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ProteomicsOptimized Sample Preparation Workflow for Improved Identification of Ghost Proteins
Large scale proteomic strategies rely on database interrogation. Thus, only referenced proteins can be identified. Recently, Alternative Proteins (AltProts) translated from nonannotated Alternative Open reading frame (AltORFs) were discovered using customized databases. Because of their small size w...
ORGANISM(S): Homo sapiens (Human) 
2021-02-15 | PXD024134 | Pride
Protein identification Fractionation Precipitation Peptides and proteins Extraction 
ProteomicsHistone proteomic associated with epigenetic studies revealed a Ghost proteome in PC1/3 KD macrophages involved in anti - tumoral resistance under IL - 10 stimulation
In our previous work, our investigation on macrophages has allowed us to show that the inhibition of the enzyme proprotein convertase (PC1/3) controls the activation of macrophages. We demonstrated that PC1/3 knockdown (KD) in macrophages would exhibit an increased secretion of pro-inflammatory and ...
ORGANISM(S): Rattus norvegicus (Rat) 
2021-02-12 | PXD020610 | Pride
Macrophage Lc-msms Altprots Histone Epigenetic 
ProteomicsProbing the Function of Alternative Proteins in Cell Reprogramming by Large Scale Proteomics and Cross - Linking Mass Spectrometry
Many proteins are lacking from reference databases because they are issued from alternative ORFs neither respecting the rules decreed for the genome annotation or for the protein translation from mRNA. It was evidenced that not only a single protein is therefore translated from an mRNA. However, the...
ORGANISM(S): Homo sapiens (Human) 
2021-02-15 | PXD014642 | Pride
Alternative proteins Proteomics Cross-linking mass spectrometry Cell reprogramming 
ProteomicsAn optimized proteomics approach reveals novel alternative proteins in mouse liver development
Alternative open reading frames (AltORFs) are unannotated sequences in genome that encode novel peptides or proteins named alternative proteins (AltProts). Although ribosome profiling and bioinformatics predict a large number of AltProts, mass spectrometry (MS) as the only direct way of identificati...
ORGANISM(S): Mus musculus (Mouse) 
2022-12-23 | PXD033940 | Pride
Liver development. Mass spectrometry Fractionation Alternative open reading frames (altorfs) Alternative proteins (altprots) Enrichment 
ProteomicsEmploying non-targeted interactomics approach and subcellular fractionation to increase our understanding of the ghost proteome
Eukaryotic mRNA has long been considered monocistronic, but nowadays, alternative proteins (AltProts) challenge this tenet. The alternative or ghost proteome has largely been neglected and the involvement of AltProts in biological processes. Here, we used subcellular fractionation to increase the in...
ORGANISM(S): Homo sapiens (Human) 
2023-03-11 | PXD035764 | Pride
Ghost proteome Alternative open reading frames Cross-linking 
ProteomicsDIA-enabled discovery of alternative proteins (AltProts) in mouse heart development
In this project, we conducted an evaluation of mass spectrometry methods using mouse heart and HCT116 cell samples. The results demonstrated that the data-independent acquisition (DIA) approach outperformed data-dependent acquisition (DDA) in the identification of Altprot and canonical proteins. Sub...
ORGANISM(S): Mus musculus (Mouse) 
2025-01-17 | PXD045956 | Pride
Altorfs  mouse heart development  mass spectroemtry 
TranscriptomicsDeciphering the ghost proteome in ovarian cancer cells by deep proteogenomic characterization
Proteogenomics is becoming a powerful tool in personalized medicine by linking genomics, transcriptomics and mass spectrometry (MS)-based proteomics. Due to increasing evidence of alternative open reading frame-encoded proteins (AltProts), proteogenomics has a high potential to unravel the character...
ORGANISM(S): Homo sapiens 
2023-11-17 | GSE248039 | GEO
ProteomicsDeciphering the ghost proteome in ovarian cancer cells by deep proteogenomic characterization.
Proteogenomics is becoming a powerful tool in personalized medicine by linking genomics, transcriptomics, and mass spectrometry (MS)-based proteomics. Due to increasing evidence of alternative open reading frame-encoded proteins (AltProts), proteogenomics has high potential to unravel the characteri...
ORGANISM(S): Homo sapiens (Human) 
2025-05-06 | PXD045689 | Pride
Alternative proteins Proteogenomics Ovarian cancer Crosslinking 
UnknownAn Optimized Proteomics Approach Reveals Novel Alternative Proteins in Mouse Liver Development.
Not available
S-EPMC9823216 | biostudies-literature
UnknownEmploying non-targeted interactomics approach and subcellular fractionation to increase our understanding of the ghost proteome.
Not available
S-EPMC9971881 | biostudies-literature
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