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 …

Mass spectrometry–based proteomics and network biology

A Bensimon, AJR Heck… - Annual review of …, 2012 - annualreviews.org
In the life sciences, a new paradigm is emerging that places networks of interacting
molecules between genotype and phenotype. These networks are dynamically modulated …

Determining target engagement in living systems

GM Simon, MJ Niphakis, BF Cravatt - Nature chemical biology, 2013 - nature.com
Chemical probes are critical tools for elucidating the biological functions of proteins and can
lead to new medicines for treating disease. The pharmacological validation of protein …

Large-scale discovery of substrates of the human kinome

N Sugiyama, H Imamura, Y Ishihama - Scientific reports, 2019 - nature.com
Kinase networks are important for cellular signal transduction. Despite tremendous efforts to
uncover these signaling pathways, huge numbers of uncharacterized phosphosites still …

Application of targeted mass spectrometry in bottom-up proteomics for systems biology research

NP Manes, A Nita-Lazar - Journal of proteomics, 2018 - Elsevier
The enormous diversity of proteoforms produces tremendous complexity within cellular
proteomes, facilitates intricate networks of molecular interactions, and constitutes a …

Functional proteomics to dissect tyrosine kinase signalling pathways in cancer

W Kolch, A Pitt - Nature Reviews Cancer, 2010 - nature.com
Advances in the generation and interpretation of proteomics data have spurred a transition
from focusing on protein identification to functional analysis. Here we review recent …

[HTML][HTML] Phosphoproteomics in cancer

HC Harsha, A Pandey - Molecular oncology, 2010 - Elsevier
Reversible protein phosphorylation serves as a basis for regulating a number of cellular
processes. Aberrant activation of kinase signaling pathways is commonly associated with …

Pathway-based identification of biomarkers for targeted therapeutics: personalized oncology with PI3K pathway inhibitors

JN Andersen, S Sathyanarayanan, A Di Bacco… - Science translational …, 2010 - science.org
Although we have made great progress in understanding the complex genetic alterations
that underlie human cancer, it has proven difficult to identify which molecularly targeted …

Spatiotemporally resolved protein detection in live cells using nanopore biosensors

H Zhang, T Zhao, P Huang, Q Wang, H Tang, X Chu… - ACS …, 2022 - ACS Publications
Spatiotemporal detection of proteins in living cells is a persistent challenge but is the key to
understanding their cellular biology and develo** theranostic technologies. We develop a …

The revolution and evolution of shotgun proteomics for large-scale proteome analysis

JR Yates III - Journal of the American Chemical Society, 2013 - ACS Publications
Mass spectrometry has evolved at an exponential rate over the last 100 years. Innovations in
the development of mass spectrometers have created powerful instruments capable of …