Mass spectrometry: analytical capabilities and potentials

Online hyphenation of in-capillary aptamer-functionalized solid-phase microextraction and extraction nanoelectrospray ionization for miniature mass spectrometry analysis

Direct mass spectrometry (MS) analysis is vital to chemical and biological investigations. However, measuring complex samples is challenging due to matrix interference, resulting in compromised MS performance. In this study, an integrated experimental protocol has been developed, combining in-capillary aptamer-functionalized solid-phase microextraction (SPME), extraction nanoelectrospray ionization (nanoESI), and miniature MS analysis. The established method was applied to analyze caffeine in electronic cigarette liquid and beverage samples as proof-of-concept demonstrations. A custom SPME strip fabricated with caffeine-binding aptamers was prepared with an immobilization density of up to 0.812 nmol cm^-2. Critical parameters affecting the effects of extraction, desorption, and ionization were optimized. A novel transition ion ratio-based strategy with enhanced quantitation accuracy was developed. The analytical performance of the proposed method was evaluated under optimized conditions. Acceptable recoveries of 87.5-111.5% with relative standard deviations of 3.1-6.1% and satisfactory sensitivity with limits of detection of 1.5 and 3 ng mL^-1 and limits of quantitation of 5 and 10 ng mL^-1 were obtained, respectively. The developed approach demonstrates a promising potential for rapid on-site applications with appealing analytical performance and efficiency.

Focus on the molecular mechanisms of cisplatin resistance based on multi-omics approaches

Cisplatin is commonly used in combination with other cytotoxic agents as a standard treatment regimen for a variety of solid tumors, such as lung, ovarian, testicular, and head and neck cancers. However, the effectiveness of cisplatin is accompanied by toxic side effects, for instance, nephrotoxicity and neurotoxicity. The response of tumors to cisplatin treatment involves multiple physiological processes, and the efficacy of chemotherapy is limited by the intrinsic and acquired resistance of tumor cells. Although enormous efforts have been made toward molecular mechanisms of cisplatin resistance, the development of omics provides new insights into the understanding of cisplatin resistance at genome, transcriptome, proteome, metabolome and epigenome levels. Mechanism studies using different omics approaches revealed the necessity of multi-omics applications, which provide information at different cellular function levels and expand our recognition of the peculiar genetic and phenotypic heterogeneity of cancer. The present work systematically describes the underlying mechanisms of cisplatin resistance in different tumor types using multi-omics approaches. In addition to the classical mechanisms such as enhanced drug efflux, increased DNA damage repair and changes in the cell cycle and apoptotic pathways, other changes like increased protein damage clearance, increased protein glycosylation, enhanced glycolytic process, dysregulation of the oxidative phosphorylation pathway, ferroptosis suppression and mRNA m6A methylation modification can also induce cisplatin resistance. Therefore, utilizing the integrated omics to identify key signaling pathways, target genes and biomarkers that regulate chemoresistance are essential for the development of new drugs or strategies to restore tumor sensitivity to cisplatin.

Electromembrane Extraction and Dual-Channel Nanoelectrospray Ionization Coupled with a Miniature Mass Spectrometer: Incorporation of a Dicationic Ionic Liquid-Induced Charge Inversion Strategy

Green analytical chemistry aims at developing analytical methods with minimum use and generation of hazardous substances for the protection of human health and the environment. To address this need, a green analytical protocol has been developed for the analysis of anionic compounds integrating electromembrane extraction (EME), dual-channel nanoelectrospray ionization (nanoESI), and a miniature mass spectrometer. Haloacetic acids (HAAs) have attracted considerable public concern due to their adverse effects on human health and were selected as model analytes for method development. A flat membrane EME device was developed and assembled in-house. Optimization of fundamental operational parameters was performed using single-factor test and response surface methodology. Both the EME acceptor phase and an imidazolium-based dicationic ionic liquid (DIL), 1,1-bis(3-methylimidazolium-1-yl) butylene difluoride (C₄(MIM)₂F₂), were subjected to dual-channel nanoESI and miniature mass spectrometry analysis based on a charge inversion strategy, where positively charged complexes were formed. Enhancement in signal intensity by as much as 2 magnitudes was achieved in the positive-ion mode compared to the negative-ion mode in the absence of the dicationic ion-pairing agent. The developed protocol was validated, obtaining good recoveries ranging from 82.7 to 109.9% and satisfactory sensitivity with limits of detection (LODs) and quantitation (LOQs) in the ranges of 1-5 and 2-10 μg/L, respectively. The greenness of the analytical procedure was assessed with a calculated score of 0.71, indicating a high degree of greenness. The developed method was applied to the analysis of real environmental or municipal water samples (n = 16), exhibiting appealing potential for outside-the-laboratory applications.

Suspect Screening of Fentanyl Analogs Using Matrix-Assisted Ionization and a Miniature Mass Spectrometer with a Custom Expandable Mass Spectral Library

The reliable identification of fentanyl and its analogs is of great significance for public security. However, with the growing prevalence of fentanyl compounds, current analytical strategies cannot fully meet the need for fast and high-throughput detection. In this study, a simple, rapid, and on-site analytical protocol was developed based on a miniature mass spectrometer. A dramatically simplified workflow was implemented using matrix-assisted ionization, bypassing complex sample pretreatment and chromatographic separation. The tandem mass spectrometry (MS/MS) capability afforded by the miniature ion trap mass spectrometer facilitated the investigation of fragmentation patterns for 49 fentanyl analogs during collision-induced dissociation, revealing valuable information on marker fragment ions and characteristic neutral loss. Calculations on Laplacian bond order values further verified the mass spectrometric behavior. A computation-assisted expandable mass spectral library was constructed in-house for fentanyl compounds. Smart suspect screening was carried out based on the full-scan MS and MS/MS data. The present study demonstrates an appealing potential for forensic applications, enabling streamlined screening for the presence of illicit fentanyl compounds at the point of seizures of suspect samples.

Characterization of ionized lignin model compounds with α-O-4 linkages by positive- and negative-ion mode electrospray ionization tandem mass spectrometry based on collision-activated dissociation

RATIONALE

The biggest obstacle in the rational conversion of biomass into aromatic chemicals is the identification of unknown compounds in lignin degradation mixtures that are highly complex. As opposed to lignin degradation products with β-O-4 linkages, very little is known about the mass spectrometric analysis of lignin degradation products with α-O-4 linkages.

METHODS

Lignin model compounds with an α-O-4 and another linkage, as well as lignin model compounds with only β-O-4 linkages, were ionized by attachment of lithium or sodium cations under positive-ion mode electrospray ionization (ESI) or by deprotonation in negative-ion mode ESI in a linear quadrupole ion trap mass spectrometer. The ions were subjected to collision-activated dissociation in multiple-stage tandem mass spectrometry experiments to characterize their fragmentation patterns.

RESULTS

All studied compounds formed abundant sodium and lithium cation adducts in positive-ion mode ESI with no fragmentation. Model compounds with β-O-4 linkages displayed stable [M - H]^- ions in negative-ion mode ESI whereas compounds with α-O-4 linkages only showed fragment ions. CAD of the lithiated α-O-4 compounds provided more structural information than CAD of sodiated compounds. However, both sodiated and lithiated compounds with α-O-4 linkages showed losses of monomer units at the MS² stage, which is useful for sequencing of lignins with this type of linkage.

CONCLUSIONS

An ionization and sequencing method has been developed for lignin model compounds with α-O-4 linkages that spontaneously fragment upon ionization via (-)ESI.

Polypyrrole-coated needle as an electrospray emitter for ambient mass spectrometry

Polypyrrole (PPy) is a polymer widely used as an extraction phase due to its ability to perform intermolecular interactions with the analyte, such as acid-base, π-π, dipole-dipole, hydrophobic, and hydrogen bonding. In this manuscript, we report the coating of a stainless steel needle with a PPy film for analyte extraction and subsequent analysis by electrospray ionization mass spectrometry (ESI-MS) under ambient and open-air conditions. The method, named PPy-ESI-MS, was optimized for analysis of 3,4-methylenedioxyamphetamine (MDA) and 3,4-methylenedioxymethamphetamine (MDMA) in synthetic urine. Seven cycles of electrodeposition of the PPy film onto the needle surface, sample at pH 8, and 40 min of extraction of analytes were determined as the best analysis conditions. The analytical performance of PPy-ESI-MS was evaluated for MDA and MDMA compounds. Analytical curves were obtained with R2 > 0.98. Limits of detection (LODs) and limits of quantification (LOQs) were determined as 20 μg L-1 and 70 μg L-1 for MDA and as 25 μg L-1 and 80 μg L-1 for MDMA, respectively. Values of precision were below 17%, and values of accuracy below 5%. The apparent recoveries ranged between 84.5% and 111.3%. In addition, the PPy-ESI-MS method was applied for the analysis of sarcosine in synthetic urine in order to evaluate the performance of the method for another class of compounds. The calibration curve was obtained with R2 > 0.98, along with LOD and LOQ of 30 μg L-1 and 100 μg L-1, respectively. The precision and accuracy values were below 5% and 8%, respectively, and the apparent recoveries close to 100%. This work demonstrates the usefulness of combining an extraction phase with ESI-MS analysis under ambient conditions to determine different classes of small molecules in a complex sample.

Distinguishing Isomeric Aromatic Radical Cations by Using Energy-Resolved Ion Trap and Medium Energy Collision-Activated Dissociation Mass Spectrometry

Different collision-activated dissociation (CAD) methods were evaluated for their effectiveness at distinguishing several ionized isomeric aromatic compounds by using a linear quadrupole ion trap/orbitrap mass spectrometer. The compounds were ionized by using atmospheric pressure chemical ionization (APCI) with carbon disulfide solvent in the positive ion mode to generate stable molecular ions with limited fragmentation. They were subjected to CAD in the linear quadrupole ion trap (ITCAD) and in an octupole collision cell (medium-energy collision-activated dissociation, MCAD; also known as HCD). Experiments conducted by attempting to vary ion activation times revealed that MCAD and ITCAD occur in the microsecond and millisecond time regimes, respectively. MCAD was found to impart substantially greater internal energies into the molecular ions compared to ITCAD. Accordingly, molecular ions subjected to MCAD favored dissociation via fast σ-bond cleavages, while molecular ions subjected to ITCAD tended to favor rearrangement reactions. MCAD used in the energy-resolved mode (ER-MCAD) enabled the distinction of six ionized isomeric compounds from each other based on modified crossing-point energies (collision energies where the molecular ions and selected fragment ions have an equal abundance). This was not true for ER-ITCAD. Overall, MCAD was superior over ITCAD at the differentiation of isomeric ions, and it provided more detailed structural information.

(-)ESI/CAD MSn Procedure for Sequencing Lignin Oligomers Based on a Study of Synthetic Model Compounds with β-O-4 and 5-5 Linkages

Seven synthesized G-lignin oligomer model compounds (ranging in size from dimers to an octamer) with 5-5 and/or β-O-4 linkages, and three synthesized S-lignin model compounds (a dimer, trimer, and tetramer) with β-O-4 linkages, were evaporated and deprotonated using negative-ion mode ESI in a linear quadrupole ion trap/Fourier transform ion cyclotron resonance mass spectrometer. The collision-activated dissociation (CAD) fragmentation patterns (obtained in MS² and MS³ experiments, respectively) for the negative ions were studied to develop a procedure for sequencing unknown lignin oligomers. On the basis of the observed fragmentation patterns, the measured elemental compositions of the most abundant fragment ions, and quantum chemical calculations, the most important reaction pathways and likely mechanisms were delineated. Many of these reactions occur via charge-remote fragmentation mechanisms. Deprotonated compounds with only β-O-4 linkages, or both 5-5 and β-O-4 linkages, showed major 1,2-eliminations of neutral compounds containing one, two, or three aromatic rings. The most likely mechanisms for these reactions are charge-remote Maccoll and retro-ene eliminations resulting in the cleavage of a β-O-4 linkage. Facile losses of H₂O and CH₂O were also observed for all deprotonated model compounds, which involve a previously published charge-driven mechanism. Characteristic "ion groups" and "key ions" were identified that, when combined with their CAD products (MS³ experiments), can be used to sequence unknown oligomers.

Mechanistic Study of the Gas-Phase In-Source Hofmann Elimination of Doubly Quaternized Cinchona-Alkaloid Based Phase-Transfer Catalysts by (+)-Electrospray Ionization/Tandem Mass Spectrometry

An unusual in-source fragmentation pattern observed for 14 doubly quaternized cinchona alkaloid-based phase-transfer catalysts (PTC) was studied using (+)-ESI high resolution mass spectrometry. Loss of the substituted benzyl cation (R1 or R2) was found to be the major product ion [M²⁺ - R₁⁺ or R₂⁺]⁺ in MS spectra of all PTC compounds. A Hofmann elimination product ion [M - H]⁺ was also observed. Only a small amount of the doubly charged M²⁺ ions were observed in the MS spectra, likely due to strong Columbic repulsion between the two quaternary ammonium cations in the gas phase. The positive voltage in the MS inlet but not the ESI probe was found to induce this extensive fragmentation for all PTC diboromo-salts. Compound 1 was used as an example to illustrate the proposed in-source fragmentation mechanism. The mechanism of formation of the Hofmann elimination product ion [M - H]⁺ was further investigated using HRMS/MS, H/D exchange, and DFT calculations. The proposed formation of 2b as the major Hofmann elimination product ion was supported both by HRMS/MS and DFT calculations. Formation of product ion 2b through a concerted unimolecular E_i elimination pathway is proposed rather than a bimolecular E2 elimination pathway for common solution Hofmann eliminations. Graphical Abstract ᅟ.

A Fundamental Tandem Mass Spectrometry Study of the Collision-Activated Dissociation of Small Deprotonated Molecules Related to Lignin

The collision-activated fragmentation pathways and reaction mechanisms of 34 deprotonated model compounds representative of lignin degradation products were explored experimentally and computationally. The compounds were evaporated and ionized by using negative-ion mode electrospray ionization doped with NaOH to produce abundant deprotonated molecules. The ions were isolated and subjected to collision-activated dissociation (CAD). Their fragment ions were then isolated and also subjected to CAD. This was repeated until no further fragmentation was observed (up to MS⁶ ). This approach enabled the identification of characteristic reaction pathways and delineation of reasonable fragmentation mechanisms for deprotonated molecules containing various functional groups. The varying fragmentation patterns observed for different types of compounds allow for the identification of the functionalities in these compounds. This information was utilized to identify the presence of specific functionalities and their combinations in molecules in an organosolv lignin sample.

Gas-phase ion-molecule reactions for the identification of the sulfone functionality in protonated analytes in a linear quadrupole ion trap mass spectrometer

RATIONALE

The oxidation of sulfur atoms is an important biotransformation pathway for many sulfur-containing drugs. In order to rapidly identify the sulfone functionality in drug metabolites, a tandem mass spectrometric method based on ion-molecule reactions was developed.

METHODS

A phosphorus-containing reagent, trimethyl phosphite (TMP), was allowed to react with protonated analytes with various functionalities in a linear quadrupole ion trap mass spectrometer. The reaction products and reaction efficiencies were measured.

RESULTS

Only protonated sulfone model compounds were found to react with TMP to form a characteristic [TMP adduct-MeOH] product ion. All other protonated compounds investigated, with functionalities such as sulfoxide, N-oxide, hydroxylamino, keto, carboxylic acid, and aliphatic and aromatic amino, only react with TMP via proton transfer and/or addition. The specificity of the reaction was further demonstrated by using a sulfoxide-containing anti-inflammatory drug, sulindac, as well as its metabolite sulindac sulfone.

CONCLUSIONS

A method based on functional group-selective ion-molecule reactions in a linear quadrupole ion trap mass spectrometer has been demonstrated for the identification of the sulfone functionality in protonated analytes. A characteristic [TMP adduct-MeOH] product ion was only formed for the protonated sulfone analytes. The applicability of the TMP reagent in identifying sulfone functionalities in drug metabolites was also demonstrated. Copyright © 2016 John Wiley & Sons, Ltd.

Rapid analysis of synthetic cannabinoids using a miniature mass spectrometer with ambient ionization capability

Synthetic cannabinoids are an emerging class of drugs of abuse and are of a great concern for transport control and usage regulation. In this study, we have developed rapid analytical methods using a miniature mass spectrometer for the identification of synthetic cannabinoids, as the traces of bulk powders on surfaces or substances in blood and urine. Significantly simplified work flows were developed by employing two ambient ionization methods, the paper spray and extraction spray ionization. Using five synthetic cannabinoids as examples, a limit of detection of 2 ng was estimated for the detection of trace powders on a bench surface and limits of quantitation as good as 10 ng/mL were obtained for the analysis of blood and urine samples.

Identification of the sulfoxide functionality in protonated analytes via ion/molecule reactions in linear quadrupole ion trap mass spectrometry

A mass spectrometric method utilizing gas-phase ion/molecule reactions of 2-methoxypropene (MOP) has been developed for the identification of the sulfoxide functionality in protonated analytes in a LQIT mass spectrometer. Protonated sulfoxide analytes react with MOP to yield an abundant addition product (corresponding to 37-99% of the product ions), which is accompanied by a much slower proton transfer. The total efficiency (percent of gas-phase collisions leading to products) of the reaction is moderate (3-14%). A variety of compounds with different functional groups, including sulfone, hydroxylamino, N-oxide, aniline, phenol, keto, ester, amino and hydroxy, were examined to probe the selectivity of this reaction. Most of the protonated compounds with proton affinities lower than that of MOP react mainly via proton transfer to MOP. The formation of adduct-MeOH ions was found to be characteristic for secondary N-hydroxylamines. N-Oxides formed abundant MOP adducts just like sulfoxides, but sulfoxides can be differentiated from N-oxides based on their high reaction efficiencies. The reaction was tested by using the anti-inflammatory drug sulindac (a sulfoxide) and its metabolite sulindac sulfone. The presence of a sulfoxide functionality in the drug but a sulfone functionality in the metabolite was readily demonstrated. The presence of other functionalities in addition to sulfoxide in the analytes was found not to influence the diagnostic reactivity.

High efficiency tandem mass spectrometry analysis using dual linear ion traps

Tandem mass spectrometry (MS/MS) plays an essential role in modern chemical analysis. It is used for differentiating isomers and isobars and suppressing chemical noise, which allows high precision quantitation. The MS/MS analysis has been typically applied by isolating the target precursor ions, while disregarding other ions, followed by a fragmentation process that produces the product ions. In this study, configurations of dual linear ion traps were explored to develop high efficiency MS/MS analysis. The ions trapped in the first linear ion trap were axially, mass-selectively transferred to the second linear ion trap for MS/MS analysis. Ions from multiple compounds simultaneously introduced into the mass spectrometer could be sequentially analyzed. This development enables highly efficient use of the sample. For miniature ion trap mass spectrometers with discontinuous atmospheric pressure interfaces, the analysis speed and the quantitation precision can be significantly improved.

Multiported pulsed valve interface for a linear quadrupole ion trap mass spectrometer to enable rapid screening of multiple functional-group selective ion-molecule reactions

Ion-molecule reactions provide a powerful tool for structural elucidation of ionized pharmaceutical analytes in tandem mass spectrometry. However, all previous interfaces for the introduction of reagents for ion-molecule reactions have utilized a single reagent approach. In this study, a multiported pulsed valve system was designed and characterized for rapid introduction of three neutral reagents into a linear quadrupole ion trap. Additionally, automatic triggering was used to allow for the introduction of the reagents on a chromatographic time scale. This system enables automatic, high throughput screening of complex mixtures by using at least three different ion-molecule reactions. Further, rapid testing of new neutral reagents is also possible.

Mini 12, miniature mass spectrometer for clinical and other applications--introduction and characterization

A benchtop miniature mass spectrometer system, Mini 12, with ambient ionization source and tandem mass spectrometry capabilities has been developed and characterized. This instrument was developed as a self-contained system to produce quantitative results for unprocessed samples of small volumes including nonvolatile analytes. The ion processing system, vacuum system, and control system are detailed. An integrated sample loading system facilitates automated operation. A user interface has been developed to acquire and to interpret analytical results for personnel who have limited mass spectrometry knowledge. Peak widths of Δm/z 0.6 Th (full width at half-maximum) and a mass range of up to m/z 900 are demonstrated with the rectilinear ion trap mass analyzer. Multistage experiments up to MS(5) are accomplished. Consumable cartridges have been designed for use in ambient paper spray ionization, and the recently developed extraction spray ionization method has been employed to improve the quantitative performance. Monitoring of trace-levels of chemicals in therapeutic drugs, as well as in food safety and environmental protection operations is demonstrated. Dual MS/MS scans are implemented to obtain the intensities of the fragment ions from the analyte and its internal standard, and the ratio is used in quantitative analysis of complex samples. Limits of quantitation (LOQ) of 7.5 ng/mL, with relative standard deviations below 10%, have been obtained for selected therapeutic drugs in whole blood throughout their individual therapeutic ranges.

Development of a mass spectrometry sampling probe for chemical analysis in surgical and endoscopic procedures

A sampling probe based on ambient desorption ionization was designed for in vivo chemical analysis by mass spectrometry in surgical and endoscopic procedures. Sampling ionization of analytes directly from tissue was achieved by sealing the sampling tip against the tissue surface without allowing leakage of the auxiliary gas used for desorption ionization. The desorbed charged species were transferred over a long distance (up to 4 m) through a flexible tube of internal diameter as small as 1/16 in. to the inlet of the mass spectrometer used for analysis. The conditions used for desorption electrospray ionization (DESI) were optimized to achieve biocompatibility for clinical applications while obtaining adequate efficiency for the analysis. This optimization involved the removal of high voltage and use of pure water as a spray solvent instead of the organic solvents or aqueous mixtures normally used. Improved sensitivity was achieved under these conditions by increasing the gas flow rate in the transfer tube. The destructive effect on tissue surfaces associated with typical desorption ionization was avoided by altering the local gas dynamics in the sample area without compromising the overall analysis efficiency.

Sensitive ionization of non-volatile analytes using protein solutions as spray liquid in desorption electrospray ionization mass spectrometry

RATIONALE

Desorption electrospray ionization (DESI) is the most popular ambient ionization technique for direct analysis of complex samples without sample pretreatment. However, for many applications, especially for trace analysis, it is of interest to improve the sensitivity of DESI-mass spectrometry (MS).

METHODS

In traditional DESI-MS, a mixture of methanol/water/acetic acid is usually used to generate the primary ions. In this article, dilute protein solutions were electrosprayed in the DESI method to create multiply charged primary ions for the desorption ionization of trace analytes on various surfaces (e.g., filter paper, glass, Al-foil) without any sample pretreatment. The analyte ions were then detected and structurally characterized using a LTQ XL mass spectrometer.

RESULTS

Compared with the methanol/water/acetic acid (49:49:2, v/v/v) solution, protein solutions significantly increased the signal levels of non-volatile compounds such as benzoic acid, TNT, o-toluidine, peptide and insulin in either positive or negative ion detection mode. For all the analytes tested, the limits of detection (LODs) were reduced to about half of the original values which were obtained using traditional DESI. The results showed that the signal enhancement is highly correlated with the molecular weight of the proteins and the selected solid surfaces.

CONCLUSIONS

The proposed DESI method is a universal strategy for rapid and sensitive detection of trace amounts of strongly bound and/or non-volatile analytes, including explosives, peptides, and proteins. The results indicate that the sensitivity of DESI can be further improved by selecting larger proteins and appropriate solid surfaces.

High-performance liquid chromatography/high-resolution multiple stage tandem mass spectrometry using negative-ion-mode hydroxide-doped electrospray ionization for the characterization of lignin degradation products

In the search for a replacement for fossil fuel and the valuable chemicals currently obtained from crude oil, lignocellulosic biomass has become a promising candidate as an alternative biorenewable source for crude oil. Hence, many research efforts focus on the extraction, degradation, and catalytic transformation of lignin, hemicellulose, and cellulose. Unfortunately, these processes result in the production of very complex mixtures. Further, while methods have been developed for the analysis of mixtures of oligosaccharides, this is not true for the complex mixtures generated upon degradation of lignin. For example, high-performance liquid chromatography/multiple stage tandem mass spectrometry (HPLC/MS(n)), a tool proven to be invaluable in the analysis of complex mixtures derived from many other biopolymers, such as proteins and DNA, has not been implemented for lignin degradation products. In this study, we have developed an HPLC separation method for lignin degradation products that is amenable to negative-ion-mode electrospray ionization (ESI doped with NaOH), the best method identified thus far for ionization of lignin-related model compounds without fragmentation. The separated and ionized compounds are then analyzed by MS(3) experiments to obtain detailed structural information while simultaneously performing high-resolution measurements to determine their elemental compositions in the two parts of a commercial linear quadrupole ion trap/Fourier-transform ion cyclotron resonance mass spectrometer. A lignin degradation product mixture was analyzed using this method, and molecular structures were proposed for some components. This methodology significantly improves the ability to analyze complex product mixtures that result from degraded lignin.

Implementation of molecular phenotyping approaches in the personalized surgical patient journey

OBJECTIVE

The present review describes commonly employed metabolic profiling platforms and discusses the current and likely future application of these technologies in surgery.

BACKGROUND

The metabolic adaptations that occur in response to surgical illness and trauma are incompletely understood. Evaluating these will be critical to the development of personalized surgical health solutions. Metabonomics is an advancing field in systems biology, which provides a means of interrogating these metabolic shifts.

METHODS

Recent literature regarding metabolic profiling technologies and their applications in surgical practice are discussed. Future strategies are proposed for the incorporation of these and next-generation technologies in the evaluation of all steps in the patient surgical pathway.

RESULTS

Metabolite-based profiling has provided valuable insights into the metabolic irregularities that occur in cancer development and progression across a variety of cancer subclasses including colorectal, breast, prostate, and lung cancers. In addition, metabolic modeling has shown considerable promise in other surgical conditions including trauma and sepsis and in the assessment of pharmacotherapeutic efficacy.

DISCUSSION

Metabonomics offers a posttranscriptional view of system activity providing functional information downstream of the genome and proteome. Information at this level will provide the surgeon with a novel means of evaluating major socioeconomic problems such as cancer and sepsis. In addition, the rapid nature of emerging next generation profiling platforms provides a viable means of "real-time" perioperative metabolic assessment and optimization.

Accelerator mass spectrometry for measurement of long-lived radioisotopes

Particle accelerators, such as those built for research in nuclear physics, can also be used together with magnetic and electrostatic mass analyzers to measure rare isotopes at very low abundance ratios. All molecular ions can be eliminated when accelerated to energies of millions of electron volts. Some atomic isobars can be eliminated with the use of negative ions; others can be separated at high energies by measuring their rate of energy loss in a detector. The long-lived radioisotopes (10)Be, (14)C,(26)A1, 36Cl, and (129)1 can now be measured in small natural samples having isotopic abundances in the range 10(-12) to 10(- 5) and as few as 10(5) atoms. In the past few years, research applications of accelerator mass spectrometry have been concentrated in the earth sciences (climatology, cosmochemistry, environmental chemistry, geochronology, glaciology, hydrology, igneous petrogenesis, minerals exploration, sedimentology, and volcanology), in anthropology and archeology (radiocarbon dating), and in physics (searches for exotic particles and measurement of halflives). In addition, accelerator mass spectrometry may become an important tool for the materials and biological sciences.

The Curtin-Hammett principle in mass spectrometry

The Curtin-Hammett principle (CHP) is an important concept in physical organic chemistry and is often utilized in the investigation of reaction mechanisms. Two reactants, A and B, in rapid equilibrium, react to form products P(A) and P(B) with rates k(A) and k(B), respectively. If the reaction is under kinetic control and the rate of equilibration between the two reactants is much faster than the reactions to form products, then the branching ratio of products P(A) and P(B) depends solely on the difference in barrier heights for the two product channels. The CHP is based on the fact that the ratio of products formed is not determined by the reactant population ratio. However, the CHP also applies to studies in other areas of chemistry, including mass spectrometry. This Account describes work from our groups in which the results must be interpreted in light of the CHP. These studies illustrate two important implications of the CHP. First, they demonstrate how product distributions cannot be used to assess reactant structure in mechanistic studies in Curtin-Hammett systems. A recent investigation of the structure of hydroxysiliconate anions demonstrated that it was not possible to distinguish between the possible reactant ion structures. A second important implication of the CHP is that the structure of the reactant does not affect the product branching ratio and therefore does not need to be a consideration if the CHP applies. We address this aspect of the discussion through kinetic method studies of the acidities of amino acids and proton affinities of bifunctional compounds. Recently reported mass spectrometric studies illustrate how the CHP puts limitations on what conclusions can be drawn from product distribution studies but also allows experimental methods, such as the kinetic method, to be carried out for complicated systems without having to know all the details of the reactant ion structures. These studies show that although the CHP is most commonly applied in mechanistic studies in physical organic chemistry, it also applies to other areas of chemistry, including mass spectrometry. Although the CHP in some cases limits the conclusions that can be drawn from an experimental study, its proper application can often be used to greatly simplify very complicated chemical systems. Therefore, it is important in mass spectrometry, and indeed, in all areas of chemistry, to recognize those systems in which the CHP should and should not apply.

Strategies to recover proteins from ocular tissues for proteomics

We present here the results of protein extraction from different ocular regions using different detergents. Extraction strategies used to determine optimal protein extraction included: pressure cycling and aqueous-organic phase extraction in combination with electrophoretic fractionation for anterior, posterior, and peripapillary sclera. Detergent extraction of proteins from freshly enucleated porcine eyes (n = 8) showed significant differences for different eye regions. Protein yield ranged from 2.3 to 50.7 mug protein/mg for different ocular tissues, with the lens yielding the most protein. ASB-14 and Triton X-100 provided the best protein yields (n = 10) for anterior and posterior sclera. The spectrophotometric measurements for ASB-14 were not consistent with SDS-PAGE densitometry. A combination of 0.5% Triton X-100, 0.5% Tween-20, and 0.1% Genapol C-100 was found optimal for extraction from sclera. Proteins from different regions of the eye are best extracted with different detergents. The pressure cycling technology provided superior extraction compared to the other methods. Additional aqueous-organic phase partitioning enables superior fractionation when compared to SDS-PAGE alone. Organic phase fractionation is compatible with MS and allowed identification of 34, 71, and 77 proteins respectively from anterior, posterior, and peripapillary sclera. The extraction strategy may affect the final outcome in protein profiling by MS or by other methods.

Feature extraction in the analysis of proteomic mass spectra

Feature extraction or biomarker selection is a critical step in disease diagnosis and knowledge discovery based on protein MS. Many studies have discussed the classification methods applied in proteomics; however, few could be found to address feature extraction in detail. In this paper, we developed a systematic approach for the extraction of mass spectrum peak apex and peak area with special emphasis on noise filtration and peak calibration. Application to a head and neck cancer data generated at the Eastern Virginia Medical School [Wadsworth, J. T., Somers, K. D., Cazares, L. H., Malik, G. et al.., Clin. Cancer Res. 2004, 10, 1625-1632] revealed that the new feature extraction method would yield consistent and highly discriminatory biomarkers.

Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation

MS-based proteomics usually involves the fragmentation of tryptic peptides (tandem MS or MS(2)) and their identification by searching protein sequence databases. In ion trap instruments fragments can be further fragmented and analyzed, a process termed MS/MS/MS or MS(3). Here, we report that efficient ion capture in a linear ion trap leads to MS(3) acquisition times and spectra quality similar to those for MS(2) experiments with conventional 3D ion traps. Fragmentation of N- or C-terminal ions resulted in informative and low-background spectra, even at subfemtomol levels of peptide. Typically C-terminal ions are chosen for further fragmentation, and the MS(3) spectrum greatly constrains the C-terminal amino acids of the peptide sequence. MS(3) spectra allow resolution of ambiguities in identification, a crucial problem in proteomics. Because of the sensitivity and rapid scan rates of the linear ion trap, several MS(3) spectra per peptide can be obtained even when sequencing very complex mixtures. We calculate the probability that an experimental MS(3) spectrum originates from fragmentation of a given N- or C-terminal ion of a peptide under consideration. This MS(3) identification score can be combined with the MS(2) scores of the precursor peptide from existing search engines. When MS(3) is performed on the linear ion trap-Fourier transform mass spectrometer combination, accurate peptide masses further increase confidence in peptide identification.

Ionization in matrix-assisted laser desorption/ionization: singly charged molecular ions are the lucky survivors

A new model for the ionization processes in UV matrix-assisted laser desorption/ionization (MALDI) which accounts for the major phenomena observed is presented and discussed. The model retains elements of earlier approaches, such as photoionization and photochemical reactions, but it redefines these in the light of new working questions, most importantly why only singly charged ions are detected. Based on experimental evidence, the formation of singly and multiply charged clusters by a deficiency/excess of ions and also by photoionization and subsequent photochemical processes is pointed out to be the major ionization processes, which typically occur in parallel. The generation of electrons and their partial loss into the surrounding vacuum and solid, on the one hand, results in a positively charged ion-neutral plume facilitating a high overall ionization yield. On the other hand, these electrons, and also the large excess of protonated matrix ions in the negative ion mode, induce effective ion reneutralization in the plume. These neutralization processes are most effective for the highly charged cluster ions initially formed. Their fragmentation behaviour is evidenced in fast metastable fragmentation characteristics and agrees well with an electron capture dissociation mechanism and the enthalpy transfer upon neutralization forms the rationale for the prominent fragmentation and intense chemical noise accompanying successful MALDI. Within the course of the paper, cross-correlations with other desorption/ionization techniques and with earlier discussions on their mechanisms are drawn.

The clinical utility and evaluation of drug screening techniques

A better understanding of the methods of drug detection, their sensitivities, and limitations increases the efficiency of medical decision making for better patient care. Many of the sociomedical and medicolegal questions are yet to be answered through court challenge. The physician must remember his or her role as a clinician, and practice the art in a fashion that best serves the interest of his or her teenage patient.

Focal Points in Mass Spectrometry

Mass spectrometry has advanced with the renaissance of time-of-flight mass analysis, the use of ion traps as analyzers and reactors, the application of tandem mass spectrometers to problems in ionic reaction mechanisms and chemical analysis, and the development of new desorption ionization techniques. These developments have allowed determination of the molecular weight distributions for polymers through the 10,000-dalton range, as well as the molecular weight and partial sequence of biopolymers of similar size. Surfaces can be characterized by use of the mass, energy, and angle distributions of particles ejected by sputtering or by laser-induced desorption. Mass spectrometry has yielded new information on the kinetics of catalytic surface reactions and on the reactivity of metal clusters.

Fourier transform mass spectrometry

Fourier transform mass spectrometry will play an important role in the future because of its unique combination of high mass resolution, high upper mass limit, and multichannel advantage. These features have already found application in gas chromatography-mass spectrometry, multiphoton ionization, laser desorption, and secondary ion mass spectrometry. However, its most notable feature is the ability to store ions. This characteristic, when combined with the others, will allow expeditious study of the interaction of gas-phase ions with both photons (photodissociation) and neutral molecules, and the convenient application of this fundamental information for chemical analysis.

Sequence analysis of derivatized peptides by high-performance liquid chromatography-mass spectrometry

N-Acetyl-N,O,S-permethylated derivatives of oligopeptides were analyzed by high-performance liquid chromatography-mass spectrometry (HPLC-MS) using a moving belt interface. A heated-gas nebulizer was employed for sample deposition, thus permitting the effective use of a water-methanol gradient covering the range from 5% to 95% water at mobile phase flow-rates of 0.5 ml/min. We demonstrate in this paper that it is possible to sequence the octapeptide derived from the C-chain of glucagon by HPLC-MS analysis of a permethylated enzymatic hydrolysate of this peptide using overlap information from the mass spectral patterns. Moreover, it is shown that peptides not readily amenable to analysis by gas chromatography-MS can be analyzed using this approach. Preliminary results suggest that N-acetyl-methyl ester derivatives of oligopeptides may in specific cases also be a useful alternative for HPLC-MS analysis of complex oligopeptide mixtures.