Dale H. Patterson

Accurate Mass Measurements Using MALDI-TOF with Delayed Extraction

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry is now an essential tool in biopolymer analysis. Sensitivity and mass range are unsurpassed, but mass measurement accuracy and resolution have been limited. With delayed extraction and a reflecting analyzer, mass measurements using MALDI-TOF can be made with an accuracy of a few parts per million (ppm). It is possible to distinguish Lys from Gln in peptides, and to determine the elemental composition of smaller molecules (mass 100–500). In database searching strategies, a smaller mass window, resulting from an increase in mass accuracy, greatly decreases the number of possible candidates. Mass measurement accuracy with errors less than 5 ppm is demonstrated on a mixture of 12 peptides ranging in mass from ca. 900 to 3700 Da. Mass measurements on 13 peaks in an unseparated tryptic digest of myoglobin gave results with an overall average error less than 3.5 ppm, with a maximum error of 7 ppm.

Dynamic modeling of electrophoretically mediated microanalysis

A dynamic model is presented for simulation of reaction-based chemical analysis of enzymes and substrates in capillary electrophoretic systems by the methodology of electrophoretically mediated microanalysis (EMMA). The mathematical model utilizes mass balance expressions describing the time-dependent effects of electromigration, chemical reaction, and diffusional band broadening upon the concentration profiles of the various reagent and product species. The model is implemented in an iterative computer program in which the capillary is segmented into arrays of bins storing the concentration profiles of each of the chemical species. During each time increment, the effects of electrophoresis, reaction kinetics, and diffusion are calculated, and the concentrations stored in the arrays are updated. The flexibility of the model to accommodate various initial capillary conditions, sample introduction methods, and voltage programming allows diverse EMMA analyses to be simulated. The simulated results are shown to be in good qualitative agreement with experimental data for zonal injection and moving boundary EMMA determinations of leucine aminopeptidase as well as an EMMA analysis of ethanol.

Electrophoretically mediated microanalysis of ethanol

Capillary electrophoresis was used to determine ethanol by the methodology of electrophoretically mediated microanalysis (EMMA). In EMMA, spatially distinct analyte and analytical reagent zones of differing electrophoretic mobility are merged under the influence of an electric field, and the resulting product is transported to the detector. The enzymatic oxidation of ethanol to acetaldehyde by alcohol dehydrogenase was utilized, and the concurrent reduction of NAD+ to NADH was monitored at 340 nm as a measure of the quantity of ethanol injected. Quantitation using an internal standard and normalization for peak migration time yielded a R.S.D. of 2.7%, and the linear range extended to that quantity of ethanol which could be reacted prior to passing by the detection window. Comparison of the EMMA technique to the Sigma spectrophotometric procedure revealed that the two methods do not yield significantly different values for the determination of ethanol. The EMMA method offered the advantages of electrophoretic mixing and miniaturization.

Electrophoretically-mediated microanalysis (EMMA)

Abstract This article describes a microanalytical technique for carrying out separations and chemical assays on biological samples at the zeptomole level using capillary electrophoretic systems. It is shown that through the use of high sensitivity detection systems, such as laser induced fluorescence, it is possible to detect components in single cells and even to detect single molecules of enzymes.

Electrophoretically mediated microanalysis of calcium

Electrophoretically mediated microanalysis (EMMA) was used for the determination of calcium. The faster analyte zone containing the calcium was injected spatially behind a slower zone of o-cresolphthalein complexone in a capillary electrophoresis based system. Upon application of the electric field the calcium zone was electrophoretically mixed with the reagent and product was formed. The bulk electroosmotic flow carried the product to the detector where the absorbance of the resulting complex at 575 nm was measured. Quantitation using an internal standard yielded a linear response with an R.S.D. of 8.1%. An inter-method comparison was performed with the standard bulk method and yielded results that did not significantly differ. The advantages of EMMA with respect to traditional methods were addressed.

Depth of Proteome Issues A Yeast Isotope-Coded Affinity Tag Reagent Study

As a test case for optimizing how to perform proteomics experiments, we chose a yeast model system in which the UPF1 gene, a protein involved in nonsense-mediated mRNA decay, was knocked out by homologous recombination. The results from five complete isotope-coded affinity tag (ICAT) experiments were combined, two using matrix-assisted laser desorption/ionization (MALDI) tandem mass spectrometry (MS/MS) and three using electrospray MS/MS. We sought to assess the reproducibility of peptide identification and to develop an informatics structure that characterizes the identification process as well as possible, especially with regard to tenuous identifications. The cleavable form of the ICAT reagent system (Gygi et al. (1999) Nat. Biotechnol. 17, 994–999) was used for quantification. Most proteins did not change significantly in expression as a consequence of the upf1 knockout. As expected, the Upf1 protein itself was down-regulated, and there were reproducible increases in expression of proteins involved in arginine biosynthesis. Initially, it seemed that about 10% of the proteins had changed in expression level, but after more thorough examination of the data it turned out that most of these apparent changes could be explained by artifacts of quantification caused by overlapping heavy/light pairs. About 700 proteins altogether were identified with high confidence and quantified. Many peptides with chemical modifications were identified, as well as peptides with noncanonical tryptic termini. Nearly all of these modified peptides corresponded to the most abundant yeast proteins, and some would otherwise have been attributed to “single hit” proteins at low confidence. To improve our confidence in the identifications, in MALDI experiments, the parent masses for the peptides were calibrated against nearby components. In addition, five novel parameters reflecting different aspects of identification were collected for each spectrum in addition to the Mascot score that was originally used. The interrelationship between these scoring parameters and confidence in protein identification is discussed.