Biomedical subjects

Jeremy E Melanson

Publications and source records attributed to Jeremy E Melanson.

5 recordsLinked to original sources

PubMed2006

High-coverage quantitative proteomics using amine-specific isotopic labeling.

Peptide dimethylation with isotopically coded formaldehydes was evaluated as a potential alternative to techniques such as the iTRAQ method for comparative proteomics. The isotopic labeling strategy and custom-designed protein quantitation software were tested using protein standards and then applied to measure proteins levels associated with Alzheimer's disease (AD). The method provided high accuracy (10% error), precision (14% RSD) and coverage (70%) when applied to the analysis of a standard solution of BSA by LC-MS/MS. The technique was then applied to measure protein abundance levels in brain tissue afflicted with AD relative to normal brain tissue. 2-D LC-MS analysis identified 548 unique proteins (p<0.05). Of these, 349 were quantified with two or more peptides that met the statistical criteria used in this study. Several classes of proteins exhibited significant changes in abundance. For example, elevated levels of antioxidant proteins and decreased levels of mitochondrial electron transport proteins were observed. The results demonstrate the utility of the labeling method for high-throughput quantitative analysis.

Alzheimer Disease↗

PubMed2006

Targeted comparative proteomics by liquid chromatography/matrix-assisted laser desorption/ionization triple-quadrupole mass spectrometry.

Here we report the first application of a matrix-assisted laser desorption/ionization (MALDI) triple-quadrupole mass spectrometer for targeted proteomics. Employing an amine-specific isotopic labelling approach, the technique was validated using five randomly selected bovine serum albumin peptides differentially labelled at known ratios. An indirect benefit of the isotopic labelling technique is a significant enhancement of the a1 ion in tandem mass (MS/MS) spectra of all peptides studied. Therefore, the a1 ion was selected as the fragment ion for multiple reaction monitoring (MRM) in all cases, eliminating tedious method development and optimization. Accurate quantification was achieved with an average relative standard deviation (RSD) of 5% (n = 5) and a detection limit of 14 amol. The technique was then applied to validate an important virulence biomarker of the fungal pathogen Candida albicans, which was not accurately quantified using global proteomics experiment employing two-dimensional liquid chromatography/electrospray ionization tandem mass spectrometry (2D-LC/ESI)-MS/MS. Using LC/MALDI-MRM analysis of five tryptic peptides, the protein PHR1 was found to be upregulated in the hyphal (pathogenic) form of C. albicans by a factor of 7.7 +/- 0.8.

Amino Acid Sequence↗

PubMed2006

Deviation from the mobile proton model in amino-modified peptides: implications for multiple reaction monitoring analysis of peptides.

The study of peptide fragmentation is important to the understanding of chemical processes occurring in the gas phase and the more practical concern of peptide identification for proteomic analysis. Using the mobile proton model as a framework, we explore the effect of amino-group modifications on peptide fragmentation. Three aldehydes are used to transform the peptides' primary amino groups into either a dimethylamino or a heterocyclic structure (five- or six-membered). The observed fragmentation patterns deviate strongly from those observed for the analogous underivatised peptides. In particular, the a1 ion is the base peak in most tandem mass spectra of the derivatised peptides. The a1 ion intensity depends strongly on the N-terminal amino acid, with tyrosine and phenylalanine having the strongest enhancement. Despite the change in fragmentation patterns of the derivatised peptides, they still provide high-quality tandem mass spectra that, in many cases, are more amenable to database searching than the spectra of underivatised peptides. In addition, the reliable presence of the a1 ion facilitates rapid quantitative measurements using the multiple reaction monitoring approach.

Aldehydes↗

PubMed2004

Noncovalent labeling of myoglobin for capillary electrophoresis with laser-induced fluorescence detection by reconstitution with a fluorescent porphyrin.

Traditional protein labeling reactions for capillary electrophoresis (CE) with laser-induced fluorescence (LIF) detection suffer from a variety of disadvantages. The reactions can be nonquantitative on a reasonable time scale, require relatively high concentrations of protein and fluorophore, and can give multiple reaction products that can not be separated. Herein, we describe a new noncovalent labeling technique that is rapid, selective for myoglobin, and gives a simple reaction product. Myoglobin is denatured with either 5.4 M urea or low pH (2.0). The denatured myoglobin releases its nonfluorescent heme group. A fluorescent porphyrin (protoporphyrin IX (PPIX) or its zinc (II) complex, Zn-PPIX), is added to the mixture and the solution conditions are altered (dilute to 0.54 M urea or adjust pH to 7.0) to allow myoglobin refolding. Upon refolding, the protein incorporates PPIX from solution, thus making the reaction product fluorescent. The experimental conditions have been optimized for both urea and low-pH denaturation of myoglobin. The latter procedure produces a detection limit of 50 nM. Alternatively, the reaction can be performed without denaturation by a simple exchange of the porphyrins. The use of Zn-PPIX yields the most efficient reaction. The low-pH reaction is unaffected by a 2000-fold excess of bovine serum albumin.

Electrophoresis, Capillary↗

PubMed2002

Enhanced detection of porphyrins by capillary electrophoresis-laser induced fluorescence.

A highly sensitive technique for the analysis of urinary porphyrins using capillary electrophoresis (CE) coupled with laser-induced fluorescence (LIF) detection is reported. Separation of mesoporphyrin IX, coproporphyrin, uroporphyrin and the penta-, hexa- and heptacarboxylic acid porphyrins was achieved in 11 min using a 10 mM 2-(N-cyclohexylamino)ethanesulfonic acid (CHES, pH 10) -75 mM sodium dodecyl sulfate (SDS) buffer. Migration time and peak area repeatability were less than 1 and 5% relative standard deviation (RSD), respectively. Limits of detection of 20 pM (2 x 10(-11) M) were achieved employing the recently introduced Nichia violet diode laser for excitation at 400 nm. This represents an enhancement in sensitivity of over two orders of magnitude compared to previous reports. This high sensitivity for urinary porphyrins was demonstrated through the quantification of coproporphyrin and uroporphyrin in urine samples after up to a 100-fold dilution.

Calibration↗