
2026-03-17 | PXD063988 | Pride
Hta-proteases Hybrid fragmentation by eacid De novo antibody sequencing Bottom-up proteomics 
TranscriptomicsGenome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting
So far, the annotation of translation initiation sites (TISs) has been based mostly upon bioinformatics rather than experimental evidence. We adapted ribosomal footprinting to puromycin-treated cells to generate a transcriptome-wide map of TISs in a human monocytic cell line. A neural network was tr...
ORGANISM(S): Homo sapiens 
2012-08-08 | E-GEOD-39561 | biostudies-arrayexpress
UnknownSequence Coverage Visualizer: A Web Application for Protein Sequence Coverage 3D Visualization.
Not available
S-EPMC10232130 | biostudies-literature
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