Electrospray and tandem mass spectrometry in biochemistry

Mass shift in mass spectrometry imaging: comprehensive analysis and practical corrective workflow

MALDI mass spectrometry imaging (MSI) allows the mapping and the tentative identification of compounds based on their m/z value. In typical MSI, a spectrum is taken at incremental 2D coordinates (pixels) across a sample surface. Single pixel mass spectra show the resolving power of the mass analyzer. Mass shift, i.e., variations of the m/z of the same ion(s), may occur from one pixel to another. The superposition of shifted masses from individual pixels peaks apparently degrades the resolution and the mass accuracy in the average spectrum. This leads to low confidence annotations and biased localization in the image. Besides the intrinsic performances of the analyzer, the sample properties (local composition, thickness, matrix deposition) and the calibration method are sources of mass shift. Here, we report a critical analysis and recommendations to mitigate these sources of mass shift. Mass shift 2D distributions were mapped to illustrate its effect and explore systematically its origin. Adapting the sample preparation, carefully selecting the data acquisition settings, and wisely applying post-processing methods (i.e., m/z realignment or individual m/z recalibration pixel by pixel) are key factors to lower the mass shift and to improve image quality and annotations. A recommended workflow, resulting from a comprehensive analysis, was successfully applied to several complex samples acquired on both MALDI ToF and MALDI FT-ICR instruments.

Laboratory Diagnosis of Lysosomal Diseases: Newborn Screening to Treatment

The goal of screening programs for inborn errors of metabolism (IEM) is early detection and timely intervention to significantly reduce morbidity, mortality and associated disabilities. Phenylketonuria exemplifies their success as neonates are identified at birth and then promptly treated allowing normal neurological development. Lysosomal diseases comprise about 50 IEM arising from a deficiency in a protein required for proper lysosomal function. Typically, these defects are in lysosomal enzymes with the concomitant accumulation of the enzyme's substrate as the cardinal feature. None of the lysosomal diseases are screened at birth in Australia and in the absence of a family history, traditional laboratory diagnosis of the majority, involves demonstrating a deficiency of the requisite enzyme. Diagnostic confusion can arise from interpretation of the degree of residual enzyme activity causative of disease and is impractical when the disorder is not due to an enzyme deficiency per se. Advances in mass spectrometry technologies has enabled simultaneous measurement of the enzymes' substrates and their metabolites which facilitates the efficiency of diagnosis. Employing urine chemistry as a reflection of multisystemic disease, individual lysosomal diseases can be identified by a characteristic substrate pattern complicit with the enzyme deficiency. Determination of lipids in plasma allows the diagnosis of a further class of lysosomal disorders, the sphingolipids. The ideal goal would be to measure biomarkers for each specific lysosomal disorder in the one mass spectrometry-based platform to achieve a diagnosis. Confirmation of the diagnosis is usually by identifying pathogenic variants in the underlying gene, and although molecular genetic technologies can provide the initial diagnosis, the biochemistry will remain important for interpreting molecular variants of uncertain significance.

Purification and characterization of 2S albumin from Nelumbo nucifera

The 2S albumins are a group of seed storage proteins that have recently attracted considerable attention in the field of allergen science due to their allergenic potential. A new 2S albumin from seeds of Nelumbo nucifera (Nn-2S alb) was purified to electrophoretic homogeneity by the combination of ammonium sulfate fractionation, gel filtration, and ion exchange chromatography. The protein has a molecular mass of about 12 kDa estimated by SDS-PAGE, in good agreement with 12.5 ± 0.01 kDa determined by ESI-MS. Circular dichroism data showed that protein contained about 66% α-helices as estimated by K2D3, indicating that the protein was predominantly helical. The sedimentation coefficient (s°_20,w) of the predicted model was 1.72 ± 0.21 S. The predicted 3-dimensional structure of the Nn-2S alb revealed that the protein has a region of 12 amino acids which largely corresponds to the conserved immuno-dominant epitope of 2S allergens.

Purification and primary structure of a novel mannose-specific lectin from Centrolobium microchaete Mart seeds

This study aimed to purify and characterize a novel mannose-binding lectin from the seeds of Centrolobium microchaete. Centrolobium microchaete lectin (CML) was purified by affinity chromatography in mannose-Sepharose-4B column. CML agglutinated rabbit erythrocytes and was inhibited by D-mannose, α-methyl-D-mannoside, D-glucose, N-Acetyl-D-glucosamine and sucrose. The lectin was stable at pH 7.0 and 8.0 and temperatures up to 60°C. The monomeric form of CML showed approximately 28kDa, and its native form is probably a homodimer, as determined by gel filtration chromatography. The primary structure of CML was determined by tandem mass spectrometry that showed CML as a protein with two distinct forms (isolectins CML-1 and CML-2) with 246 and 247 residues, respectively. CML-2 possesses one residue of Asn more than CML-1 in C-terminal. The primary structure of CML agrees with the molecular weights found by electrospray ionization mass spectrometry: 27,224 and 27,338Da for CML-1 and CML-2, respectively. CML is a metal-dependent glycoprotein. Moreover, the glycan composition of CML and its structure were predicted.

Interfacing low-energy SAW nebulization with Liquid Chromatography-Mass Spectrometry for the analysis of biological samples

Soft ionization methods for the introduction of labile biomolecules into a mass spectrometer are of fundamental importance to biomolecular analysis. Previously, electrospray ionization (ESI) and matrix assisted laser desorption-ionization (MALDI) have been the main ionization methods used. Surface acoustic wave nebulization (SAWN) is a new technique that has been demonstrated to deposit less energy into ions upon ion formation and transfer for detection than other methods for sample introduction into a mass spectrometer (MS). Here we report the optimization and use of SAWN as a nebulization technique for the introduction of samples from a low flow of liquid, and the interfacing of SAWN with liquid chromatographic separation (LC) for the analysis of a protein digest. This demonstrates that SAWN can be a viable, low-energy alternative to ESI for the LC-MS analysis of proteomic samples.

The Role of Mass Spectrometry in the "Omics" Era

Mass spectrometry (MS) is one of the key analytical technology on which the emerging ''-omics'' approaches are based. It may provide detection and quantization of thousands of proteins and biologically active metabolites from a tissue, body fluid or cell culture working in a ''global'' or ''targeted'' manner, down to ultra-trace levels. It can be expected that the high performance of MS technology, coupled to routine data handling, will soon bring fruit in the request for a better understanding of human diseases, leading to new molecular biomarkers, hence affecting drug targets and therapies. In this review, we focus on the main advances in the MS technologies, influencing genomics, transcriptomics, proteomics, lipidomics and metabolomics fields, up to the most recent MS applications to meta-omic studies.

Antibody screening identifies 78 putative host proteins involved in Cyprinid herpesvirus 3 infection or propagation in common carp, Cyprinus carpio L

Cyprinid herpesvirus 3 (CyHV-3) is the aetiological agent of a serious and notifiable disease afflicting common and koi carp, Cyprinus carpio L., termed koi herpesvirus disease (KHVD). Significant progress has been achieved in the last 15 years, since the initial reports surfaced from Germany, USA and Israel of the CyHV-3 virus, in terms of pathology and detection. However, relatively few studies have been carried out in understanding viral replication and propagation. Antibody-based affinity has been used for detection of CyHV-3 in enzyme-linked immunosorbent assay and PCR-based techniques, and immunohistological assays have been used to describe a CyHV-3 membrane protein, termed ORF81. In this study, monoclonal antibodies linked to N-hydroxysuccinimide (NHS)-activated spin columns were used to purify CyHV-3 and host proteins from tissue samples originating in either CyHV-3 symptomatic or asymptomatic fish. The samples were next analysed either by polyacrylamide gel electrophoresis (PAGE) and subsequently by electrospray ionization coupled to mass spectrometry (ESI-MS) or by ESI-MS analysis directly after purification. A total of 78 host proteins and five CyHV-3 proteins were identified in the two analyses. These data can be used to develop novel control methods for CyHV-3, based on pathways or proteins identified in this study.

Lipidomics of oxidized polyunsaturated fatty acids

Lipid mediators are produced from the oxidation of polyunsaturated fatty acids through enzymatic and free radical-mediated reactions. When subject to oxygenation via cyclooxygenases, lipoxygenases, and cytochrome P450 monooxygenases, polyunsaturated fatty acids give rise to an array of metabolites including eicosanoids, docosanoids, and octadecanoids. These potent bioactive lipids are involved in many biochemical and signaling pathways, with inflammation being of particular importance. Moreover, because they are produced by more than one pathway and substrate, and are present in a variety of biological milieus, their analysis is not always possible with conventional assays. Liquid chromatography coupled to electrospray mass spectrometry offers a versatile and sensitive approach for the analysis of bioactive lipids, allowing specific and accurate quantitation of multiple species present in the same sample. Here we explain the principles of this approach to mediator lipidomics and present detailed protocols for the assay of enzymatically produced oxygenated metabolites of polyunsaturated fatty acids that can be tailored to answer biological questions or facilitate assessment of nutritional and pharmacological interventions.

Tandem mass spectrometry in hormone measurement

Mass spectrometry methods have the potential to measure different hormones during the same analysis and have improved specificity and a wide analytical range compared with many immunoassay methods. Increasingly in clinical laboratories liquid chromatography-tandem mass spectrometry (LC-MS/MS) assays are replacing immunoassays for the routine measurement of testosterone, 17-hydroxyprogesterone, and other steroid hormones. Reference LC-MS/MS methods for steroid, thyroid, and peptide hormones are being used for assessment of the performance and calibration of commercial immunoassays. In this chapter, the general principles of tandem mass spectrometry and examples of hormone assays are described.

Sub-cellular proteomics of Medicago truncatula

Medicago truncatula is a leading model species and substantial molecular, genetic, genomics, proteomics, and metabolomics resources have been developed for this species to facilitate the study of legume biology. Currently, over 60 proteomics studies of M. truncatula have been published. Many of these have focused upon the unique symbiosis formed between legumes and nitrogen fixing rhizobia bacteria, while others have focused on seed development and the specialized proteomes of distinct tissues/organs. These include the characterization of sub-cellular organelle proteomes such as nuclei and mitochondria, as well as proteins distributed in plasma or microsomal membranes from various tissues. The isolation of sub-cellular proteins typically requires a series of steps that are labor-intensive. Thus, efficient protocols for sub-cellular fractionation, purification, and enrichment are necessary for each cellular compartment. In addition, protein extraction, solubilization, separation, and digestion prior to mass spectral identification are important to enhance the detection of low abundance proteins and to increase the overall detectable proportion of the sub-cellular proteome. This review summarizes the sub-cellular proteomics studies in M. truncatula.

Retrobiosynthetic approach delineates the biosynthetic pathway and the structure of the acyl chain of mycobacterial glycopeptidolipids

Glycopeptidolipids (GPLs) are dominant cell surface molecules present in several non-tuberculous and opportunistic mycobacterial species. GPLs from Mycobacterium smegmatis are composed of a lipopeptide core unit consisting of a modified C(26)-C(34) fatty acyl chain that is linked to a tetrapeptide (Phe-Thr-Ala-alaninol). The hydroxyl groups of threonine and terminal alaninol are further modified by glycosylations. Although chemical structures have been reported for 16 GPLs from diverse mycobacteria, there is still ambiguity in identifying the exact position of the hydroxyl group on the fatty acyl chain. Moreover, the enzymes involved in the biosynthesis of the fatty acyl component are unknown. In this study we show that a bimodular polyketide synthase in conjunction with a fatty acyl-AMP ligase dictates the synthesis of fatty acyl chain of GPL. Based on genetic, biochemical, and structural investigations, we determine that the hydroxyl group is present at the C-5 position of the fatty acyl component. Our retrobiosynthetic approach has provided a means to understand the biosynthesis of GPLs and also resolve the long-standing debate on the accurate structure of mycobacterial GPLs.

Microfluidic integration of photonic crystal fibers for online photochemical reaction analysis

Liquid-filled hollow-core photonic crystal fibers (HC-PCFs) are perfect optofluidic channels, uniquely providing low-loss optical guidance in a liquid medium. As a result, the overlap of the dissolved specimen and the intense light field in the micronsized core is increased manyfold compared to conventional bioanalytical techniques, facilitating highly-efficient photoactivation processes. Here we introduce a novel integrated analytical technology for photochemistry by microfluidic coupling of a HC-PCF nanoflow reactor to supplementary detection devices. Applying a continuous flow through the fiber, we deliver photochemical reaction products to a mass spectrometer in an online and hence rapid fashion, which is highly advantageous over conventional cuvette-based approaches.

Liquid chromatography-nuclear magnetic resonance coupling as alternative to liquid chromatography-mass spectrometry hyphenations: curious option or powerful and complementary routine tool?

Combining the most powerful separation techniques, i.e. liquid chromatography (LC) or capillary electrophoresis (CE) with a information rich detection system - the mass spectrometer or the nuclear magnetic resonance (NMR) spectrometer - has been pursued for more than three decades. This compilation shall provide an overview of the advantages and limitations of the LC-NMR hyphenation in the light of its most valued application-the unequivocal analyte identification. Especially the post LC trapping of analytes with an in-line solid phase extraction (SPE) device prior to transferring the analyte of interest to the NMR spectrometer (LC-SPE-NMR) proved to be a robust installation allowing a significant cut-down of the amount of analyte needed for the generation of high quality heteronuclear NMR shift correlation data. Different available technical realizations will be discussed and typical application examples from natural product research and from industrial settings will be given.

Proteomics-based investigation in C2C12 myoblast differentiation

Skeletal muscle cell differentiation is a multistage process extensively studied over the years. Even if great improvements have been achieved in defining biological process underlying myogenesis, many molecular mechanisms need still to be clarified.

To further highlight this process, we studied cells at undifferentiated, intermediate and highly differentiated stages, and we analyzed, for each condition, morphological and proteomic changes. We also identified the proteins that showed statistical significant changes by a ESI-Q-TOF mass spectrometer. This work provides further evidence of the involvement of particular proteins in skeletal muscle development. Furthermore, the high level of expression of many heat shock proteins, suggests a relationship between differentiation and cellular stress. Intriguingly, the discovery of myogenesis-correlated proteins, known to play a role in apoptosis, suggests a link between differentiation and this type of cell death.

Electrospray ionization mass spectrometry: a technique to access the information beyond the molecular weight of the analyte

The Electrospray Ionization (ESI) is a soft ionization technique extensively used for production of gas phase ions (without fragmentation) of thermally labile large supramolecules. In the present review we have described the development of Electrospray Ionization mass spectrometry (ESI-MS) during the last 25 years in the study of various properties of different types of biological molecules. There have been extensive studies on the mechanism of formation of charged gaseous species by the ESI. Several groups have investigated the origin and implications of the multiple charge states of proteins observed in the ESI-mass spectra of the proteins. The charged analytes produced by ESI can be fragmented by activating them in the gas-phase, and thus tandem mass spectrometry has been developed, which provides very important insights on the structural properties of the molecule. The review will highlight recent developments and emerging directions in this fascinating area of research.

Strong associations of short-chain perfluoroalkyl acids with serum albumin and investigation of binding mechanisms

Interactions of perfluoroalkyl acids (PFAAs) with tissue and serum proteins likely contribute to their tissue distribution and bioaccumulation patterns. Protein-water distribution coefficients (K(PW) ) based on ligand associations with bovine serum albumin (BSA) as a model protein were recently proposed as biologically relevant parameters to describe the environmental behavior of PFAAs, yet empirical data on such protein binding behavior are limited. In the present study, associations of perfluoroalkyl carboxylates (PFCAs) with two to 12 carbons (C₂-C₁₂) and perfluoroalkyl sulfonates with four to eight carbons (C₄, C₆, and C₈) with BSA are evaluated at low PFAA:albumin mole ratios and various solution conditions using equilibrium dialysis, nanoelectrospray ionization mass spectrometry, and fluorescence spectroscopy. Log K(PW) values for C₄ to C₁₂ PFAAs range from 3.3 to 4.3. Affinity for BSA increases with PFAA hydrophobicity but decreases from the C₈ to C₁₂ PFCAs, likely due to steric hindrances associated with longer and more rigid perfluoroalkyl chains. The C₄-sulfonate exhibits increased affinity relative to the equivalent chain-length PFCA. Fluorescence titrations support evidence that an observed dependence of PFAA-BSA binding on pH is attributable to conformational changes in the protein. Association constants determined for perfluorobutanesulfonate and perfluoropentanoate with BSA are on the order of those for long-chain PFAAs (K(a) ∼10⁶/M), suggesting that physiological implications of strong binding to albumin may be important for short-chain PFAAs.

Analysis of Staphylococcus enterotoxin B using differential isotopic tags and liquid chromatography quadrupole ion trap mass spectrometry

Staphylococcus aureus produces enterotoxins, which are causative agents of foodborne intoxications. Enterotoxins are single-chain polypeptides and have a molecular weight of about 26-28 kDa. The consumption of food contaminated with Staphylococcus aureus enterotoxins results in the onset of acute gastroenteritis within 2-6 h. The objective of this study was the development of a new method for the quantification of Staphylococcal enterotoxin B (SEB) in food matrices. Tryptic peptide map was generated and nine proteolytic fragments were clearly identified (sequence coverage of 35%). Among these, three specific tryptic peptides were selected to be used as surrogate peptides and internal standards for quantitative analysis using an isotopic tagging strategy along with analysis by LC-MS/MS. The linearity of the measurement by LC-MS/MS was evaluated by combining mixtures of both isotopes at 0.1, 0.2, 0.5, 1.0 and 2.0 ¹H/²H molar ratios with a slope near to 1, values of R² above 0.98 and %CV obtained from six repeated measurement was below 8%. The precision and accuracy of the method were assessed using SEB spiked in chicken meat homogenate samples. SEB was fortified at 0.2, 1 and 2 pmol/g. The accuracy results indicated that the method can provide accuracy within a 84.9-91.1% range. Overall, the results presented in this manuscript show that proteomics-based methods can be effectively used to detect, confirm and quantify SEB in food matrices.

Evidence of molecular fragmentation inside the charged droplets produced by electrospray process

The behavior of the analyte molecules inside the neutral core of the charged droplet produced by the electrospray (ES) process is not unambiguously known to date. We have identified interesting molecular transformations of two suitably chosen analytes inside the ES droplets. The highly stable Ni(II) complex of 1,8-dimethyl-1,3,6,8,10,13-hexaazacyclotetradecane (1) that consists of a positive charge at the metal center, and the allyl pendant armed tertiary amine containing macrocycle 3,4,5:12,13,14-dipyridine-2,6,11,15-tetramethyl-1,7,10,16-tetraallyl-1,4,7,10,13,16-hexaazacyclooctadeca-3,13-diene (M(4p)) have been studied by ESI mass spectrometry as the model analytes. We have shown that these two molecules are not representatively transferred from solution to gas phase by ESI; rather, they undergo fragmentation inside the charged droplets. The results indicated that a charged analyte such as 1 was possibly unstable inside the neutral core of the ES droplet and undergoes fragmentation due to the Coulombic repulsion imparted by the surface protons. Brownian motion of the neutral analyte such as M(4p) inside the droplet, on the other hand, may lead to proton attachment on interaction with the charged surface causing destabilization that leads to fragmentation of M(4p) and release of resonance stabilized allyl cations from the core of the droplet. Detailed solvent dependence and collision-induced dissociation (CID) studies provided compelling evidences that the fragmentation of the analytes indeed occurs inside the charged ES droplets. A viable model of molecular transformations inside the ES droplet was proposed based on these results to rationalize the behavior of the analyte molecules inside the charged ES droplets.

Developments in Electrospray Ionization Mass Spectrometry of Non-Covalent DNA–Ligand Complexes

Many anti-cancer drugs function by binding non-covalently to double-stranded (ds) DNA. Electrospray ionization mass spectrometry (ESI-MS) has emerged over the past decade as a sensitive technique for the determination of stoichiometries and relative binding affinities of DNA–ligand interactions. The chromosome contains nucleotide sequences, for example, guanosine-rich regions, that predispose them to the formation of higher order structures such as quadruplex DNA (qDNA). Sequences that form qDNA are found in the telomeres. The proposal that ligands that stabilize qDNA might interfere with the activity of telomerase in cancer cells has stimulated the search for ligands that are selective for qDNA over dsDNA. The insights gained from the development of ESI-MS methods for analysis of non-covalent dsDNA–ligand complexes are now being applied in the search for qDNA-selective ligands. ESI-MS is a useful first-pass screening technique for qDNA-binding ligands. This short review describes some experimental considerations for ESI-MS analysis of DNA–ligand complexes, briefly addresses the question of whether non-covalent DNA–ligand complexes are faithfully transferred from solution to the gas phase, discusses ion mobility mass spectrometry as a technique for probing this issue, and highlights some recent ESI-MS studies of qDNA-selective ligands.

Measurement of steroid concentrations in brain tissue: methodological considerations

It is well recognized that steroids are synthesized de novo in the brain (neurosteroids). In addition, steroids circulating in the blood enter the brain. Steroids play numerous roles in the brain, such as influencing neural development, adult neuroplasticity, behavior, neuroinflammation, and neurodegenerative diseases such as Alzheimer's disease. In order to understand the regulation and functions of steroids in the brain, it is important to directly measure steroid concentrations in brain tissue. In this brief review, we discuss methods for the detection and quantification of steroids in the brain. We concisely present the major advantages and disadvantages of different technical approaches at various experimental stages: euthanasia, tissue collection, steroid extraction, steroid separation, and steroid measurement. We discuss, among other topics, the potential effects of anesthesia and saline perfusion prior to tissue collection; microdissection via Palkovits punch; solid phase extraction; chromatographic separation of steroids; and immunoassays and mass spectrometry for steroid quantification, particularly the use of mass spectrometry for "steroid profiling." Finally, we discuss the interpretation of local steroid concentrations, such as comparing steroid levels in brain tissue with those in the circulation (plasma vs. whole blood samples; total vs. free steroid levels). We also present reference values for a variety of steroids in different brain regions of adult rats. This brief review highlights some of the major methodological considerations at multiple experimental stages and provides a broad framework for designing studies that examine local steroid levels in the brain as well as other steroidogenic tissues, such as thymus, breast, and prostate.

Electrospray ionization mass spectrometry from discrete nanoliter-sized sample volumes

We describe a method for nanoelectrospray ionization mass spectrometry (nESI-MS) of very small sample volumes. Nanoliter-sized sample droplets were taken up by suction into a nanoelectrospray needle from a silicon microchip prior to ESI. To avoid a rapid evaporation of the small sample volumes, all manipulation steps were performed under a cover of fluorocarbon liquid. Sample volumes down to 1.5 nL were successfully analyzed, and an absolute limit of detection of 105 attomole of insulin (chain B, oxidized) was obtained. The open access to the sample droplets on the silicon chip provides the possibility to add reagents to the sample droplets and perform chemical reactions under an extended period of time. This was demonstrated in an example where we performed a tryptic digestion of cytochrome C in a nanoliter-sized sample volume for 2.5 h, followed by monitoring the outcome of the reaction with nESI-MS. The technology was also utilized for tandem mass spectrometry (MS/MS) sequencing analysis of a 2 nL solution of angiotensin I.

Steroid measurement with LC-MS/MS. Application examples in pediatrics

The correct measurement of steroids is vital for the diagnosis of congenital adrenal hyperplasia (CAH), apparent mineralocorticoid excess, familial hyperaldosteronism type I, primary aldosteronism, Cushing's disease, adrenal insufficiency, etc. Steroid diagnostics also plays an important role in disorders of sexual differentiation and gonadal function. Steroid metabolism is involved in evaluations for precocious puberty, premature thelarche, and polycystic-ovary disease. Finally, the hypothalamo-pituitary-adrenal (HPA) axis is considered to be one of the major systems involved in fetal programming or in stress regulation. Most methods for the determination of steroid hormones are based on immunoassays, which are rapid and easy to perform. However, the reliability of several steroid immunoassays has been shown to be questionable because of the lack of specificity and of matrix effects. Immunological methods, especially direct assays, often overestimate true steroid values. Patient follow-up over time or between laboratories, as well as longitudinal studies, are therefore extremely difficult. This is of particular importance in pediatrics. Liquid chromatography triple quadrupole mass spectrometry (LC-MS/MS) is an increasingly common tool in the clinical laboratory and has the potential to overcome the limitations of immunoassays. LC-MS/MS affords the specificity, imprecision, and limits of quantification necessary for the reliable measurement of steroids, expanding diagnostic capabilities. In addition to the high throughput, the method requires minimal sample preparation and a small sample volume. All these features make it an attractive method to use in a clinical setting. Moreover, LC-MS/MS has the advantage that a spectrum of steroid hormones can be measured simultaneously. Steroid profiling is a very effective method for distinguishing almost all steroid-related disorders. It allows accurate diagnosis and is very useful in many clinical situations. Steroid profiles open up new vistas. The applicability for clinical samples and questions in pediatric endocrinology will be discussed.

A statistically rigorous test for the identification of parent-fragment pairs in LC-MS datasets

Untargeted global metabolic profiling by liquid chromato-graphy−mass spectrometry generates numerous signals that are due to unknown compounds and whose identification forms an important challenge. The analysis of metabolite fragmentation patterns, following collision-induced dissociation, provides a valuable tool for identification, but can be severely impeded by close chromatographic coelution of distinct metabolites. We propose a new algorithm for identifying related parent−fragment pairs and for distinguishing these from signals due to unrelated compounds. Unlike existing methods, our approach addresses the problem by means of a hypothesis test that is based on the distribution of the recorded ion counts, and thereby provides a statistically rigorous measure of the uncertainty involved in the classification problem. Because of technological constraints, the test is of primary use at low and intermediate ion counts, above which detector saturation causes substantial bias to the recorded ion count. The validity of the test is demonstrated through its application to pairs of coeluting isotopologues and to known parent−fragment pairs, which results in test statistics consistent with the null distribution. The performance of the test is compared with a commonly used Pearson correlation approach and found to be considerably better (e.g., false positive rate of 6.25%, compared with a value of 50% for the correlation for perfectly coeluting ions). Because the algorithm may be used for the analysis of high-mass compounds in addition to metabolic data, we expect it to facilitate the analysis of fragmentation patterns for a wide range of analytical problems.

Size effect on fragmentation in tandem mass spectrometry

The collision energy or collision voltage necessary to obtain 50% fragmentation (characteristic collision energy/voltage, CCE or CCV) has been systematically determined for different types of molecules [poly(ethylene glycols) (PEG), poly(tetrahydrofuran) (PTHF), and peptides] over a wide mass (degrees of freedom) range. In the case of lithium-cationized PEGs a clear linear correlation (R(2) > 0.996) has been found between CCE and precursor ion mass on various instrument types up to 4.5 kDa. A similar linear correlation was observed between CCV and the mass-to-charge ratio. For singly and multiply charged polymers studied under a variety of experimental conditions and on several instruments, all data were plotted together and showed correlation coefficient R(2) = 0.991. A prerequisite to observe such a good linear correlation is that the energy and entropy of activation in a class of polymers is likely to remain constant. When compounds of different structure are compared, the CCV will depend not only on the molecular mass but the activation energy and entropy as well. This finding has both theoretical and practical importance. From a theoretical point of view it suggests fast energy randomization up to at least 4.5 kDa so that statistical rate theories are applicable in this range. These results also suggest an easy method for instrument tuning for high-throughput structural characterization through tandem MS: after a standard compound is measured, the optimum excitation voltage is in a simple proportion with the mass of any structurally similar analyte at constant experimental conditions.

Ambient mass spectrometry: bringing MS into the "real world"

Mass spectrometry has recently undergone a second contemporary revolution with the introduction of a new group of desorption/ionization (DI) techniques known collectively as ambient mass spectrometry. Performed in an open atmosphere directly on samples in their natural environments or matrices, or by using auxiliary surfaces, ambient mass spectrometry (MS) has greatly simplified and increased the speed of MS analysis. Since its debut in 2004 there has been explosive growth in the applications and variants of ambient MS, and a very comprehensive set of techniques based on different desorption and ionization mechanisms is now available. Most types of molecules with a large range of masses and polarities can be ionized with great ease and simplicity with the outstanding combination of the speed, selectivity, and sensitivity of MS detection. This review describes and compares the basis of ionization and the concepts of the most promising ambient MS techniques known to date and illustrates, via typical analytical and bioanalytical applications, how ambient MS is helping to bring MS analysis deeper than ever into the "real world" open atmosphere environment--to wherever MS is needed.

Microfluidic Device for Coupling Capillary Electrophoresis and Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry

We have designed and fabricated a polydimethylsiloxane (PDMS) microfluidic device for coupling capillary electrophoresis (CE) and matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS). The coupling is advantageous in biological research because CE has the power of separating analytes in a sample based on mobility difference and MALDI-MS provides accurate and sensitive mass analysis of the analytes. The goal is realized by fractionating the separated analytes inside the microfluidic device and pushing the analyte fractions into open reservoirs. Each analyte fraction is then mixed with a matrix solution and deposited on a MALDI target for MALDI-MS. Therefore, a two-step analysis of analytes in the form of CE-MALDI-MS is achieved by using the microfluidic device.

Microfluidics with MALDI analysis for proteomics--a review

Various microfluidic devices have been developed for proteomic analyses and many of these have been designed specifically for mass spectrometry detection. In this review, we present an overview of chip fabrication, microfluidic components, and the interfacing of these devices to matrix-assisted laser desorption ionization (MALDI) mass spectrometry. These devices can be directly coupled to the mass spectrometer for on-line analysis in real-time, or samples can be analyzed on-chip or deposited onto targets for off-line readout. Several approaches for combining microfluidic devices with analytical functions such as sample cleanup, digestion, and separations with MALDI mass spectrometry are discussed.

Sequence Analysis of Native Oligosaccharides Using Negative ESI Tandem MS

Carbohydrates exhibit many physiologically and pharmacologically important activities, yet their complicated structure and sequence pose major analytical challenges. Although their structural complexity makes analysis of carbohydrate difficult, mass spectrometry (MS) with high sensitivity, resolution and accuracy has become a vital tool in many applications related to analysis of carbohydrates or oligosaccharides. This application is essentially based on soft ionization technique which facilitates the ionization and vaporization of large, polar and thermally labile biomolecules. Electrospray-ionization (ESI), one of the soft ionization technique, tandem MS has been used in the sequencing of peptides, proteins, lipids, nucleic acids and more recently carbohydrates. The development of the ESI and tandem MS has begun to make carbohydrate analysis more routine. This review will focus on the application of the ESI tandem MS for the sequence analysis of native oligosaccharides, including neutral saccharides with multiple linkages, and the uronic acid polymers, alginate and glycosaminoglycans structures containing epimers.

Analysis of protein posttranslational modifications by mass spectrometry: With special reference to haemoglobin

Mass spectrometry provides a convenient platform for the study of different protein post translational modifications from clinical specimen. Analysis of different post translational modifications of hemoglobin like glycation and glutathionylation can provide useful information on the disease progression and the possible outcome of therapies. In the present study, we have addressed post translational modifications of hemoglobin like glutathionylation and glycation in relation to diabetes and chronic renal failure. We found that both alpha and beta chains of human hemoglobin are glycated irrespective of the extent of glycemia as evidenced by a mass increment of 162 Da. The phenomenon of glutathionylation was observed with only the beta globin chain of hemoglobin probably due to the presence of an accessible cysteine residue indicated by a mass increment of 305 Da. Also, the extent of gltuathionylation observed in the CRF patients could correlate with the severity of the oxidative stress owing to renal replacement therapies like dialysis and transplantation.