Biomedical subjects

Gregor McCombie

Publications and source records attributed to Gregor McCombie.

9 recordsLinked to original sources

PubMed2006

Enhanced MALDI ionization efficiency at the metal-matrix interface: practical and mechanistic consequences of sample thickness and preparation method.

Electrosprayed spots of varying thickness were evaluated for use as reproducible, homogenous, high efficiency MALDI samples. Thin samples on stainless steel plates were found to give exceptionally strong signals, as did the last layers of thick samples, when ablated down to the steel substrate. A small enhancement was also observed for thin samples on a gold substrate, and with a few-nanometer gold coating on top of a thick sample. Ion yields and intensity ratios can be understood in the context of the previously described quantitative MALDI model including the matrix-metal interfacial ionization potential reduction effect (Knochenmuss, R.; Anal. Chem. 2004, 76, 3179-3184). The absolute and relative stabilities of ion signals were found to be at least a factor of two better for the thin electrosprayed spots, compared to spots prepared by dried droplet methods.

Animals↗

PubMed2006

Recombinant antibodies for the depletion of abundant proteins from human serum.

The identification of biomarkers from serum or plasma is often hindered by a few proteins present at high concentrations, which may obscure less abundant proteins. Ideal serum depletion strategies would be flexible as regards the proteins to be removed, and would feature the use of reagents with long shelf-lives. In this article, we describe a novel protein depletion methodology based on the incubation of serum samples with phage-derived recombinant antibody fragments, which are able to bind to staphylococcal Protein A, and which carry a C-terminal peptide tag capable of streptavidin binding. The resulting protein-antibody complexes can be removed by simultaneous capture on Protein A and/or streptavidin resin. The depletion methodology was exemplified by the isolation of recombinant human mAb fragments specific to abundant human serum Ags and by the simultaneous depletion of albumin, immunoglobulins, alpha2-macroglobulin, hemoglobin, transferrin and haptoglobin. The depleted serum samples were analyzed by 2-DE and by gel-free MS-based methodologies, confirming the efficiency and selectivity of the depletion process. The methodology presented is modular in nature, since several recombinant antibodies can be combined in a single depletion experiment. Furthermore, antibodies do not have to be covalently coupled to a solid support facilitating long-term storage.

Antibodies↗

PubMed2006

MALDI MS imaging of amyloid.

Label-free molecular imaging by mass spectrometry allows simultaneous mapping of multiple analytes in biological tissue sections. In this chapter, the application of this new technology to the detection Abeta peptides in mouse brain sections is discussed.

Amyloid↗

PubMed2005

Spatial and spectral correlations in MALDI mass spectrometry images by clustering and multivariate analysis.

Matrix-assisted laser desorption/ionization mass spectrometry imaging is a technique for direct analysis of tissue sections without the use of molecular tags or contrast agents. The combination of spatial and mass resolution results in large and complex data sets that require powerful and efficient analysis and interpretation tools. Conventional images, derived from a specific analyte mass, do not identify the spatially localized correlations between analytes that are latent in the data. A new approach to find and visualize these correlations is presented. Clustering methods are used to classify pixels by spectral similarity, facilitating definition of distinct spatial regions. Principal component and discriminant analyses are combined to comprehensively identify changes in the mass spectra between regions. Images are generated by projecting the spectra of each pixel on the discriminant spectra; contrast is then a function of multiple correlated peaks.

Algorithms↗

PubMed2005

FT-ICR mass spectrometry in the drug discovery process.

The high mass accuracy and resolution of Fourier transform (FT)-ion cyclotron resonance (ICR) mass spectrometry are making it an increasingly useful tool in drug discovery and development. The basics of FT-ICR are described here, including modern ion sources and fragmentation methods. Although FT-ICR is not a high-throughput method in the traditional sense, previously difficult and complex problems are being efficiently approached using steadily improving instruments and magnets. Applications are surveyed in fields such as proteomics, metabonomics, natural product analysis and non-covalent complexes.

Chemistry, Pharmaceutical↗

PubMed2004

Small-molecule MALDI using the matrix suppression effect to reduce or eliminate matrix background interferences.

The matrix suppression effect (MSE) can lead to high-quality MALDI mass spectra: strong analyte signals and weak or negligible matrix background peaks. Experiment and theory suggest that MSE should be widespread and, therefore, generally applicable to measurement of low molecular weight (LMW) substances. These are otherwise impractical with MALDI due to interference from matrix. Appropriate conditions for MSE were investigated and tested on a variety of LMW substances. Straightforward and semiautomated interpretation was possible for 87.7% of these. Another 3.5% gave poor MSE due to sodium cationization rather than protonation of the analyte, but interpretation was possible. MALDI imaging shows that MSE varies significantly across a typical sample. Selective data accumulation could further increase the utility of the method. Samples containing more than one analyte were also studied. Analyte-analyte suppression was not found to be excessive, and moderately abundant minority species can be adequately detected.

Molecular Weight↗

PubMed2004

Zinc metalloproteinase-mediated cleavage of the human Nogo-66 receptor.

The central nervous system myelin components oligodendrocyte-myelin glycoprotein, myelin-associated glycoprotein and the Nogo-66 domain of Nogo-A inhibit neurite outgrowth by binding the neuronal glycosyl-phosphatidylinositol-anchored Nogo-66 receptor (NgR) that transduces the inhibitory signal to the cell interior via a transmembrane co-receptor, p75NTR. Here, we demonstrate that human NgR expressed in human neuroblastoma cells is constitutively cleaved in a post-ER compartment to generate a lipid-raft associated C-terminal fragment that is present on the cell surface and a soluble N-terminal fragment that is released into the medium. Mass spectrometric analysis demonstrated that the N-terminal fragment terminated just after the C-terminus of the ligand-binding domain of NgR. In common with other shedding mechanisms, the release of this fragment was blocked by a hydroxamate-based inhibitor of zinc metalloproteinases, but not by inhibitors of other protease classes and up-regulated by treatment with the cellular cholesterol depleting agent methyl-beta-cyclodextrin. The N-terminal fragment bound Nogo-66 and blocked Nogo-66 binding to cell surface NgR but failed to associate with p75NTR, indicative of a role as a Nogo-66 antagonist. Furthermore, the N- and C-terminal fragments of NgR were detectable in human brain cortex and the N-terminal fragment was also present in human cerebrospinal fluid, demonstrating that NgR proteolysis occurs within the human nervous system. Our findings thus identify a potential cellular mechanism for the regulation of NgR function at the level of the receptor.

Animals↗

PubMed2003

Quantitative evaluation of noncovalent chorismate mutase-inhibitor binding by ESI-MS.

Electrospray time-of-flight mass spectrometry was used to quantitatively determine the dissociation constant of chorismate mutase and a transition state analogue inhibitor. This system presents a fairly complex stoichiometry because the native protein is a homotrimer with three equal and independent substrate binding sites. We can detect the chorismate mutase trimer as well as chorismate mutase-inhibitor complexes by choosing appropriate conditions in the ESI source. To verify that the protein-inhibitor complexes are specific, titration experiments with different enzyme variants and different inhibitors were performed. A plot of the number of bound inhibitors versus added inhibitor concentration revealed saturation behavior with 3:1 (inhibitor:functional trimer) stoichiometry for the TSA. The soft ESI conditions, the relatively high protein mass of 43.5 kDa, and the low charge state (high m/z) result in broad peaks, a typical problem in analyzing noncovalent protein complexes. Due to the low molecular weight of the TSA (226 Da) the peaks of the free protein and the protein with one, two or three inhibitors bound cannot be clearly resolved. For data analysis, relative peak areas of the deconvoluted spectra of chorismate mutase-inhibitor complexes were obtained by fitting appropriate peak shapes to the signals corresponding to the free enzyme and its complexes with one, two, or three inhibitor molecules. From the relative peak areas we were able to calculate a dissociation constant that agreed well with known solution-phase data. This method may be generally useful for interpreting mass spectra of noncovalent complexes that exhibit broad peaks in the high m/z range.

Bacillus subtilis↗

PubMed2003

Mass spectrometric determination of association constants of adenylate kinase with two noncovalent inhibitors.

Noncovalent complexes between chicken muscle adenylate kinase and two inhibitors, P(1),P(4)-di(adenosine-5')tetraphosphate (Ap4A) and P(1),P(5)-di(adenosine-5') pentaphosphate (Ap5A), were investigated with electrospray ionization mass spectrometry under non-denaturing conditions. The nonconvalent nature and the specificity of the complexes are demonstrated with a number of control experiments. Titration experiments allowed the association constants for inhibitor binding to be determined. Problems with concentration dependent ion yields are circumvented by a data evaluation method that is insensitive to the overall ionization efficiency. The K(a) values found were 9.0 x 10(4) M(-1) (Ap4A) and 4.0 x 10(7) M(-1) (Ap5A), respectively, in very good agreement with available literature data.

Adenylate Kinase↗