Cancer proteogenomics: current impact and future prospects

DR Mani, K Krug, B Zhang, S Satpathy… - Nature Reviews …, 2022 - nature.com
Genomic analyses in cancer have been enormously impactful, leading to the identification of
driver mutations and development of targeted therapies. But the functions of the vast majority …

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 …

diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition

F Meier, AD Brunner, M Frank, A Ha, I Bludau… - Nature …, 2020 - nature.com
Data-independent acquisition modes isolate and concurrently fragment populations of
different precursors by cycling through segments of a predefined precursor m/z range …

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 …

Biological nanopore approach for single‐molecule protein sequencing

ZL Hu, MZ Huo, YL Ying, YT Long - Angewandte Chemie, 2021 - Wiley Online Library
Proteins are responsible for the occurrence and treatment of many diseases, and therefore
protein sequencing will revolutionize proteomics and clinical diagnostics. Biological …

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 …

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 …

Bioinformatics methods for mass spectrometry-based proteomics data analysis

C Chen, J Hou, JJ Tanner, J Cheng - International journal of molecular …, 2020 - mdpi.com
Recent advances in mass spectrometry (MS)-based proteomics have enabled tremendous
progress in the understanding of cellular mechanisms, disease progression, and the …

Illuminating the dark phosphoproteome

EJ Needham, BL Parker, T Burykin, DE James… - Science …, 2019 - science.org
Protein phosphorylation is a major regulator of protein function and biological outcomes.
This was first recognized through functional biochemical experiments, and in the past …

BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes

F Meier, PE Geyer, S Virreira Winter, J Cox, M Mann - Nature methods, 2018 - nature.com
Great advances have been made in sensitivity and acquisition speed on the Orbitrap mass
analyzer, enabling increasingly deep proteome coverage. However, these advances have …