Electrospray ionization and matrix-assisted laser desorption ionization mass spectrometry. Emerging technologies in biomedical sciences

Mass spectrometric based analysis, characterization and applications of circulating cell free DNA isolated from human body fluids

In the past decade, cell free DNA, or circulating cell free DNA, or cell free circulating DNA, isolated from body fluids such as plasma/serum/urine has emerged as an important tool for clinical diagnostics. The molecular biology of circulating cell free DNA is poorly understood but there is currently an increased effort to understand the origin, mechanism of its circulation, and sensitive characterization for the development of diagnostic applications. There has been considerable progress towards these goals using real time polymerase chain reaction technique (rt-PCR). More recently, new attempts to incorporate mass spectrometric techniques to develop accurate and highly sensitive high-throughput clinical diagnostic tests have been reported. This review focuses on the methods to isolate circulating cell free DNA from body fluids, their quantitative analysis and mass spectrometry based characterization in evolving applications as prenatal and cancer diagnostic tools.

Surface plasmon resonance mass spectrometry in proteomics

Due to the enormous complexity of the proteome, focus in proteomics shifts more and more from the study of the complete proteome to the targeted analysis of part of the proteome. The isolation of this specific part of the proteome generally includes an affinity-based enrichment. Surface plasmon resonance (SPR), a label-free technique able to follow enrichment in real-time and in a semiquantitative manner, is an emerging tool for targeted affinity enrichment. Furthermore, in combination with mass spectrometry (MS), SPR can be used to both selectively enrich for and identify proteins from a complex sample. Here we illustrate the use of SPR-MS to solve proteomics-based research questions, describing applications that use very different types of immobilized components: such as small (drug or messenger) molecules, peptides, DNA and proteins. We evaluate the current possibilities and limitations and discuss the future developments of the SPR-MS technique.

Probing the non-covalent binding interaction of the Na+ channel inactivation gate peptide in a linker between domain III and IV with 5,5-diphenyhydantoin in electrospray ion trap tandem mass spectrometry

The Na(+) channel-subunit containing an Ile1488, Phe1489 and Met1490 (IFM) motif is critical for a fast inactivation process. BL-1, a model IFM-containing peptide with a sequence of acetyl-GGQDIFMTEEK-OH, was observed as a doubly charged potassium-adduct ion by electrospray ionization mass spectrometry (ESI-MS) and a singly charged ion by atmospheric-pressure matrix-assisted laser desorption/ionization mass spectrometry (AP-MALDI-MS). Two crown ethers were applied to demonstrate their desalting ability and then to confirm the potassium-adduct assignments. In order to probe the best binding condition for BL-1 with a local anesthetic drug, 5,5-diphenyhydantoin (DPH), a series of experiments were performed and the parameters affecting complexation were carefully investigated including molar ratios, reaction time and reaction temperature. The most effective conditions for the observation of the complex by ESI-MS were molar ratio of BL-1 and DPH of 1:28 after 18 h of incubation at 40 degrees C. In addition, collision-activated dissociation (CAD) was successfully applied to confirm the formation of the complex between BL-1 with DPH that is via a weak non-covalent bonding with a 1:1 stoichiometry.

Pulsed Oscillating Mass Spectrometer: A Miniaturized Type of Time-of-Flight Mass Spectrometer

We report the development, characterization, and performance of a new type of time-of-flight mass analyzer that employs an oscillatory ion flight path and uses secondary electrons to record the mass spectrum. The analyzer is simple in concept and design and inexpensive to build and has been made as small as 6-cm total length. The oscillating ions produce a periodic secondary electron signal whose frequency is mass dependent in mathematically the same way as a conventional time-of-flight analyzer. Because of the oscillating nature of the ions, we have called the analyzer the pulsed oscillating mass spectrometer.

Investigation of intact protein complexes by mass spectrometry

Mass spectrometry has grown in recent years to a well-accepted and increasingly important complementary technique in structural biology. Especially electrospray ionization mass spectrometry is well suited for the detection of non-covalent protein complexes and their interactions with DNA, RNA, ligands, and cofactors. Over the last decade, significant advances have been made in the ionization and mass analysis techniques, which makes the investigation of even larger and more heterogeneous intact assemblies feasible. These technological developments have paved the way to study intact non-covalent protein-protein interactions, assembly and disassembly in real time, subunit exchange, cooperativity effects, and effects of cofactors, allowing us a better understanding of proteins in cellular processes. In this review, we describe some of the latest developments and several highlights.

Effect of different solution flow rates on analyte ion signals in nano-ESI MS, or: when does ESI turn into nano-ESI?

In nano-ESI MS, the qualitative and quantitative characteristics of mass spectra vary considerably upon the use of different spraying conditions, i.e., aperture of the spraying needle and the voltage applied. The major parameters affected by the aperture size is the liquid flow rate which determines the initial droplet size and the current emitted upon the spray process, as described by different models of the ESI process. In the present study, the effect of flow rate on ion signals was studied systematically using mixtures of compounds with different physicochemical properties (i.e., detergent/oligosaccharide and oligosaccharide/peptide). For these model systems, the functional dependence of certain analyte-ion ratios upon the flow rate can be correlated to changes in analyte partition during droplet fission prior to ion release. Analyte suppression is practically absent at minimal flow rates below 20 nL/min.

Profiling and in vivo Quantification of Proteins by High Resolution Mass Spectrometry: The Example of Goserelin, an Analogue of Luteinizing Hormone-Releasing Hormone

Proteins are essential biomolecules which are frequently involved in major pathological syndromes and are widely used as diagnostic markers or therapeutic agents. The emergence of proteomics will doubtless further increase the significance of proteins both in the clinic and in the life sciences in general. Our main objective is to offer innovative solutions to what we like to call the "post-proteomics era". To achieve our goal, we intend to develop novel approaches and technologies for in vivo metabolic studies of proteins using mass spectrometry (MS), focusing on pharmacokinetics and pharmacodynamics. Using goserelin as a model, we have successfully developed and validated a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the detection and quantification of an intact analogue of luteinizing hormone-releasing hormone (LHRH) in small volumes of rat plasma samples at concentrations ranging from 0.3 to 405.0 microg/l. To this end, a microbore reversed-phase-HPLC system was coupled on-line to a tandem high resolution quadrupole time-of-flight (Q-TOF) instrument fitted with an electrospray ion source and operated in LC-MS/MS mode. External calibration was used and the high resolution was crucial to discard contaminating signals, which would not have been possible with the more conventional triple quadrupole mass spectrometers operated in a static mode. For low sample amounts, calibration curves were constructed corresponding to rat plasma levels of 0.3 to 16.4 microg/l and found to be of third order with a coefficient of determination greater than 0.999. The relative standard deviation was found to be lower than 15%. A lower limit of detection (LLOD) of 0.17 microg/l and a lower limit of quantification (LLOQ) of 0.3 microg/l were determined.

Mutation scanning by ion-pair reversed-phase high-performance liquid chromatography-electrospray ionization mass spectrometry (ICEMS)

Partially denaturing high-performance liquid chromatography has emerged as the most sensitive physical mutation scanning method. However, there are a few reports of mutations missed or only detectable at unique temperatures. The combined use of ion-pair reversed-phase high-performance liquid chromatography under completely denaturing conditions and electrospray ionization quadrupole ion trap mass spectrometry (ICEMS) obviates the need for selecting appropriate temperatures for resolving heteroduplices and allows the discrimination of different alleles even when they co-elute due to distinct mass differences between nucleobases. This was demonstrated for the detection of four mutations (259G>A, 286A>G, 300T>G, and 331+1G>A) in exon 5 and intron 5 of BRCA1, respectively. Current mass resolution of quadrupole ion trap mass spectrometers limits the identification of single A>T or T>A transversions with a mass difference of 9 Da to fragments <80 base pairs (bp). The presence of all other mutations can be detected in fragments up to approximately 105 bp. The approach may prove particularly useful in the mutational scanning of AT- or GC-rich sequences that are recalcitrant to most other methods.

An overview of some recent developments in ionization methods for mass spectrometry

An overview of some recent advances in ionization sources for mass spectrometry is presented. Limitations were set so that the overview covers ionization techniques relevant to organic and biological analysis that have appeared in the literature since the year 2000. No effort is made to be comprehensive. Rather, a broad sweep overview of author-subjective highlights among a wide variety of sources is presented. These ionization sources include electron ionization, chemical ionization, various atmospheric plasma ionization sources, laser desorption sources, sonic spray and electrospray ionization sources.

Contributions of mass spectrometry in the study of nucleic acid-binding proteins and of nucleic acid-protein interactions

Nucleic-acid-protein (NA-P) interactions play essential roles in a variety of biological processes-gene expression regulation, DNA repair, chromatin structure regulation, transcription regulation, RNA processing, and translation-to cite only a few. Such biological processes involve a broad spectrum of NA-P interactions as well as protein-protein (P-P) interactions. These interactions are dynamic, in terms of the chemical composition of the complexes involved and in terms of their mere existence, which may be restricted to a given cell-cycle phase. In this review, the contributions of mass spectrometry (MS) to the deciphering of these intricate networked interactions are described along with the numerous applications in which it has proven useful. Such applications include, for example, the identification of the partners involved in NA-P or P-P complexes, the identification of post-translational modifications that (may) regulate such complexes' activities, or even the precise molecular mapping of the interaction sites in the NA-P complex. From a biological standpoint, we felt that it was worth the reader's time to be as informative as possible about the functional significance of the analytical methods reviewed herein. From a technical standpoint, because mass spectrometry without proper sample preparation would serve no purpose, each application described in this review is detailed by duly emphasizing the sample preparation-whenever this step is considered innovative-that led to significant analytical achievements.

Mass spectrometry of nicotinic acetylcholine receptors and associated proteins as models for complex transmembrane proteins

Studies were conducted to optimize matrix-assisted laser desorption/ionization, time-of-flight mass spectrometry (MALDI TOF MS) in analyzing the composition of nicotinic acetylcholine receptors (nAChR) from Torpedo californica electric tissue in their membrane-bound, detergent-solubilized, and affinity-purified states. Mass spectra obtained from nAChR-rich membrane fractions gave reasonably good representations of protein compositions indicated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of those same samples. Efficiency of extraction of nAChR from membranes was not markedly different for most detergents, but quality and signal size of mass spectra were clearly influenced by detergent composition and concentration, protein concentration, and MALDI matrix composition. The best spectra, allowing detection and accurate size determinations for samples containing as little as 10 fmol of pure nAChR, were obtained for samples solubilized in Triton X-100 and assayed by use of a sinapinic acid matrix. Although informative spectra could be obtained for nAChR affinity purified on alpha-cobratoxin (Naja naja siamensis) columns and extracted using sinapinic acid, superior spectra with much higher signal:noise were obtained if extraction media contained Triton X-100 or sodium dodecyl sulfate. nAChR subunit masses determined were similar regardless of the membrane-associated, detergent-solubilized, or affinity-purified state of the preparation. These studies illustrate how masses can be determined for nAChR subunits and for other protein components in Torpedo membrane preparations, such as RAPsyn and Na(+)-K(+)-ATPase alpha and beta subunits. They also provide an underpinning for streamlined analysis of the composition of complex transmembrane proteins using MALDI TOF MS.

Influence of pressure in the first pumping stage on analyte desolvation and fragmentation in nano-ESI MS

In ESI MS, some classes of biomolecules are detected only with low signal intensities due to difficulties in achieving efficient analyte desolvation, either because an analyte tends to fragment already at gentle desolvation conditions (i.e., noncovalent protein complexes or nucleotides) or because an analyte requires very strong activation in order to remove solvent molecules (i.e., carbohydrates). Even though the pressure in the first pumping stage of the ESI instrument is known to have an influence on the desolvation conditions, it has never been the focus of a detailed investigation. The role of the pressure in the first pumping stage is systematically interrogated in this study for several model substances. Ion signal intensities and signal-to-noise ratios are significiantly enhanced if the pressure in the first pumping stage is increased and adjusted, and analyte fragmentation can be substantially reduced. Thus, besides thermal heating and the acceleration in the nozzle-skimmer region, which are usually optimized, the pressure in the first pumping stage is an additional important desolvation parameter.

Characterization of Cryptosporidium parvum by matrix-assisted laser desorption ionization-time of flight mass spectrometry

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was used to investigate whole and freeze-thawed Cryptosporidium parvum oocysts. Whole oocysts revealed some mass spectral features. Reproducible patterns of spectral markers and increased sensitivity were obtained after the oocysts were lysed with a freeze-thaw procedure. Spectral-marker patterns for C. parvum were distinguishable from those obtained for Cryptosporidium muris. One spectral marker appears specific for the genus, while others appear specific at the species level. Three different C. parvum lots were investigated, and similar spectral markers were observed in each. Disinfection of the oocysts reduced and/or eliminated the patterns of spectral markers.

High-throughput chiral liquid chromatography/tandem mass spectrometry

Chiral liquid chromatography is a well-established area of bioanalytical chemistry and is often used during the processes of drug discovery and development. The development and use of a chiral drug require the understanding of the pharmacokinetic characteristics of each of the enantiomers, including potential differences in their absorption, distribution, metabolism, and excretion. Chromatographic techniques coupled to atmospheric pressure ionization-tandem mass spectrometry have shown potential as sensitive and robust tools in the quantitative and qualitative determination of enantiomers in biologic fluids and tissue extracts. However, development of a chiral liquid chromatography method requires time-consuming procedures that are devised empirically. Clearly, there is an incentive to design chromatographic approaches that are easy to use, compatible with mass spectrometry ionization interface conditions, exhibit relatively short run times without compromising sensitivity, and offer a broad analyte specificity. For these reasons, the present paper explores the feasibility of the bonded macrocyclic glycopeptide phases (teicoplanin and vancomycin) for analysis by chiral liquid chromatography/tandem mass spectrometry. Ritalinic acid, pindolol, fluoxetine, oxazepam, propranolol, terbutaline, metoprolol, and nicardipine were tested in this study. Furthermore, an example of a simultaneous chiral LC/MS/MS detection (chromatographic run time approximately 10 min) of four pharmaceutical products resulting in baseline resolutions of all four pairs of enantiomers is presented. Methanol, an MS-compatible mobile phase, was utilized in all the experiments.

High-throughput approaches to the quantitative analysis of ketoconazole, a potent inhibitor of cytochrome P450 3A4, in human plasma

Ketoconazole, an imidazole-piperazine compound, is an orally active antimycotic agent. In addition, ketoconazole is a specific inhibitor of cytochrome P450 3A4. As about 60% of oxidized drugs are biotransformed by this isoform, the potential effect of a concomitant administration of ketoconazole on drug disposition may be of interest during drug development. The present paper describes three different approaches (methods A, B, and C) to attain high-throughput sample preparation and analysis in the quantification of ketoconazole in human plasma. Method A consisted of acetonitrile precipitation in a 96-well plate, transfer of the supernatant via a Tomtec Quadra 96 Model 320, and subsequent injection onto a 50 x 4.6 mm (i.d.) Develosil Combi-RP-5 column (packed with C30 bonded silica particles). Method B consisted of an identical sample preparation to method A with the exception that a Michrom Magic Bullet(trade mark) column, 2.0 --> 0.50 mm (i.d., tapered bore) x25 mm length, was used. Lastly, in method C, a turbulent-flow chromatography (TurboFlow LC/APCI-MS/MS) module was used for the direct analysis of ketoconazole in human plasma. A Sciex API 3000 was used in methods A and B, while a Micromass Quattro LC was employed in method C. Based on the values obtained for the calibrator (standard) and quality control samples, all three protocols yielded satisfactory accuracy, precision, and reduced manual sample preparation time.

Liquid-liquid extraction using 96-well plate format in conjunction with liquid chromatography/tandem mass spectrometry for quantitative determination of methylphenidate (Ritalin) in human plasma

Methylphenidate (MPH; Ritalin: methyl-alpha-phenyl-2-piperidinacetate hydrochloride) is utilized for the treatment of attention deficit hyperactivity disorder (ADHD) and narcolepsy. Recently, we described a rapid enantioselective liquid chromatography/tandem mass spectrometry (LC/MS/MS) method for the determination of the enantiomers of MPH (Rapid Commun. Mass Spectrom. 1999; 13: 2054). A lower limit of quantification (LLOQ) of 87 pg/mL was attained for the human plasma assay. The present paper describes a high-throughput sample preparation procedure in conjunction with racemic LC/MS/MS analysis for MPH with a LLOQ of 50 pg/mL. A semi-automated robotics method using liquid-liquid extraction (LLE) in a 96-well plate format was developed and validated. The correlation coefficients were > or =0.998 for MPH indicating good fits of the regression models over the range of the calibration curve. The accuracy and precision of the semi-automated approach were comparable to those obtained using the manual sample preparation technique reported previously (vide supra). The current method can easily be adapted to the enantioselective LC/MS/MS assay of MPH. The assay was simple, fast, specific, and exhibited excellent ruggedness.