Instrumentation at the leading edge of proteomics

TM Peters-Clarke, JJ Coon, NM Riley - Analytical Chemistry, 2024 - ACS Publications
The proteome, or collection of proteoforms expressed in a biological system, is dynamic and
heterogeneous. As our appreciation for the complexity of the proteome has evolved, so have …

ROS-induced ribosome impairment underlies ZAKα-mediated metabolic decline in obesity and aging

G Snieckute, L Ryder, AC Vind, Z Wu, FS Arendrup… - Science, 2023 - science.org
The ribotoxic stress response (RSR) is a signaling pathway in which the p38-and c-Jun N-
terminal kinase (JNK)–activating mitogen-activated protein kinase kinase kinase (MAP3K) …

Mass spectrometry-based proteomic landscape of rice reveals a post-transcriptional regulatory role of N6-methyladenosine

ST Li, Y Ke, Y Zhu, TY Zhu, H Huang, L Li, Z Hou… - Nature Plants, 2024 - nature.com
Rice is one of the most important staple food and model species in plant biology, yet its
quantitative proteomes are largely uncharacterized. Here we quantify the relative protein …

Oktoberfest: Open‐source spectral library generation and rescoring pipeline based on Prosit

M Picciani, W Gabriel, VG Giurcoiu, O Shouman… - …, 2024 - Wiley Online Library
Abstract Machine learning (ML) and deep learning (DL) models for peptide property
prediction such as Prosit have enabled the creation of high quality in silico reference …

Fast and deep phosphoproteome analysis with the Orbitrap Astral mass spectrometer

NM Lancaster, P Sinitcyn, P Forny… - Nature …, 2024 - nature.com
Owing to its roles in cellular signal transduction, protein phosphorylation plays critical roles
in myriad cell processes. That said, detecting and quantifying protein phosphorylation has …

A large-scale proteogenomic atlas of pear

P Wang, X Wu, Z Shi, S Tao, Z Liu, K Qi, Z ** protein states and interactions across the tree of life with co-fractionation mass spectrometry
MA Skinnider, MO Akinlaja, LJ Foster - Nature communications, 2023 - nature.com
We present CFdb, a harmonized resource of interaction proteomics data from 411 co-
fractionation mass spectrometry (CF-MS) datasets spanning 21,703 fractions. Meta-analysis …

Mass spectrometry-based atlas of extracellular matrix proteins across 25 mouse organs

MC McCabe, AJ Saviola… - Journal of proteome …, 2023 - ACS Publications
The extracellular matrix (ECM) is a critical non-cellular component of multicellular organisms
containing a variety of proteins, glycoproteins, and proteoglycans which have been …

Quantitative map** of the in vivo O-GalNAc glycoproteome in mouse tissues identifies GalNAc-T2 O-glycosites in metabolic disorder

W Yang, E Tian, A Chernish, P McCluggage… - Proceedings of the …, 2023 - pnas.org
The family of GalNAc-Ts (GalNAcpolypeptide: N-Acetylgalactosaminyl transferases)
catalyzes the first committed step in the synthesis of O-glycans, which is an abundant and …

[HTML][HTML] Data-independent acquisition-based global phosphoproteomics reveal the diverse roles of casein kinase 1 in plant development

L Qu, M Liu, L Zheng, X Wang, H Xue - Science Bulletin, 2023 - Elsevier
Abstract Casein kinase 1 (CK1) is serine/threonine protein kinase highly conserved among
eukaryotes, and regulates multiple developmental and signaling events through …