Understudied proteins: opportunities and challenges for functional proteomics

G Kustatscher, T Collins, AC Gingras, T Guo… - Nature …, 2022 - nature.com
Most research aiming at understanding the molecular foundations of life and disease has
focused on a limited set of increasingly well-known proteins while the biological functions of …

Tutorial: best practices and considerations for mass-spectrometry-based protein biomarker discovery and validation

ES Nakayasu, M Gritsenko, PD Piehowski, Y Gao… - Nature …, 2021 - nature.com
Mass-spectrometry-based proteomic analysis is a powerful approach for discovering new
disease biomarkers. However, certain critical steps of study design such as cohort selection …

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 …

Parallelized acquisition of orbitrap and astral analyzers enables high-throughput quantitative analysis

HI Stewart, D Grinfeld, A Giannakopulos… - Analytical …, 2023 - ACS Publications
The growing trend toward high-throughput proteomics demands rapid liquid
chromatography–mass spectrometry (LC–MS) cycles that limit the available time to gather …

Ultra-high-throughput clinical proteomics reveals classifiers of COVID-19 infection

CB Messner, V Demichev, D Wendisch, L Michalick… - Cell systems, 2020 - cell.com
The COVID-19 pandemic is an unprecedented global challenge, and point-of-care
diagnostic classifiers are urgently required. Here, we present a platform for ultra-high …

Proteomic landscape of Alzheimer's Disease: novel insights into pathogenesis and biomarker discovery

B Bai, D Vanderwall, Y Li, X Wang, S Poudel… - Molecular …, 2021 - Springer
Mass spectrometry-based proteomics empowers deep profiling of proteome and protein
posttranslational modifications (PTMs) in Alzheimer's disease (AD). Here we review the …

[HTML][HTML] Single-cell proteomics: progress and prospects

RT Kelly - Molecular & Cellular Proteomics, 2020 - Elsevier
MS-based proteome profiling has become increasingly comprehensive and quantitative, yet
a persistent shortcoming has been the relatively large samples required to achieve an in …

Sex differences in brain protein expression and disease

AP Wingo, Y Liu, ES Gerasimov, SM Vattathil, J Liu… - Nature medicine, 2023 - nature.com
Most complex human traits differ by sex, but we have limited insight into the underlying
mechanisms. Here, we investigated the influence of biological sex on protein expression …

[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 …

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 …