Proteomic landscape of Alzheimer's Disease: novel insights into pathogenesis and biomarker discovery
Mass spectrometry-based proteomics empowers deep profiling of proteome and protein
posttranslational modifications (PTMs) in Alzheimer's disease (AD). Here we review the …
posttranslational modifications (PTMs) in Alzheimer's disease (AD). Here we review the …
Overlapping genes in natural and engineered genomes
BW Wright, MP Molloy, PR Jaschke - Nature Reviews Genetics, 2022 - nature.com
Modern genome-scale methods that identify new genes, such as proteogenomics and
ribosome profiling, have revealed, to the surprise of many, that overlap in genes, open …
ribosome profiling, have revealed, to the surprise of many, that overlap in genes, open …
dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts
The dia-PASEF technology uses ion mobility separation to reduce signal interferences and
increase sensitivity in proteomic experiments. Here we present a two-dimensional peak …
increase sensitivity in proteomic experiments. Here we present a two-dimensional peak …
Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform
Liquid chromatography (LC) coupled with data-independent acquisition (DIA) mass
spectrometry (MS) has been increasingly used in quantitative proteomics studies. Here, we …
spectrometry (MS) has been increasingly used in quantitative proteomics studies. Here, we …
MSBooster: improving peptide identification rates using deep learning-based features
Peptide identification in liquid chromatography-tandem mass spectrometry (LC-MS/MS)
experiments relies on computational algorithms for matching acquired MS/MS spectra …
experiments relies on computational algorithms for matching acquired MS/MS spectra …
IonQuant enables accurate and sensitive label-free quantification with FDR-controlled match-between-runs
Missing values weaken the power of label-free quantitative proteomic experiments to
uncover true quantitative differences between biological samples or experimental …
uncover true quantitative differences between biological samples or experimental …
Spectral entropy outperforms MS/MS dot product similarity for small-molecule compound identification
Compound identification in small-molecule research, such as untargeted metabolomics or
exposome research, relies on matching tandem mass spectrometry (MS/MS) spectra against …
exposome research, relies on matching tandem mass spectrometry (MS/MS) spectra against …
A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides
We describe pLink 2, a search engine with higher speed and reliability for proteome-scale
identification of cross-linked peptides. With a two-stage open search strategy facilitated by …
identification of cross-linked peptides. With a two-stage open search strategy facilitated by …
MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics
There is a need to better understand and handle the'dark matter'of proteomics—the vast
diversity of post-translational and chemical modifications that are unaccounted in a typical …
diversity of post-translational and chemical modifications that are unaccounted in a typical …
Most non-canonical proteins uniquely populate the proteome or immunopeptidome
Combining RNA sequencing, ribosome profiling, and mass spectrometry, we elucidate the
contribution of non-canonical translation to the proteome and major histocompatibility …
contribution of non-canonical translation to the proteome and major histocompatibility …