Instrumentation at the leading edge of proteomics

TM Peters-Clarke, JJ Coon, NM Riley - Analytical Chemistry, 2023 - 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 …

High-throughput analysis of hazards in novel food based on the density functional theory and multimodal deep learning

L Shi, W Jia, R Zhang, Z Fan, W Bian, H Mo - Food Chemistry, 2024 - Elsevier
The emergence of cultured meat presents the potential for personalized food additive
manufacturing, offering a solution to address future food resource scarcity. Processing raw …

Systematic optimization of automated phosphopeptide enrichment for high-sensitivity phosphoproteomics

P Bortel, I Piga, C Koenig, C Gerner… - Molecular & Cellular …, 2024 - ASBMB
Improving coverage, robustness, and sensitivity is crucial for routine phosphoproteomics
analysis by single-shot liquid chromatography-tandem mass spectrometry (LC-MS/MS) from …

Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition

UH Guzman, A Martinez-Val, Z Ye, E Damoc… - Nature …, 2024 - nature.com
Mass spectrometry (MS)-based proteomics aims to characterize comprehensive proteomes
in a fast and reproducible manner. Here we present the narrow-window data-independent …

In-Depth Endogenous Phosphopeptidomics of Serum with Zirconium (IV)-Grafted Mesoporous Silica Enrichment

C Wu, S Zhang, C Hou, S Byers, J Ma - Analytical Chemistry, 2024 - ACS Publications
Detection of endogenous peptides, especially those with modifications (such as
phosphorylation) in biofluids, can serve as an indicator of intracellular pathophysiology …

Gas-Phase Fractionation Data-Independent Acquisition Analysis of 3D Cocultured Spheroid Tumor Model Reveals Altered Translational Processes and Signaling …

AE Shannon, CE Boos, BC Searle… - Journal of Proteome …, 2024 - ACS Publications
Colorectal cancer (CRC) contains considerable heterogeneity; therefore, models of the
disease must also reflect the multifarious components. Compared to traditional 2D models …

Benefit of In Silico Predicted Spectral Libraries in Data-Independent Acquisition Data Analysis Workflows

A Staes, T Mendes Maia, S Dufour… - Journal of Proteome …, 2024 - ACS Publications
Data-independent acquisition (DIA) has become a well-established method for MS-based
proteomics. However, the list of options to analyze this type of data is quite extensive, and …

Emerging potential of immunopeptidomics by mass spectrometry in cancer immunotherapy

Y Minegishi, Y Haga, K Ueda - Cancer Science, 2024 - Wiley Online Library
With significant advances in analytical technologies, research in the field of cancer
immunotherapy, such as adoptive T cell therapy, cancer vaccine, and immune checkpoint …

Acquisition and analysis of DIA-based proteomic data: a comprehensive survey in 2023

R Lou, W Shui - Molecular & Cellular Proteomics, 2024 - ASBMB
Data-independent acquisition (DIA) mass spectrometry (MS) has emerged as a powerful
technology for high-throughput, accurate, and reproducible quantitative proteomics. This …

[HTML][HTML] Protocol for high-throughput semi-automated label-free-or TMT-based phosphoproteome profiling

C Koenig, A Martinez-Val, P Naicker, S Stoychev… - STAR protocols, 2023 - Elsevier
Tandem mass tags data-dependent acquisition (TMT-DDA) as well as data-independent
acquisition-based label-free quantification (LFQ-DIA) have become the leading workflows to …