Negative ion mode matrix-assisted laser desorption/ionisation time-of-flight mass spectrometric analysis of oligosaccharides using halide adducts and 9-aminoacridine matrix

Reactive Matrices for Analytical Matrix-Assisted Laser Desorption/Ionization (MALDI) Mass Spectrometry

In recent years, a special focus is placed on the usage of reactive matrices for analytical matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS). Since 2003, when the term "reactive matrices" was suggested and the dignity of compounds, possessing dualistic properties as matrices and derivatization agents was demonstrated, corresponding approach has found application in various fields and, in particular, in bioanalysis (metabolomics, lipidomics, etc.). The main advantage of this methodology is that it reduces sample treatment time, simplifies the procedure of sample handling, improves the sensitivity of analysis, enhances the molecular identification and profiling. Within the framework of this review, the main attention is paid to "true" reactive matrices that interact with analyte molecules through an exchange or addition reactions. A special section discusses practical application of reactive matrices in the determination of the distribution of targeted and non-targeted organic substances on the surface of biological tissue sections by MALDI-MS imaging. In this critical review, a controversial proposal is made to consider protonating and deprotonating matrices as reactive, because they can undergo a chemical reaction such as proton transfer that occurs in both target solution and MALDI plume. In this respect, special attention is paid to "proton sponge" matrices that have found a wide application in the analysis of various acidic compounds by MALDI-MS in the negative mode. Historical data on the formation of ions and the fate of matrices in MALDI are considered at the beginning of this article.

Disruption of DNA Damage-Response by Propyl Gallate and 9-Aminoacridine

The DNA-damage response (DDR) protects the genome from various types of endogenous and exogenous DNA damage, and can itself be a target of certain chemicals that give rise to chromosomal aberrations. Here, we developed a screening method to detect inhibition of Mediator of DNA damage Checkpoint 1 (MDC1) foci formation (the Enhanced Green Fluorescent Protein (EGFP)-MDC1 foci formation-inhibition assay) using EGFP-MDC1-expressing human cells. The assay identified propyl gallate (PG) and 9-aminoacridine (9-AA) as inhibitors of camptothecin (CPT)-induced MDC1 foci formation. We demonstrated that the inhibition of CPT-induced MDC1 foci formation by PG was caused by the direct suppression of histone H2AX phosphorylation at Ser139 (γH2AX), which is required for MDC1 foci formation, by quantifying γH2AX in cells and in vitro 9-AA also directly suppressed H2AX Ser139-phosphorylation in vitro but the concentration was much higher than that required to suppress CPT-induced MDC1 foci formation in cells. Consistent with these findings, PG and 9-AA both suppressed CPT-induced G2/M cell-cycle arrest and increased the number of abnormal nuclei. Our results suggest that early DDR-inhibitory effects of PG and 9-AA contribute to their chromosome-damaging potential, and that the EGFP-MDC1 foci formation-inhibition assay is useful for detection of and screening for H2AX Ser139-phosphorylation-inhibitory effects of chemicals.

Negative ion MALDI-TOF MS, ISD and PSD of neutral underivatized oligosaccharides without anionic dopant strategies, using 2,5-DHAP as a matrix

Oligosaccharides represent complex class of analytes for mass spectrometric analysis due to the high variety of structural isomers concerning glycosidic linkages and possible branching. A systematic study of the negative ion mode matrix-assisted laser desorption/ionization (MALDI) mass spectrometry of various neutral oligosaccharides under selection of an appropriate matrix, like 2,5-dihydroxyacetophenone (2,5-DHAP) is reported here, without commonly used anion dopant strategies. Nevertheless, we were able to generate relevant in-source decay (ISD) cross-ring fragment ions, typically obtained in the negative ion mode. Data observed indicate that the intrinsic property of the terminal non-reduced aldose is crucial for this behavior. A systematic study of the post source decay (PSD) of molecular, pseudomolecular and ISD cross-ring cleavage precursor ions is reported here. A direct comparison of the positive and negative ion mode MALDI MS1 and PSD behavior of neutral oligosaccharides could also be performed under the use of the same matrix preparation, because 2,5-DHAP is fully compatible with positive ion mode acquisition. We found that PSD spectra of deprotonated neutral oligosaccharides obtained in the negative ion mode are richer, because they contained both glycosidic and cross-ring fragment ions. However, we also found that cross-ring fragment ions are readily produced in the positive ion mode when potassiated precursor ions were selected. In addition, we show evidence that non-anionic dopants and specific instrumental parameters can also significantly influence the ISD fragmentation. Taken together, our results should increase our understanding of oligosaccharide behavior in the negative ion mode as well as increase our knowledge regarding many aspects of in-source MALDI chemistry.

Current metabolomics: technological advances

Metabolomics, the global quantitative assessment of metabolites in a biological system, has played a pivotal role in various fields of science in the post-genomic era. Metabolites are the result of the interaction of the system's genome with its environment and are not merely the end product of gene expression, but also form part of the regulatory system in an integrated manner. Therefore, metabolomics is often considered a powerful tool to provide an instantaneous snapshot of the physiology of a cell. The power of metabolomics lies on the acquisition of analytical data in which metabolites in a cellular system are quantified, and the extraction of the most meaningful elements of the data by using various data analysis tool. In this review, we discuss the latest development of analytical techniques and data analyses methods in metabolomics study.

MALDI-MS/MS with traveling wave ion mobility for the structural analysis of N-linked glycans

The preference for singly charged ion formation by MALDI makes it a better choice than electrospray ionization for profiling mixtures of N-glycans. For structural analysis, fragmentation of negative ions often yields more informative spectra than fragmentation of positive ones but such ions are more difficult to produce from neutral glycans under MALDI conditions. This work investigates conditions for the formation of both positive and negative ions by MALDI from N-linked glycans released from glycoproteins and their subsequent MS/MS and ion mobility behaviour. 2,4,6-Trihydroxyacetophenone (THAP) doped with ammonium nitrate was found to give optimal ion yields in negative ion mode. Ammonium chloride or phosphate also yielded prominent adducts but anionic carbohydrates such as sulfated N-glycans tended to ionize preferentially. Carbohydrates adducted with all three adducts (phosphate, chloride, and nitrate) produced good negative ion CID spectra but those adducted with iodide and sulfate did not yield fragment ions although they gave stronger signals. Fragmentation paralleled that seen following electrospray ionization providing superior spectra than could be obtained by PSD on MALDI-TOF instruments or with ion traps. In addition, ion mobility drift times of the adducted glycans and the ability of this technique to separate isomers also mirrored those obtained following ESI sample introduction. Ion mobility also allowed profiles to be obtained from samples whose MALDI spectra showed no evidence of such ions allowing the technique to be used in conditions where sample amounts were limiting. The method was applied to N-glycans released from the recombinant human immunodeficiency virus glycoprotein, gp120.

N-(1-naphthyl) ethylenediamine dinitrate: a new matrix for negative ion MALDI-TOF MS analysis of small molecules

An organic salt, N-(1-naphthyl) ethylenediamine dinitrate (NEDN), with rationally designed properties of a strong UV absorbing chromophore, hydrogen binding and nitrate anion donors, has been employed as a matrix to analyze small molecules (m/z < 1000) such as oligosaccharides, peptides, metabolites and explosives using negative ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Compared with conventional matrixes such as α-cyano-4-hydroxycinnamic acid (CCA) and 2,5-dihydroxybenzoic acid (DHB), NEDN provides a significant improvement in detection sensitivity and yields very few matrix-associated fragment and cluster ions interfering with MS analysis. For low-molecular-weight saccharides, the lowest detection limit achieved ranges from 500 amol to 5 pmol, depending on the molecular weight and the structure of the analytes. Additionally, the mass spectra in the lower mass range (m/z < 200) consist of only nitrate and nitric acid cluster ions, making the matrix particularly useful for structural identification of oligosaccharides by post-source decay (PSD) MALDI-MS. Such a characteristic is illustrated by using maltoheptaose as a model system. This work demonstrates that NEDN is a novel negative ion-mode matrix for MALDI-MS analysis of small molecules with nitrate anion attachment.

Production and fragmentation of negative ions from neutral N-linked carbohydrates ionized by matrix-assisted laser desorption/ionization

Although negative ion fragmentation mass spectra of neutral N-linked carbohydrates (those attached to Asn in glycoproteins) provide much more structural information than spectra recorded in positive ion mode, neutral carbohydrates are reluctant to form negative ions by matrix-assisted laser desorption/ionization (MALDI) unless ionized from specific matrices such as nor-harmane or adducted with anions such as chloride. This paper reports the results of experiments to optimize negative ion formation from adducts of N-linked glycans with respect to ion abundance and fragment ion production. The best results were obtained with 2,4,6-trihydroxyacetophenone (THAP) as the matrix with added ammonium nitrate as the salt providing the anion. This approach is demonstrated to be applicable for a wide range of N-linked glycan structures. Phosphate adducts, analogous to those that are usually encountered in electrospray spectra from N-glycans released by protein N-glycosidase F, were produced by addition of ammonium phosphate to the matrix but in relatively low yield allowing competitive ionization of endogenous anionic compounds leading to complex spectra. Fragmentation of the nitrate adducts, which were formed in higher yield, generally paralleled that seen by collision-induced dissociation following ionization by electrospray, with the first stage of the dissociation being the elimination of the nitrate with a proton from one of the hydroxyl groups of the sugar. The spectra of the resulting [M-H](-) species displayed very specific fragment ions, mainly cross-ring and C-type glycosidic cleavage products, that revealed more structural (linkage and branching) information of the compounds than the mainly glycosidic cleavage products that dominated the positive ion spectra.

Sphingomyelin is more sensitively detectable as a negative ion than phosphatidylcholine: a matrix-assisted laser desorption/ionization time-of-flight mass spectrometric study using 9-aminoacridine (9-AA) as matrix

Phospholipids (PLs) are increasingly analyzed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) and imaging MS. Different classes of PLs are preferentially detectable either as positive or negative ions depending on the charges of their headgroups. Sphingomyelin (SM) and phosphatidylcholine (PC) occur in virtually all biological samples and both are assumed to be detectable with the same sensitivity (in the positive ion mode) because their headgroups are identical. We will show here that the detectabilities of PC and SM depend on the matrix used. In the presence of 2,5-dihydroxybenzoic acid (DHB) SM is more sensitively detectable in positive ion mode than PC while the use of 9-aminoacridine (9-AA) as matrix inverts the detectabilities. Our explanation is that the preferred generation of negative ions from SM if 9-AA is used as matrix results in a reduced yield of positive ions. It will also be shown that this is not only valid if a simplified model system is investigated, but also if, for instance, extracts from human erythrocytes are investigated. It will also be outlined that this finding is particularly important in the context of imaging studies where no previous separation of the lipids of interest can be performed.

Lithographically patterned silicon nanowire arrays for matrix free LDI-TOF/MS analysis of lipids

Silicon nanowire arrays were patterned onto silicon chips by a combination of lithography and chemical vapor deposition using the vapor-liquid-solid growth method. Thus, highly reproducible sample deposition zones were obtained that were used for laser desorption ionization (LDI) mass spectrometric analysis of lipidic species with lithium salts as dopants. Using a conventional UV laser (337 nm), hydrocarbons and numerous lipids (triglycerides, diglycerides, wax esters) could be effectively lithiated yielding [M + Li](+) ions. Upon doping with lithium hydroxide the SiNW arrays yielded high signal-to-noise ratios with low limits of detection (e.g. 750 pg tripalmitin on target with S/N 5) and efficient ionization for a range of fatty acids (FA), mono-, di- and triglycerides and hydrocarbons (HC), in the form of [FA-H + 2Li](+), [mono- or diglyceride-H(2)O + Li](+), or [triglyceride + Li](+) and [HC + Li](+), respectively. It is expected that these chips will find a broad range of applications in the analysis of natural compounds and food control.

Elemental sulfur as a versatile low-mass-range calibration standard for laser desorption ionization mass spectrometry

Facile generation of series of singly charged radical anions (S(n)(-*); n = 1-15) and cations (S(n)(+*); n = 2-11) by direct laser ionization renders elemental sulfur an excellent material for the low-mass-region calibration of time of flight (TOF) mass spectrometers. Upon irradiation by a 337-nm UV laser, elemental sulfur undergoes facile ionization without the need of an additional laser-absorbing matrix. An intense and evenly spaced set of peaks is obtained in both modes.