False discovery rate: the Achilles' heel of proteogenomics
Proteogenomics refers to the integrated analysis of the genome and proteome that
leverages mass-spectrometry (MS)-based proteomics data to improve genome annotations …
leverages mass-spectrometry (MS)-based proteomics data to improve genome annotations …
[HTML][HTML] Proteogenomic characterization of human early-onset gastric cancer
We report proteogenomic analysis of diffuse gastric cancers (GCs) in young populations.
Phosphoproteome data elucidated signaling pathways associated with somatic mutations …
Phosphoproteome data elucidated signaling pathways associated with somatic mutations …
Proteogenomics from a bioinformatics angle: A growing field
G Menschaert, D Fenyö - Mass spectrometry reviews, 2017 - Wiley Online Library
Proteogenomics is a research area that combines areas as proteomics and genomics in a
multi‐omics setup using both mass spectrometry and high‐throughput sequencing …
multi‐omics setup using both mass spectrometry and high‐throughput sequencing …
[HTML][HTML] Integrated pharmaco-proteogenomics defines two subgroups in isocitrate dehydrogenase wild-type glioblastoma with prognostic and therapeutic …
The prognostic and therapeutic relevance of molecular subtypes for the most aggressive
isocitrate dehydrogenase 1/2 (IDH) wild-type glioblastoma (GBM) is currently limited due to …
isocitrate dehydrogenase 1/2 (IDH) wild-type glioblastoma (GBM) is currently limited due to …
[HTML][HTML] An analysis of proteogenomics and how and when transcriptome-informed reduction of protein databases can enhance eukaryotic proteomics
L Fancello, T Burger - Genome Biology, 2022 - Springer
Background Proteogenomics aims to identify variant or unknown proteins in bottom-up
proteomics, by searching transcriptome-or genome-derived custom protein databases …
proteomics, by searching transcriptome-or genome-derived custom protein databases …
[HTML][HTML] PROTEOFORMER 2.0: further developments in the ribosome profiling-assisted proteogenomic hunt for new proteoforms
PROTEOFORMER is a pipeline that enables the automated processing of data derived from
ribosome profiling (RIBO-seq, ie the sequencing of ribosome-protected mRNA fragments) …
ribosome profiling (RIBO-seq, ie the sequencing of ribosome-protected mRNA fragments) …
Integrating next-generation genomic sequencing and mass spectrometry to estimate allele-specific protein abundance in human brain
Gene expression contributes to phenotypic traits and human disease. To date,
comparatively less is known about regulators of protein abundance, which is also under …
comparatively less is known about regulators of protein abundance, which is also under …
Connecting proteomics to next‐generation sequencing: proteogenomics and its current applications in biology
Understanding the relationship between genotypes and phenotypes is essential to
disentangle biological mechanisms and to unravel the molecular basis of diseases. Genes …
disentangle biological mechanisms and to unravel the molecular basis of diseases. Genes …
Glycoproteogenomics: setting the course for next-generation cancer neoantigen discovery for cancer vaccines
Molecular-assisted precision oncology gained tremendous ground with high-throughput
next-generation sequencing (NGS), supported by robust bioinformatics. The quest for …
next-generation sequencing (NGS), supported by robust bioinformatics. The quest for …
ProteomeGenerator: a framework for comprehensive proteomics based on de novo transcriptome assembly and high-accuracy peptide mass spectral matching
Modern mass spectrometry now permits genome-scale and quantitative measurements of
biological proteomes. However, analysis of specific specimens is currently hindered by the …
biological proteomes. However, analysis of specific specimens is currently hindered by the …