Data‐independent acquisition mass spectrometry‐based proteomics and software tools: a glimpse in 2020
F Zhang, W Ge, G Ruan, X Cai, T Guo - Proteomics, 2020 - Wiley Online Library
This review provides a brief overview of the development of data‐independent acquisition
(DIA) mass spectrometry‐based proteomics and selected DIA data analysis tools. Various …
(DIA) mass spectrometry‐based proteomics and selected DIA data analysis tools. Various …
Bottom-up proteomics: advancements in sample preparation
Liquid chromatography–tandem mass spectrometry (LC–MS/MS)-based proteomics is a
powerful technique for profiling proteomes of cells, tissues, and body fluids. Typical bottom …
powerful technique for profiling proteomes of cells, tissues, and body fluids. Typical bottom …
Itaconate and itaconate derivatives target JAK1 to suppress alternative activation of macrophages
The Krebs cycle-derived metabolite itaconate and its derivatives suppress the inflammatory
response in pro-inflammatory" M1" macrophages. However, alternatively activated" M2" …
response in pro-inflammatory" M1" macrophages. However, alternatively activated" M2" …
[HTML][HTML] Mucus sialylation determines intestinal host-commensal homeostasis
Intestinal mucus forms the first line of defense against bacterial invasion while providing
nutrition to support microbial symbiosis. How the host controls mucus barrier integrity and …
nutrition to support microbial symbiosis. How the host controls mucus barrier integrity and …
HSP70 chaperones RNA-free TDP-43 into anisotropic intranuclear liquid spherical shells
INTRODUCTION Aggregation of the RNA binding protein TDP-43 (TAR DNA-binding protein
43) is a common pathological hallmark shared by several age-related neurodegenerative …
43) is a common pathological hallmark shared by several age-related neurodegenerative …
AlphaPeptDeep: a modular deep learning framework to predict peptide properties for proteomics
Abstract Machine learning and in particular deep learning (DL) are increasingly important in
mass spectrometry (MS)-based proteomics. Recent DL models can predict the retention …
mass spectrometry (MS)-based proteomics. Recent DL models can predict the retention …
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 …
Precise, fast and comprehensive analysis of intact glycopeptides and modified glycans with pGlyco3
Great advances have been made in mass spectrometric data interpretation for intact
glycopeptide analysis. However, accurate identification of intact glycopeptides and modified …
glycopeptide analysis. However, accurate identification of intact glycopeptides and modified …
Identification of modified peptides using localization-aware open search
Identification of post-translationally or chemically modified peptides in mass spectrometry-
based proteomics experiments is a crucial yet challenging task. We have recently introduced …
based proteomics experiments is a crucial yet challenging task. We have recently introduced …
The cytosolic thiol peroxidase PRXIIB is an intracellular sensor for H2O2 that regulates plant immunity through a redox relay
G Bi, M Hu, L Fu, X Zhang, J Zuo, J Li, J Yang, JM Zhou - Nature plants, 2022 - nature.com
Rapid production of H2O2 is a hallmark of plant responses to diverse pathogens and plays a
crucial role in signalling downstream of various receptors that perceive immunogenic …
crucial role in signalling downstream of various receptors that perceive immunogenic …