Biomedical subjects

Duncan H L Robertson

Publications and source records attributed to Duncan H L Robertson.

8 recordsLinked to original sources

PubMed2005

Positional proteomics: selective recovery and analysis of N-terminal proteolytic peptides.

Bottom-up proteomics is the analysis of peptides derived from single proteins or protein mixtures, and because each protein generates tens of peptides, there is scope for controlled reduction in complexity. We report here a new strategy for selective isolation of the N-terminal peptides of a protein mixture, yielding positionally defined peptides. The method is tolerant of several fragmentation methods, and the databases that must be searched are substantially less complex.

Animals↗

PubMed2005

Structural and functional differences in isoforms of mouse major urinary proteins: a male-specific protein that preferentially binds a male pheromone.

The MUPs (major urinary proteins) of the house mouse, Mus domesticus, are lipocalins that bind and slowly release male-specific pheromones in deposited scent marks. However, females also express these proteins, consistent with a second role in encoding individual signatures in scent marks. We have purified and characterized an atypical MUP from the urine of male C57BL/6J inbred mice, which is responsible for the binding of most of the male pheromone, 2-sec-butyl-4,5-dihydrothiazole, and which is also responsible for the slow release of this pheromone from scent marks. This protein is absent from the urine of female mice of the same strain. The protein has been characterized by MS, leading to unequivocal identification as a previously uncharacterized gene product, providing compelling evidence for the expression of this gene in liver and manifestation in urine. These properties contrast strongly with those of the other MUPs in the same urine sample, and suggest that the requirement to manifest a male-specific pheromone has been met by evolution of a cognate protein specifically adapted to the binding and release of this ligand. This atypical MUP is also present in a random sample of wild-caught male mice, confirming that this protein is not specific to the inbred mouse strain but is present in natural populations also.

Amino Acid Sequence↗

PubMed2004

Copper-associated liver disease: a proteomics study of copper challenge in a sheep model.

Sheep display a variant phenotype with respect to their susceptibility to copper and derivative pathology. The North Ronaldsay sheep are acutely sensitive to environmental copper while the Cambridge breed is much more copper-tolerant. A study of protein expression in the liver of the two different breeds of sheep as a result of copper challenge would aid in the understanding of their differing pathophysiologies and contribute to knowledge of copper toxicosis in man. In this initial study, Cambridge breed sheep were challenged with oral copper and liver proteins were analyzed by two-dimensional (2-D) gel electrophoresis. Proteins whose expression pattern was modified by copper exposure were then identified by peptide mass fingerprinting using matrix assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry. In conclusion, the pattern of changes in protein expression were consistent with an early adaptive response to oxidative challenge. This was followed by evidence of an impaired ability of the liver to compensate as copper loading increased, accompanied by oxidative stress-induced injury.

Animals↗

PubMed2004

The proteome of chicken skeletal muscle: changes in soluble protein expression during growth in a layer strain.

The whole animal, and the pectoralis muscle in particular, grows at a greatly enhanced rate in chickens selected for meat production (broilers) when compared to those selected for egg production (layers). As part of an ongoing study to analyse muscle protein dynamics under conditions of rapid growth, we have embarked upon a preliminary characterisation of the proteome of layer chicken pectoralis muscle, at specified time-points from 1 to 27 days after hatching. Soluble extracts of muscle homogenates were separated by two-dimensional (2-D) gel electrophoresis and selected spots were analysed by in-gel tryptic digestion and matrix assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry. Of 90 spots, 51 gave mass spectra that matched to existing chicken proteins present in on-line databases, 12 matched equivalent proteins from non-avian species and 11 yielded good quality spectra but were unable to be matched against existing databases. For many of these proteins, growth over 27 days elicited dramatic changes in relative expression levels. Chicken skeletal muscle offers an excellent system for developmental proteomics.

Animals↗

PubMed2003

Proteome analysis of intact proteins in complex mixtures.

Analysis of intact protein mixtures by electrospray ionization mass spectrometry requires the resolution of a complex, overlapping set of multiply charged envelopes. To ascertain the ability of a moderate resolution mass spectrometer to resolve such mixtures, we have analyzed the soluble proteins of adult chick skeletal muscle. This is a highly specialized tissue showing a marked bias in expression of glycolytic enzymes in the soluble fraction. SDS-PAGE-resolved proteins were first identified by a combination of matrix-assisted laser desorption ionization time-of-flight (TOF) and electrospray ionization tandem mass spectrometry. Then the mixture of intact proteins was introduced into the electrospray source of a Q-TOF mass spectrometer either by direct infusion or via a C4 desalting trap. In both instances, the complex pattern of peaks could be resolved into true masses, and these masses could in many instances be reconciled with the masses predicted from the known protein sequences when qualified by expected co- and post-translational modifications. These included loss of the N-terminal initiator methionine residue and N-terminal acetylation. The ability to resolve such a complex mixture of proteins with a routine instrument is of considerable value in analyses of protein expression and in the confirmation of post-translational changes in mature proteins.

Amino Acid Sequence↗

PubMed2002

Stable isotope labelling in vivo as an aid to protein identification in peptide mass fingerprinting.

Peptide mass fingerprinting (PMF) is a powerful technique for identification of proteins derived from in-gel digests by virtue of their matrix-assisted laser desorption/ionization-time of flight mass spectra. However, there are circumstances where the under-representation of peptides in the mass spectrum and the complexity of the source proteome mean that PMF is inadequate as an identification tool. In this paper, we show that identification is substantially enhanced by inclusion of composition data for a single amino acid. Labelling in vivo with a stable isotope labelled amino acid (in this paper, decadeuterated leucine) identifies the number of such amino acids in each digest fragment, and show a considerable gain in the ability of PMF to identify the parent protein. The method is tolerant to the extent of labelling, and as such, may be applicable to a range of single cell systems.

Deuterium↗

PubMed2002

Polymorphism in major urinary proteins: molecular heterogeneity in a wild mouse population.

Major urinary proteins (MUPs) are present in high levels in the urine of mice, and the specific profile of MUPs varies considerably among wild-caught individuals. We have conducted a detailed study of the polymorphic variation within a geographically constrained island population, analyzing the MUP heterogeneity by isoelectric focusing and analytical ion exchange chromatography. Several MUPs were purified in sufficient quantities for analysis by electrospray ionization mass spectrometry and MALDI-TOF mass spectrometry of endopeptidase Lys-C peptide maps. The results of such analyses permitted the identification of three new MUP allelic variants. In each of these proteins, the sites of variation were located to a restricted segment of the polypeptide chain, projecting to a patch on the surface of the protein, and connected to the central lipocalin calyx through the polypeptide backbone. The restriction of the polymorphic variation to one segment of the polypeptide may be of functional significance, either in the modulation of ligand release or in communication of individuality signals within urinary scent marks.

Animal Communication↗

PubMed2002

Dynamics of protein turnover, a missing dimension in proteomics.

Functional genomic experiments frequently involve a comparison of the levels of gene expression between two or more genetic, developmental, or physiological states. Such comparisons can be carried out at either the RNA (transcriptome) or protein (proteome) level, but there is often a lack of congruence between parallel analyses using these two approaches. To fully interpret protein abundance data from proteomic experiments, it is necessary to understand the contributions made by the opposing processes of synthesis and degradation to the transition between the states compared. Thus, there is a need for reliable methods to determine the rates of turnover of individual proteins at amounts comparable to those obtained in proteomic experiments. Here, we show that stable isotope-labeled amino acids can be used to define the rate of breakdown of individual proteins by inspection of mass shifts in tryptic fragments. The approach has been applied to an analysis of abundant proteins in glucose-limited yeast cells grown in aerobic chemostat culture at steady state. The average rate of degradation of 50 proteins was 2.2%/h, although some proteins were turned over at imperceptible rates, and others had degradation rates of almost 10%/h. This range of values suggests that protein turnover is a significant missing dimension in proteomic experiments and needs to be considered when assessing protein abundance data and comparing it to the relative abundance of cognate mRNA species.

Amino Acids↗