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Protein Dynamics Viewer Splash

Protein Dynamics Viewer

The Lamond Lab have performed large-scale proteomics experiments to study proteome dynamics. The aim of these mass spectrometry experiments is to generate protein annotations, such as synthesis, degradation, turnover and half-life rates; subcellular localisation and abundance; and potential isoforms. This viewer aims to communicate these protein annotations via easy-to-access graphical representations.



publications

Mark Larance, Yasmeen Ahmad, Kathryn J Kirkwood, Tony Ly and Angus I. Lamond (2013)
Global Subcellular Characterization of Protein Degradation Using Quantitative Proteomics
Molecular & Cellular Proteomics

Yasmeen Ahmad, Francois-Michel Boisvert, Emma Lundberg, Mathias Uhlen and Angus I. Lamond (2011)
Systematic Analysis of Protein Pools, Isoforms and Modifications Affecting Turnover and Subcellular Localisation
Molecular & Cellular Proteomics

Francois-Michel Boisvert, Yasmeen Ahmad, Marek Gierlinski, Fabien Charriere, Douglas Lamont, Michelle Scott, Geoff Barton and Angus I. Lamond (2011)
A Quantitative Spatial Proteomics Analysis of Proteome Turnover in Human Cells
Molecular & Cellular Proteomics

Francois-Michel Boisvert, Yun Wah Lam, Douglas Lamont and Angus I. Lamond (2010)
A Quantitative Proteomics Analysis of Subcellular Proteome Localization and Changes Induced by DNA Damage
Molecular & Cellular Proteomics



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Proteome Dynamics

Multi-dimensional Analysis

Proteomics technology has now become truly quantitative, multidimensional and amazingly versatile. The simple goal of protein identification has thus been superseded by more ambitious aims involving large-scale protein quantification in a panoply of applications.

Proteomics has now extended beyond simple high sensitivity protein detection. Rapid and efficient protein quantification, as well as identification, has opened the doors to a wide range of new applications for the systematic analysis of cell proteins.

These advances promise to revolutionise our understanding of the functional interpretation of genomic information. This leads us into what we can define as the third generation phase of modern MS-based proteomics.

The first generation was marked by the development of MS-based technologies for peptide analysis that enhanced the sensitivity of protein identification. The second generation arose from the development of SILAC and other quantitative methods that allowed the use of MS analysis for high throughput measurement of protein dynamics and interactions, rather than just identification.

As we now enter the third generation phase, we anticipate that MS-based proteomics will be used routinely to measure absolute protein levels and survey the dynamic responses of entire proteomes.



Abundance & Localisation

Localisation and Abundance

Using mass spectrometry techniques, we have measured protein abundance and localisation for over 8,000 proteins, spanning three cellular compartments, namely the cytoplasm, nucleus and nucleolus. Data has been gathered for two human cell lines: HeLa and HCT116.

The data show that the proteome predominantly partitions into a specific subcellular location, however the majority of proteins do show a signal in two or more compartments. Often the cellular compartment in which a protein complex is formed is not the primary functional location for the protein complex.




Turnover & Half-Life

Turnover and Half-Life

Using a combined PULSE SILAC mass spectrometry technique, we have been able to measure protein synthesis and degradation rates for over 6,000 proteins in HeLa cells, spanning three cellular compartments, namely cytoplasm, nucleus and the nucleolus. From this data, bioinformatics approaches were used to calculate turnover and half-life values.

The protein turnover is calculated by first measuring the separate curves of synthesis and degradation rates for each protein, and then identifying the point at which these curves cross. This measurement corresponds to the time it takes for 50% of the protein to turn over.

The half-life of a protein is defined as the time taken for 50% of the pool of the pre-existing protein species to be degraded.



Systematic Detection of Protein Pools, Isoforms and Modifications

Localisation and Abundance

Our recent published work has outlined systematic approaches for detection of either distinct isoforms, or separate pools of the same isoform, with differential biological properties.

Protein isoforms were detected using the following data analysis strategies that evaluate differences between groups of peptides assigned to a protein: