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Virtually all modern chemical instrumentation is controlled by computers. While software packages are continually becoming easier to use, allowing for more researchers to utilize more complex instruments, conveying some level of understanding as to how computers and instruments communicate is still an important part of the undergraduate curriculum. Understanding how digital and analog signals are used to allow the smooth operation of an instrument allows the user to better understand the possible sources or problems when instruments stop working optimally. The experiment presented here allows students to investigate the communication between the computer and a high-performance liquid chromatography (HPLC) system by allowing them to construct a LabVIEW-based control program. Student understanding of instrument control is reinforced by having them control pump speed, detector zeroing, and a solvent recycling valve while also monitoring the injection port status and the detector output. Students gain an understanding of the HPLC process by incorporating all of the instrument tasks into their control software and then use their system to analyze a mixture of five small organic molecules, thereby gaining insight into the chemical concepts underlying HPLC separations.

Capillary electrophoresis is an important analytical separation method used to study a wide variety of samples, including those of biological origin. Capillary electrophoresis may be covered in the classroom, especially in advanced analytical courses, and while many students are exposed to gel electrophoresis in biology or biochemistry laboratories, capillary electrophoresis is not as commonly found in undergraduate lab curricula. Published lab experiments that incorporate capillary electrophoresis include the analysis of caffeine in beverages and cations in water samples but not of more biological samples such as a peptide mixture. This paper introduces a peptide separation based on capillary zone electrophoresis that is both qualitative and quantitative. It describes the separation of four small peptides where two of the analytes have similar migration times, forcing students to think about how they can best identify which peak corresponds to which analyte, while exposing them to a bioanalytical application of capillary electrophoresis.

An in-depth understanding of all parameters that affect an instrumental analysis method, allowing students to explore how these instruments work so that they are not just a "black box," is key to being able to optimize the technique and obtain the best possible results. It is, however, impractical to provide such in depth coverage of every technique and instrument in the classroom, and even more so in the laboratory. Exploring various instrumental parameters can be time consuming in the lab assuming that hands-on access is even available. One alternative to exploring different instrumental situations in the lab is to use computer simulations to model instrument performance under different conditions. Here, we present a simulation of a time-of-flight (TOF) mass spectrometer using the LabVIEW software platform. LabVIEW is routinely used for instrument interfacing and control and can be used to create simulations of a wide variety of chemical instruments. Because of their relatively high cost, mass spectrometers may not be readily available at all institutions, which makes a computer simulation an attractive alternative. Because TOF mass spectrometers, at least basic instruments, are relatively easy to understand, we chose to simulate a TOF in this exercise. This approach could be used to simulate other types of chemical instrumentation. (Contains 4 figures.)

A high-performance liquid chromatography (HPLC) laboratory experiment based on the separation of four prescription drugs (disopyramide, lidocaine, procainamide, and quinidine) is presented. The experiment is set within the forensic science context of the discovery of a patient's mysterious death where a drug overdose is suspected. Each lab group is provided with drug standards of known concentration and a simulated "blood" extract from the patient. Each group must determine whether the patient died of a drug overdose or through natural causes. This requires each drug standard to be analyzed separately to determine its retention time. The group must then analyze the "blood" to identify which drugs are present. After establishing the identity of any drugs present in the "blood", multiple drug injections of varying concentrations are performed to construct a calibration curve of peak area versus concentration. This can be used to determine the quantity of each drug present in the "blood". The students must also search the literature to determine possible drug interactions as well as normal and lethal doses of each drug, before reaching a conclusion about whether the patient died of a drug overdose, and if so whether it was likely accidental or intentional. (Contains 2 figures and 1 table.)

Mass spectrometry has become a routine analytical tool in the undergraduate curriculum in the form of GC-MS. While relatively few undergraduate programs have incorporated biological mass spectrometry into their programs, the importance of these techniques, as demonstrated by their recognition with the 2002 Nobel Prize, will hopefully lead to increased opportunities for undergraduate students to experience the power of these techniques. We present a laboratory experiment that allows students to determine the molecular mass of a peptide based on the spectrum obtained from analysis using electrospray ionization mass spectrometry (ESI-MS). Since ESI-MS often produces multiply charged ions, students must use isotopic patterns to first determine the charge state on the ion signals prior to calculating the molecular mass and thus the identity of the peptide. If the charge state determination is not done correctly, large mass errors larger can occur, while students routinely observe mass errors of approximately 0.01% when the analysis is done correctly. (Contains 1 table and 2 figures.) [For Part 1, see EJ820900.]

Biological mass spectrometry is an important analytical technique in drug discovery, proteomics, and research at the biology-chemistry interface. Currently, few hands-on opportunities exist for undergraduate students to learn about this technique. With the 2002 Nobel Prize being awarded, in part, for the development of biological mass spectrometry, more academic institutions will hopefully incorporate these techniques into their curricula. We present the first in a series of experiments designed to introduce students to the analysis of biological molecules using mass spectrometry. In this experiment, students analyze a medium-sized protein using electrospray ionization and identify it based on molecular weight. Since electrospray ionization produces multiply charged ions and since isotopic distributions cannot be easily observed for highly charged ions, a mathematical treatment of sequentially charged ions is used to determine the charge state on the ion signals and thus calculate the molecular weight. Averages of several differently-charged ion signals from the same analyte are used to obtain an average molecular weight. We have included several representative protein spectra, suitable for classroom use, in the Supplemental Material. (Contains 1 table, 1 figure, and 2 notes.)

The study of forensic science is found throughout undergraduate programs in growing numbers, both as stand-alone courses as well as specific examples within existing courses. Part of the driving force for this trend is the ability to apply common chemistry techniques to everyday situations, all couched in the context of a mystery that must be solved. The paint analysis lab is meant to allow students to determine if paint samples that may appear similar to the human eye are really the same or if they have measurable differences. The forensic aspect of the experiment lies in the application of spectroscopy to determine if the paint sample found at a crime scene is indistinguishable to paint found in a suspect's possession. Since observed colors are due to light reflected from a surface, reflectance spectroscopy is used to analyze the various paint samples. Samples containing various percentages of white and blue paints are analyzed using the 1976 CIELab color space system. As part of this experiment, students learn about reflectance spectroscopy, sampling techniques, basic statistics, and the fact that they can not always rely on initial observations. (Contains 1 figure and 1 table.)

Students are given an unknown protein and are asked to analyze and identify the molecular mass of medium -sized proteins using ESI-MS or Electrospray ionization-Mass spectrometer.

A tandem time-of-flight (TOF) mass spectrometer has been designed to obtain complete MS/MS spectra from compounds eluting from a gas chromatograph. This application requires high spectral generation rate, unit mass resolution for both precursor selection and product spectra, and efficient ion utilization. These objectives are achieved by refiectron TOF mass separation in both stages and laser photoinduced dissociation as the ion fragmentation method. Careful timing of the laser pulse relative to ion extraction allows ions of a single m/z value up to m/z 1000 to be photodissociated while ions with adjacent m/z values are essentially unaffected. The convergent foci of the ion packet and laser pulse results in ion fragmentation efficiencies as high as 79%. An ion gate prevents the nonselected precursor ions from convoluting the product spectra. Product spectra can be generated at the maximum laser repetition rate (currently 200 Hz). To achieve unit mass resolution for all product m/z values simultaneously, a novel reflectron was designed for the second TOF stage.

A tandem mass spectrometry experiment designed for a peptide ion is presented. The experiment aims to teach students how to use the results for de novo peptide sequencing. The importance of learning how to sequence the peptide de novo without a database is also explained.

Ketamine can be used to facilitate date-rape when unknowingly spiked into a victim's beverage. If a biological sample is not available from the victim, the beverage container might be the only remaining source of forensic evidence. We present a rapid, simple analysis method for the detection of ketamine in wet or dry beverage residues based on liquid chromatography-mass spectrometry (LC-MS). Wet residues consist of the final few drops (<1 ml) in a container while dry residues are the remains once all liquid has evaporated. By using LC-MS, which readily handles aqueous samples, often no derivatization or sample extraction is needed, thus reducing analysis time and lab technician involvement. Tandem mass spectrometry (MS/MS) provides an enhancement in both selectivity and sensitivity. We have studied a range of beverages and determined limits of detection between 1.2 × 10-3 and 1.3 × 10-4 mg/ml, compared to 0.21-0.85 mg/ml used in most date-rape scenarios. This paper represents the first published report of using LC-MS/MS for the analysis of beverage residues for the presence of a date-rape drug. This method could replace the current gas chromatography-mass spectrometry (GC-MS) methods and provide a faster, more selective method for the analysis of date-rape drugs, requiring virtually no sample preparation. Copyright © 2011 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

We set out to find the “ fenestrin” gene, a gene whose protein is associated with numerous cellular apertures, including the nuclear exchange junction in mating Tetrahymena thermophila. First we developed protocols for imaging and isolating intact nuclear exchange junctions from conjugating cells. Proteins from these junctions were purified using SDS-PAGE, subjected to limited proteolysis, and precise molecular weights were determined by mass spectrometry. Using Protein Prospector® software and the published Tetrahymena Genome Database, genes for 15 of the most abundant proteins found in our extracts were identified. The most promising candidate was cloned by PCR, fused to yellow fluorescent protein (YFP), and placed under the control of an inducible metallothionein promoter. YFP-localization within live Tetrahymena transformants strongly suggested that one of these genes encoded the fenestrin protein, a result that was subsequently confirmed by Western blotting. [ABSTRACT FROM AUTHOR]