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 …

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 …

Cyclic immonium ion of lactyllysine reveals widespread lactylation in the human proteome

N Wan, N Wang, S Yu, H Zhang, S Tang, D Wang… - Nature …, 2022 - nature.com
Lactylation was initially discovered on human histones. Given its nascence, its occurrence
on nonhistone proteins and downstream functional consequences remain elusive. Here we …

MS-GF+ makes progress towards a universal database search tool for proteomics

S Kim, PA Pevzner - Nature communications, 2014 - nature.com
Mass spectrometry (MS) instruments and experimental protocols are rapidly advancing, but
the software tools to analyse tandem mass spectra are lagging behind. We present a …

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] Wnt signaling through inhibition of β-catenin degradation in an intact Axin1 complex

VSW Li, SS Ng, PJ Boersema, TY Low, WR Karthaus… - Cell, 2012 - cell.com
Degradation of cytosolic β-catenin by the APC/Axin1 destruction complex represents the key
regulated step of the Wnt pathway. It is incompletely understood how the Axin1 complex …

Lgr5 homologues associate with Wnt receptors and mediate R-spondin signalling

W De Lau, N Barker, TY Low, BK Koo, VSW Li… - Nature, 2011 - nature.com
The adult stem cell marker Lgr5 and its relative Lgr4 are often co-expressed in Wnt-driven
proliferative compartments. We find that conditional deletion of both genes in the mouse gut …

Proteomics beyond trypsin

L Tsiatsiani, AJR Heck - The FEBS journal, 2015 - Wiley Online Library
Peptide‐centered shotgun analysis of proteins has been the core technology in mass
spectrometry based proteomics and has enabled numerous biological discoveries, such as …

The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent '+ 4'cell markers

J Muñoz, DE Stange, AG Schepers… - The EMBO …, 2012 - embopress.org
Two types of stem cells are currently defined in small intestinal crypts: cycling crypt base
columnar (CBC) cells and quiescent '+ 4'cells. Here, we combine transcriptomics with …

Toward a comprehensive characterization of a human cancer cell phosphoproteome

H Zhou, S Di Palma, C Preisinger, M Peng… - Journal of proteome …, 2013 - ACS Publications
Mass spectrometry (MS)-based phosphoproteomics has achieved extraordinary success in
qualitative and quantitative analysis of cellular protein phosphorylation. Considering that an …