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 …

Recent advances of small extracellular vesicle biomarkers in breast cancer diagnosis and prognosis

Y Lee, J Ni, J Beretov, VC Wasinger, P Graham, Y Li - Molecular cancer, 2023 - Springer
Current clinical tools for breast cancer (BC) diagnosis are insufficient but liquid biopsy of
different bodily fluids has recently emerged as a minimally invasive strategy that provides a …

Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography–mass spectrometry

P Mertins, LC Tang, K Krug, DJ Clark, MA Gritsenko… - Nature protocols, 2018 - nature.com
Here we present an optimized workflow for global proteome and phosphoproteome analysis
of tissues or cell lines that uses isobaric tags (TMT (tandem mass tags)-10) for multiplexed …

A review on quantitative multiplexed proteomics

N Pappireddi, L Martin, M Wühr - Chembiochem, 2019 - Wiley Online Library
Over the last few decades, mass spectrometry‐based proteomics has become an
increasingly powerful tool that is now able to routinely detect and quantify thousands of …

MultiNotch MS3 enables accurate, sensitive, and multiplexed detection of differential expression across cancer cell line proteomes

GC McAlister, DP Nusinow, MP Jedrychowski… - Analytical …, 2014 - ACS Publications
Multiplexed quantitation via isobaric chemical tags (eg, tandem mass tags (TMT) and
isobaric tags for relative and absolute quantitation (iTRAQ)) has the potential to revolutionize …

Protein analysis by shotgun/bottom-up proteomics

Y Zhang, BR Fonslow, B Shan, MC Baek… - Chemical …, 2013 - ACS Publications
According to Genome Sequencing Project statistics (http://www. ncbi. nlm. nih.
gov/genomes/static/gpstat. html), as of February 16, 2012, complete gene sequences have …

Isobaric labeling-based relative quantification in shotgun proteomics

N Rauniyar, JR Yates III - Journal of proteome research, 2014 - ACS Publications
Mass spectrometry plays a key role in relative quantitative comparisons of proteins in order
to understand their functional role in biological systems upon perturbation. In this review, we …

NOREVA: normalization and evaluation of MS-based metabolomics data

B Li, J Tang, Q Yang, S Li, X Cui, Y Li… - Nucleic acids …, 2017 - academic.oup.com
Diverse forms of unwanted signal variations in mass spectrometry-based metabolomics data
adversely affect the accuracies of metabolic profiling. A variety of normalization methods …

Thermal proteome profiling for interrogating protein interactions

A Mateus, N Kurzawa, I Becher, S Sridharan… - Molecular systems …, 2020 - embopress.org
Thermal proteome profiling (TPP) is based on the principle that, when subjected to heat,
proteins denature and become insoluble. Proteins can change their thermal stability upon …

Benchmarking common quantification strategies for large-scale phosphoproteomics

A Hogrebe, L von Stechow, DB Bekker-Jensen… - Nature …, 2018 - nature.com
Comprehensive mass spectrometry (MS)-based proteomics is now feasible, but
reproducible quantification remains challenging, especially for post-translational …