Post-translational modifications and mass spectrometry detection

In this review, we provide a comprehensive bibliographic overview of the role of mass spectrometry and the recent technical developments in the detection of post-translational modifications (PTMs). We briefly describe the principles of mass spectrometry for detecting PTMs and the protein and peptide enrichment strategies for PTM analysis, including phosphorylation, acetylation and oxidation. This review presents a bibliographic overview of the scientific achievements and the recent technical development in the detection of PTMs is provided. In order to ascertain the state of the art in mass spectrometry and proteomics methodologies for the study of PTMs, we analyzed all the PTM data introduced in the Universal Protein Resource (UniProt) and the literature published in the last three years. The evolution of curated data in UniProt for proteins annotated as being post-translationally modified is also analyzed. Additionally, we have undertaken a careful analysis of the research articles published in the years 2010 to 2012 reporting the detection of PTMs in biological samples by mass spectrometry. © 2013 Elsevier Inc.

Dynamics of linear polymers in random media

We study phenomenological scaling theories of the polymer dynamics in random media, employing the existing scaling theories of polymer chains and the percolation statistics. We investigate both the Rouse and the Zimm model for Brownian dynamics and estimate the diffusion constant of the center-of-mass of the chain in such disordered media. For internal dynamics of the chain, we estimate the dynamic exponents. We propose similar scaling theory for the reptation dynamics of the chain in the framework of Flory theory for the disordered medium. The modifications in the case of correlated disorders are also discussed. .

The thermal performance of the polysaccharides extracted from hardwood:cellulose and hemicellulose

The pyrolytic behaviour of individual component in biomass needs to be understood to gain insight into the mechanism of biomass pyrolysis. A comparative study on the pyrolysis of cellulose (hexose-based polysaccharides) and hemicallulose (pentose-based polysaccharides) is performed by two sets of experiments including TG analysis and Py-GC-MS/FTIR. The samples of these two polysaccharide components are thermally decomposed in TGA at the heating rate of 5 and 60 K/min to demonstrate the different characteristics of mass loss stage(s) between them. The yield of pyrolytic products is examined by a fluidized-bed fast pyrolysis unit. The experiment confirms that cellulose mainly contributes to bio-oil production (reaching the maximum of 72% at 580 °C), while hemicellulose works as an important precursor for the char production (∼25%). The compounds in the gaseous mixture (CO and CO2) and bio-oil (levoglucosan, furfural, aldehyde, acetone and acetic acid) are further characterized by GC-MS for cellulose and GC-FTIR for hemicellulose, and their formations are investigated thoroughly. © 2010 Elsevier Ltd. All rights reserved.

The role of protein oxidation in ageing & disease

Ageing is a natural phenomenon of the human lifecycle, yet it is still not understood what causes the deterioration of the human body near the end of the lifespan. One popular theory is the Free Radical Theory of Ageing, which proposes that oxidative damage to biomolecules causes ageing of tissues. The ageing population is affected by many chronic diseases. This study focused on sarcopenia (muscle loss in ageing) and obesity as two models for comparison of oxidative damage in muscle proteins in mice. The aim of the study was to develop advanced mass spectrometry methods to detect specific oxidative modifications to mouse muscle proteins, including oxidation, nitration, chlorination, and carbonyl group formation, but western blotting was also used to provide complementary information on the oxidative state of proteins from aged and obese muscle. Mass spectrometry proved to be a powerful tool, enabling identification of the types of modifications present, the sites at which they were present and percentage of the peptide populations that were modified. Targeted and semi-targeted mass spectrometry methods were optimised for the identification and quantitation of the oxidised residues in muscle proteins. The development of the quantitative methods enabled comparisons of mass spectrometry instruments. Both the Time of Flight and QTRAP systems showed advantages of using the different mass analysers to quantify oxidative modifications. Several oxidised residues were characterised and quantified in both the obese and sarcopenic models, and higher levels of oxidation were found compared to their control counterparts. Residues found to be oxidised were oxidation of proline, tyrosine and tryptophan, dioxidation of methionine, allysine and nitration of tyrosine. However quantification was performed on methionine dioxidation and cysteine trioxidation containing residues in SERCA. The combination of measuring residue susceptibility and functional studies could contribute to understanding the overall role of oxidation in ageing and obesity.