Using MetaboAnalyst 5.0 for LC–HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data

Z Pang, G Zhou, J Ewald, L Chang, O Hacariz… - Nature protocols, 2022 - nature.com
Liquid chromatography coupled with high-resolution mass spectrometry (LC–HRMS) has
become a workhorse in global metabolomics studies with growing applications across …

[HTML][HTML] High-throughput proteomics: a methodological mini-review

M Cui, C Cheng, L Zhang - Laboratory investigation, 2022 - Elsevier
Proteomics plays a vital role in biomedical research in the post-genomic era. With the
technological revolution and emerging computational and statistic models, proteomic …

Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism

T Vatanen, KS Jabbar, T Ruohtula, J Honkanen… - Cell, 2022 - cell.com
The perinatal period represents a critical window for cognitive and immune system
development, promoted by maternal and infant gut microbiomes and their metabolites. Here …

System-wide analysis of RNA and protein subcellular localization dynamics

E Villanueva, T Smith, M Pizzinga, M Elzek… - Nature …, 2024 - nature.com
Although the subcellular dynamics of RNA and proteins are key determinants of cell
homeostasis, their characterization is still challenging. Here we present an integrative …

Deciphering the immunopeptidome in vivo reveals new tumour antigens

AM Jaeger, LE Stopfer, R Ahn, EA Sanders, DA Sandel… - Nature, 2022 - nature.com
Immunosurveillance of cancer requires the presentation of peptide antigens on major
histocompatibility complex class I (MHC-I) molecules,,,–. Current approaches to profiling of …

Transcription-coupled repair of DNA–protein cross-links depends on CSA and CSB

CJ Carnie, AC Acampora, AS Bader, C Erdenebat… - Nature Cell …, 2024 - nature.com
Covalent DNA–protein cross-links (DPCs) are toxic DNA lesions that block replication and
require repair by multiple pathways. Whether transcription blockage contributes to the …

[HTML][HTML] Map** diversity in African trypanosomes using high resolution spatial proteomics

NM Moloney, K Barylyuk, E Tromer, OM Crook… - Nature …, 2023 - nature.com
African trypanosomes are dixenous eukaryotic parasites that impose a significant human
and veterinary disease burden on sub-Saharan Africa. Diversity between species and life …

N1-methylpseudouridine found within COVID-19 mRNA vaccines produces faithful protein products

KQ Kim, BD Burgute, SC Tzeng, C **g, C Jungers… - Cell Reports, 2022 - cell.com
Synthetic mRNA technology is a promising avenue for treating and preventing disease. Key
to the technology is the incorporation of modified nucleotides such as N1 …

LFQ-based peptide and protein intensity differential expression analysis

M Bai, J Deng, C Dai, J Pfeuffer… - Journal of Proteome …, 2023 - ACS Publications
Testing for significant differences in quantities at the protein level is a common goal of many
LFQ-based mass spectrometry proteomics experiments. Starting from a table of protein …

Cardiac glycosides protect wormseed wallflower (Erysimum cheiranthoides) against some, but not all, glucosinolate‐adapted herbivores

GC Younkin, ML Alani, A Páez‐Capador… - New …, 2024 - Wiley Online Library
The chemical arms race between plants and insects is foundational to the generation and
maintenance of biological diversity. We asked how the evolution of a novel defensive …