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 …

Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial

C Ludwig, L Gillet, G Rosenberger, S Amon… - Molecular systems …, 2018 - embopress.org
Many research questions in fields such as personalized medicine, drug screens or systems
biology depend on obtaining consistent and quantitatively accurate proteomics data from …

Cerebrospinal fluid proteomics define the natural history of autosomal dominant Alzheimer's disease

ECB Johnson, S Bian, RU Haque, EK Carter… - Nature medicine, 2023 - nature.com
Alzheimer's disease (AD) pathology develops many years before the onset of cognitive
symptoms. Two pathological processes—aggregation of the amyloid-β (Aβ) peptide into …

MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database

X Shao, CD Gomez, N Kapoor… - Nucleic acids …, 2023 - academic.oup.com
The extracellular matrix (ECM) is a complex assembly of proteins that constitutes the scaffold
organizing cells, tissues, and organs. Over the past decade, mass-spectrometry-based …

Mass-spectrometric exploration of proteome structure and function

R Aebersold, M Mann - Nature, 2016 - nature.com
Numerous biological processes are concurrently and coordinately active in every living cell.
Each of them encompasses synthetic, catalytic and regulatory functions that are, almost …

The next horizon in precision oncology: Proteogenomics to inform cancer diagnosis and treatment

H Rodriguez, JC Zenklusen, LM Staudt, JH Doroshow… - Cell, 2021 - cell.com
When it comes to precision oncology, proteogenomics may provide better prospects to the
clinical characterization of tumors, help make a more accurate diagnosis of cancer, and …

Revisiting biomarker discovery by plasma proteomics

PE Geyer, LM Holdt, D Teupser… - Molecular systems biology, 2017 - embopress.org
Clinical analysis of blood is the most widespread diagnostic procedure in medicine, and
blood biomarkers are used to categorize patients and to support treatment decisions …

The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics

LK Pino, BC Searle, JG Bollinger… - Mass spectrometry …, 2020 - Wiley Online Library
Skyline is a freely available, open‐source Windows client application for accelerating
targeted proteomics experimentation, with an emphasis on the proteomics and mass …

Proteogenomics connects somatic mutations to signalling in breast cancer

P Mertins, DR Mani, KV Ruggles, MA Gillette… - Nature, 2016 - nature.com
Somatic mutations have been extensively characterized in breast cancer, but the effects of
these genetic alterations on the proteomic landscape remain poorly understood. Here we …

[HTML][HTML] The extracellular matrix: Tools and insights for the “omics” era

A Naba, KR Clauser, H Ding, CA Whittaker, SA Carr… - Matrix Biology, 2016 - Elsevier
The extracellular matrix (ECM) is a fundamental component of multicellular organisms that
provides mechanical and chemical cues that orchestrate cellular and tissue organization …