Quantitation in mass-spectrometry-based proteomics

WX Schulze, B Usadel - Annual review of plant biology, 2010 - annualreviews.org
Mass-spectrometry-based proteomics, the large-scale analysis of proteins by mass
spectrometry, has emerged as a new technology over the last decade and become routine …

Application of machine learning in spatial proteomics

M Mou, Z Pan, M Lu, H Sun, Y Wang… - Journal of Chemical …, 2022 - ACS Publications
Spatial proteomics is an interdisciplinary field that investigates the localization and dynamics
of proteins, and it has gained extensive attention in recent years, especially the subcellular …

Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics

A Geladaki, N Kočevar Britovšek, LM Breckels… - Nature …, 2019 - nature.com
The study of protein localisation has greatly benefited from high-throughput methods
utilising cellular fractionation and proteomic profiling. Hyperplexed Localisation of Organelle …

Novel asymmetrically localizing components of human centrosomes identified by complementary proteomics methods

L Jakobsen, K Vanselow, M Skogs, Y Toyoda… - The EMBO …, 2011 - embopress.org
Centrosomes in animal cells are dynamic organelles with a proteinaceous matrix of
pericentriolar material assembled around a pair of centrioles. They organize the microtubule …

A comparison of labeling and label-free mass spectrometry-based proteomics approaches

VJ Patel, K Thalassinos, SE Slade… - Journal of proteome …, 2009 - ACS Publications
The proteome of the recently discovered bacterium Methylocella silvestris has been
characterized using three profiling and comparative proteomics approaches. The organism …

Using hyperLOPIT to perform high-resolution mapping of the spatial proteome

CM Mulvey, LM Breckels, A Geladaki, NK Britovšek… - Nature protocols, 2017 - nature.com
The organization of eukaryotic cells into distinct subcompartments is vital for all functional
processes, and aberrant protein localization is a hallmark of many diseases. Microscopy …

Deep proteome coverage based on ribosome profiling aids mass spectrometry-based protein and peptide discovery and provides evidence of alternative translation …

G Menschaert, W Van Criekinge, T Notelaers… - Molecular & cellular …, 2013 - ASBMB
An increasing number of studies involve integrative analysis of gene and protein expression
data, taking advantage of new technologies such as next-generation transcriptome …

Protein neighbors and proximity proteomics

JS Rees, XW Li, S Perrett, KS Lilley… - Molecular & Cellular …, 2015 - ASBMB
Within cells, proteins can co-assemble into functionally integrated and spatially restricted
multicomponent complexes. Often, the affinities between individual proteins are relatively …

Putative glycosyltransferases and other plant Golgi apparatus proteins are revealed by LOPIT proteomics

N Nikolovski, D Rubtsov, MP Segura, GP Miles… - Plant …, 2012 - academic.oup.com
The Golgi apparatus is the central organelle in the secretory pathway and plays key roles in
glycosylation, protein sorting, and secretion in plants. Enzymes involved in the biosynthesis …

Proteomics technologies for the global identification and quantification of proteins

IA Brewis, P Brennan - Advances in protein chemistry and structural biology, 2010 - Elsevier
This review provides an introduction for the nonspecialist to proteomics and in particular the
major approaches available for global protein identification and quantification. Proteomics …