Multidimensional proteomics for cell biology

M Larance, AI Lamond - Nature reviews Molecular cell biology, 2015‏ - nature.com
The proteome is a dynamic system in which each protein has interconnected properties—
dimensions—that together contribute to the phenotype of a cell. Measuring these properties …

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 …

A subcellular map of the human proteome

PJ Thul, L Åkesson, M Wiking, D Mahdessian… - Science, 2017‏ - science.org
INTRODUCTION A complete view of human biology can only be achieved by studying the
molecular components of its smallest functional unit, the cell. Cells are internally organized …

A comprehensive subcellular atlas of the Toxoplasma proteome via hyperLOPIT provides spatial context for protein functions

K Barylyuk, L Koreny, H Ke, S Butterworth, OM Crook… - Cell host & …, 2020‏ - cell.com
Apicomplexan parasites cause major human disease and food insecurity. They owe their
considerable success to highly specialized cell compartments and structures. These …

System-wide analysis of RNA and protein subcellular localization dynamics

E Villanueva, T Smith, M Pizzinga, M Elzek… - Nature …, 2024‏ - nature.com
Although the subcellular dynamics of RNA and proteins are key determinants of cell
homeostasis, their characterization is still challenging. Here we present an integrative …

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 …

A draft map of the mouse pluripotent stem cell spatial proteome

A Christoforou, CM Mulvey, LM Breckels… - Nature …, 2016‏ - nature.com
Abstract Knowledge of the subcellular distribution of proteins is vital for understanding
cellular mechanisms. Capturing the subcellular proteome in a single experiment has proven …

MSnbase, efficient and elegant R-based processing and visualization of raw mass spectrometry data

L Gatto, S Gibb, J Rainer - Journal of Proteome Research, 2020‏ - ACS Publications
We present version 2 of the MSnbase R/Bioconductor package. MSnbase provides
infrastructure for the manipulation, processing, and visualization of mass spectrometry data …

[HTML][HTML] SOS1 tonoplast neo-localization and the RGG protein SALTY are important in the extreme salinity tolerance of Salicornia bigelovii

OR Salazar, K Chen, VJ Melino, MP Reddy… - Nature …, 2024‏ - nature.com
The identification of genes involved in salinity tolerance has primarily focused on model
plants and crops. However, plants naturally adapted to highly saline environments offer …

[HTML][HTML] A portrait of the human organelle proteome in space and time during cytomegalovirus infection

PMJ Beltran, RA Mathias, IM Cristea - Cell systems, 2016‏ - cell.com
The organelles within a eukaryotic host are manipulated by viruses to support successful
virus replication and spread of infection, yet the global impact of viral infection on host …