Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial
Many research questions in fields such as personalized medicine, drug screens or systems
biology depend on obtaining consistent and quantitatively accurate proteomics data from …
biology depend on obtaining consistent and quantitatively accurate proteomics data from …
Bioinformatics methods for mass spectrometry-based proteomics data analysis
Recent advances in mass spectrometry (MS)-based proteomics have enabled tremendous
progress in the understanding of cellular mechanisms, disease progression, and the …
progress in the understanding of cellular mechanisms, disease progression, and the …
Philosopher: a versatile toolkit for shotgun proteomics data analysis
To the Editor—Here we introduce Philosopher (https://philosopher. nesvilab. org), a free,
open-source, versatile and robust data analysis toolkit designed to bring easy access to a …
open-source, versatile and robust data analysis toolkit designed to bring easy access to a …
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 …
Gasdermin D is an executor of pyroptosis and required for interleukin-1β secretion
Inflammasome is an intracellular signaling complex of the innate immune system. Activation
of inflammasomes promotes the secretion of interleukin 1β (IL-1β) and IL-18 and triggers …
of inflammasomes promotes the secretion of interleukin 1β (IL-1β) and IL-18 and triggers …
MS-GF+ makes progress towards a universal database search tool for proteomics
S Kim, PA Pevzner - Nature communications, 2014 - nature.com
Mass spectrometry (MS) instruments and experimental protocols are rapidly advancing, but
the software tools to analyse tandem mass spectra are lagging behind. We present a …
the software tools to analyse tandem mass spectra are lagging behind. We present a …
DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics
CC Tsou, D Avtonomov, B Larsen, M Tucholska… - Nature …, 2015 - nature.com
As a result of recent improvements in mass spectrometry (MS), there is increased interest in
data-independent acquisition (DIA) strategies in which all peptides are systematically …
data-independent acquisition (DIA) strategies in which all peptides are systematically …
Protein analysis by shotgun/bottom-up proteomics
According to Genome Sequencing Project statistics (http://www. ncbi. nlm. nih.
gov/genomes/static/gpstat. html), as of February 16, 2012, complete gene sequences have …
gov/genomes/static/gpstat. html), as of February 16, 2012, complete gene sequences have …
Identification of novel lipid droplet factors that regulate lipophagy and cholesterol efflux in macrophage foam cells
S Robichaud, G Fairman, V Vijithakumar, E Mak… - Autophagy, 2021 - Taylor & Francis
Macrophage autophagy is a highly anti-atherogenic process that promotes the catabolism of
cytosolic lipid droplets (LDs) to maintain cellular lipid homeostasis. Selective autophagy …
cytosolic lipid droplets (LDs) to maintain cellular lipid homeostasis. Selective autophagy …
The 2022 report on the human proteome from the HUPO human proteome project
The 2022 Metrics of the Human Proteome from the HUPO Human Proteome Project (HPP)
show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 …
show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 …