Advances and utility of the human plasma proteome

EW Deutsch, GS Omenn, Z Sun, M Maes… - Journal of proteome …, 2021 - ACS Publications
The study of proteins circulating in blood offers tremendous opportunities to diagnose,
stratify, or possibly prevent diseases. With recent technological advances and the urgent …

[HTML][HTML] Acquisition and analysis of DIA-based proteomic data: A comprehensive survey in 2023

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

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 …

dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts

V Demichev, L Szyrwiel, F Yu, GC Teo… - Nature …, 2022 - nature.com
The dia-PASEF technology uses ion mobility separation to reduce signal interferences and
increase sensitivity in proteomic experiments. Here we present a two-dimensional peak …

MSBooster: improving peptide identification rates using deep learning-based features

KL Yang, F Yu, GC Teo, K Li, V Demichev… - Nature …, 2023 - nature.com
Peptide identification in liquid chromatography-tandem mass spectrometry (LC-MS/MS)
experiments relies on computational algorithms for matching acquired MS/MS spectra …

Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation

AD Brunner, M Thielert, C Vasilopoulou… - Molecular systems …, 2022 - embopress.org
Single‐cell technologies are revolutionizing biology but are today mainly limited to imaging
and deep sequencing. However, proteins are the main drivers of cellular function and in …

Increasing the throughput of sensitive proteomics by plexDIA

J Derks, A Leduc, G Wallmann, RG Huffman… - Nature …, 2023 - nature.com
Current mass spectrometry methods enable high-throughput proteomics of large sample
amounts, but proteomics of low sample amounts remains limited in depth and throughput. To …

M2 macrophage hybrid membrane‐camouflaged targeted biomimetic nanosomes to reprogram inflammatory microenvironment for enhanced enzyme‐thermo …

R Chen, J Yang, M Wu, D Zhao, Z Yuan… - Advanced …, 2023 - Wiley Online Library
Excessive inflammatory reactions caused by uric acid deposition are the key factor leading
to gout. However, clinical medications cannot simultaneously remove uric acid and eliminate …

Advances in data‐independent acquisition mass spectrometry towards comprehensive digital proteome landscape

RB Kitata, JC Yang, YJ Chen - Mass spectrometry reviews, 2023 - Wiley Online Library
The data‐independent acquisition mass spectrometry (DIA‐MS) has rapidly evolved as a
powerful alternative for highly reproducible proteome profiling with a unique strength of …

Natural proteome diversity links aneuploidy tolerance to protein turnover

J Muenzner, P Trébulle, F Agostini, H Zauber… - Nature, 2024 - nature.com
Accessing the natural genetic diversity of species unveils hidden genetic traits, clarifies gene
functions and allows the generalizability of laboratory findings to be assessed. One notable …