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 …

Recent advances in mass spectrometry based clinical proteomics: applications to cancer research

A Macklin, S Khan, T Kislinger - Clinical proteomics, 2020 - Springer
Cancer biomarkers have transformed current practices in the oncology clinic. Continued
discovery and validation are crucial for improving early diagnosis, risk stratification, and …

Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells

Y Zhu, PD Piehowski, R Zhao, J Chen, Y Shen… - Nature …, 2018 - nature.com
Nanoscale or single-cell technologies are critical for biomedical applications. However,
current mass spectrometry (MS)-based proteomic approaches require samples comprising a …

Ultrasensitive proteome analysis using paramagnetic bead technology

CS Hughes, S Foehr, DA Garfield… - Molecular systems …, 2014 - embopress.org
In order to obtain a systems‐level understanding of a complex biological system, detailed
proteome information is essential. Despite great progress in proteomics technologies …

Proteomic analysis of single mammalian cells enabled by microfluidic nanodroplet sample preparation and ultrasensitive NanoLC‐MS

Y Zhu, G Clair, WB Chrisler, Y Shen, R Zhao… - Angewandte …, 2018 - Wiley Online Library
We report on the quantitative proteomic analysis of single mammalian cells. Fluorescence‐
activated cell sorting was employed to deposit cells into a newly developed nanodroplet …

Evaluation of FASP, SP3, and iST protocols for proteomic sample preparation in the low microgram range

M Sielaff, J Kuharev, T Bohn, J Hahlbrock… - Journal of proteome …, 2017 - ACS Publications
Efficient and reproducible sample preparation is a prerequisite for any robust and sensitive
quantitative bottom-up proteomics workflow. Here, we performed an independent …

Metabolic reprogramming toward oxidative phosphorylation identifies a therapeutic target for mantle cell lymphoma

L Zhang, Y Yao, S Zhang, Y Liu, H Guo… - Science translational …, 2019 - science.org
Metabolic reprogramming is linked to cancer cell growth and proliferation, metastasis, and
therapeutic resistance in a multitude of cancers. Targeting dysregulated metabolic pathways …

Next-generation proteomics: towards an integrative view of proteome dynamics

AFM Altelaar, J Munoz, AJR Heck - Nature Reviews Genetics, 2013 - nature.com
Next-generation sequencing allows the analysis of genomes, including those representing
disease states. However, the causes of most disorders are multifactorial, and systems-level …

[HTML][HTML] Automated mass spectrometry imaging of over 2000 proteins from tissue sections at 100-μm spatial resolution

PD Piehowski, Y Zhu, LM Bramer, KG Stratton… - Nature …, 2020 - nature.com
Biological tissues exhibit complex spatial heterogeneity that directs the functions of
multicellular organisms. Quantifying protein expression is essential for elucidating …

Proteomic challenges: sample preparation techniques for microgram-quantity protein analysis from biological samples

P Feist, AB Hummon - International journal of molecular sciences, 2015 - mdpi.com
Proteins regulate many cellular functions and analyzing the presence and abundance of
proteins in biological samples are central focuses in proteomics. The discovery and …