Ultraviolet Matrix-assisted Laser Desorption Ionization Research Articles

Infrared MALDI Mass Spectrometry with Laser-Induced Postionization for Imaging of Bacterial Colonies.

Ultraviolet matrix-assisted laser desorption ionization mass spectrometry imaging (UV-MALDI-MSI) is a powerful tool to visualize bacterial metabolites in microbial colonies and in biofilms. However, a challenge for the method is the efficient extraction of analytes from deeper within the bacterial colonies and from the cytoplasm of individual cells during the matrix coating step. Here, we used a pulsed infrared (IR) laser of 2.94 μm wavelength to disrupt and ablate bacterial cells without a prior coating with a MALDI matrix. Instead, tissue water or, in some experiments, in addition a small amount of glycerol was exploited for the deposition of the IR laser energy and for supporting the ionization of the analytes. Compared to water, glycerol exhibits a lower vapor pressure, which prolonged the available measurement time window within an MSI experiment. Mass spectra were acquired with a hybrid Synapt G2-S HDMS instrument at a pixel size of 120 μm. A frequency-quadrupled q-switched Nd:YAG laser with 266 nm wavelength served for laser-induced postionization (MALDI-2). In this way, the ion abundances of numerous small molecules such as nucleobases, 2-alkyl-quinolones, a prominent class of Pseudomonas aeruginosa signaling molecules involved in one of the three quorum-sensing pathways, and also the signals of various bacterial phospholipids were boosted, partially by orders of magnitude. We analyzed single and cocultured colonies of Gram-negative P. aeruginosa and of Gram-positive Bacillus subtilis and Staphylococcus aureus as exemplary bacterial systems. To enable a rapid (within 5 s) MSI-compatible steam inactivation in a custom-made autoclave filled with hot water steam, bacterial cultures were grown on porous polyamide membranes. Compared to a UV-MALDI-2-MS measurement of the same systems, mass spectra with a reduced low mass background were generally generated. This resulted in the unequivocal detection of numerous metabolites only with the IR laser. In a fundamental part of our study, and to optimize the IR-MALDI-2 approach for the highest analytical sensitivity, we characterized the expansion dynamics of the particle plume as generated by the IR laser. Here, we recorded the total ion count and the intensities of selected signals registered from P. aeruginosa samples as a function of the interlaser delay and buffer gas pressure in the ion source. The data revealed that the IR-MALDI-2 ion signals are primarily generated from slow particles having mean velocities of ∼10 m/s. Interestingly, two different pressure/delay time regimes of the optimized ionization efficiency for phospholipids and smaller metabolites, respectively, were revealed, a result pointing to yet-unknown convoluted reaction cascades. The described IR-MALDI-2 method could be a helpful new tool for a microbial mass spectrometry imaging of small molecules requiring little sample preparation.

Temperature Dependence of Desorbed Ions and Neutrals and Ionization Mechanism of Matrix-Assisted Laser Desorption/Ionization.

Two separate temperature-dependent experiments were performed to investigate the ionization mechanism of ultraviolet matrix-assisted laser desorption/ionization (UV-MALDI) of matrix 2,5-dihydroxybenzoic acid (2,5-DHB). First, the angular resolved intensity and velocity distributions of neutrals desorbed from the 2,5-DHB solid sample through UV laser (355 nm) pulse irradiation were measured using a rotating quadrupole mass spectrometer. Second, the desorbed neutrals, at an angle normal to the surface, and the desorbed ions were simultaneously detected for each laser shot using the quadrupole mass spectrometer and a time-of-flight mass spectrometer, respectively. Both experiments were conducted at two initial temperatures: 100 and 300 K. The measurements from these two experiments were used to calculate the initial temperature dependence of the ion-to-neutral ratio. The results closely agreed with the predictions of the temperature-dependent ion-to-neutral ratio using the thermal model, indicating that thermally induced proton transfer is the dominant reaction that generates initial ions of 2,5-DHB in UV-MALDI.

MALDI- and LDI-MS saponin fingerprint of leaves and stick components of commercial yerba mate (Ilex paraguariensis).

Yerba mate (YM) is massively produced and consumed as an infusion in South America and spreading all over the world. This product is obtained from dried leaves of Ilex paraguariensis Saint Hilaire, mixed with fragments of dried branches (sticks). For its commercialization, YM must have a minimum percentage of leaves because its presence determines YM quality and price. Till today, a mechanical methodology to determine the relative amount of components (sticks, leaves, and powder) is used. There is not any modern analytical method that provides information for quick characterization of the YM components. Typical saponin fingerprints for leaves and sticks were found by using ultraviolet matrix-assisted laser desorption ionization and ultraviolet laser desorption ionization mass spectrometry. Then, their possible application as useful tools for quick characterization of components of commercial YM (leaves and sticks) is presented. Furthermore, fingerprints obtained from authentic samples of Ilex paraguariensis and Ilex dumosa are also included and discussed. Each Ilex show typical saponin fingerprints for leaves and sticks.

Vacuum Ultraviolet Single-Photon Postionization of Amino Acids

In this study, ultraviolet (UV) laser desorption and vacuum UV single-photon (VUV SP) postionization were performed to ionize and successfully analyze 20 common amino acids. The analytical merit and efficiency of the ionization was compared with those of conventional UV matrix-assisted laser desorption ionization (UV-MALDI). A VUV light source (118 nm) was generated from the ninth harmonic of a Q-switched Nd:YAG laser, and the photon number was determined to be larger than 1012 for each laser pulse in the ionization region. In general, the detection sensitivity of VUV-SP-postionization was 10–100 times higher than that of conventional UV-MALDI. In particular, the ion signal from VUV-SP-postionization was considerably larger than that from UV-MALDI for analytes with low proton affinity such as glycine. However, some fragmentation of intact ions was observed in VUV-SP-postionization. Quantitative analysis performed using a glycine/histidine mixture and tryptophan/phenylalanine mixture revealed that the dynamic range of VUV-SP-postionization was one order of magnitude larger than that of UV-MALDI, indicating that VUV-SP-postionization is suitable for the quantitative analysis of amino acids.

Biospectroscopy, biospectrometry and imaging of Ilex paraguariensis. Basis for non-destructive quality evaluation using artificial vision.

Yerba mate (YM) is massively produced and consumed as an infusion in South America and is gaining popularity all over the world. This product is obtained from the dried leaves of Ilex paraguariensis Saint Hilaire, mixed with fragments of its dried branches. For its commercialization YM must have a minimum percentage of leaves according to a standard classification. Until now, composition quantification has been mechanically performed, thus development of new methods is still pending. In this work a quantification method using solid-phase molecular fluorescence, alternately diffuse reflectance spectroscopy and an imaging technique using a scanner have been proposed. Strong differences between the spectroscopic properties of leaves and sticks were observed and in all the cases linear correlations between the processed signals and composition were observed. Interesting differences in chemical composition of YM leaves and sticks were additionally obtained in this work by means of total phenol content quantification, ultraviolet matrix assisted laser-desorption ionization mass spectrometry and ultraviolet laser-desorption ionization mass spectrometry.

Bacillus subtilis subsp. subtilis CBMDC3f with antimicrobial activity against Gram-positive foodborne pathogenic bacteria: UV-MALDI-TOF MS analysis of its bioactive compounds.

In this work a new Bacillus sp. strain, isolated from honey, was characterized phylogenetically. Its antibacterial activity against three relevant foodborne pathogenic bacteria was studied; the main bioactive metabolites were analyzed using ultraviolet matrix assisted laser desorption-ionization mass spectrometry (UV-MALDI MS). Bacillus CBMDC3f was phylogenetically characterized as Bacillus subtilis subsp. subtilis after rRNA analysis of the 16S subunit and the gyrA gene (access codes Genbank JX120508 and JX120516, respectively). Its antibacterial potential was evaluated against Listeria monocytogenes (9 strains), B. cereus (3 strains) and Staphylococcus aureus ATCC29213. Its cell suspension and cell-free supernatant (CFS) exerted significant anti-Listeria and anti-S. aureus activities, while the lipopeptides fraction (LF) also showed anti-B. cereus effect. The UV-MALDI-MS analysis revealed surfactin, iturin and fengycin in the CFS, whereas surfactin predominated in the LF. The CFS from CBMDC3f contained surfactin, iturin and fengycin with four, two and four homologues per family, respectively, whereas four surfactin, one iturin and one fengycin homologues were identified in the LF. For some surfactin homologues, their UV-MALDI-TOF/TOF (MS/MS; Laser Induced Decomposition method, LID) spectra were also obtained. Mass spectrometry analysis contributed with relevant information about the type of lipopeptides that Bacillus strains can synthesize. From our results, surfactin would be the main metabolite responsible for the antibacterial effect.

Ion Intensity and Thermal Proton Transfer in Ultraviolet Matrix-Assisted Laser Desorption/Ionization

The ionization mechanism of ultraviolet matrix-assisted laser desorption/ionization (UV-MALDI) was investigated by measuring the total cation intensity (not including sodiated and potasiated ions) as a function of analyte concentration (arginine, histidine, and glycine) in a matrix of 2,4,6-trihydroxyacetophenone (THAP). The total ion intensity increased up to 55 times near the laser fluence threshold as the arginine concentration increased from 0% to 1%. The increases were small for histidine, and a minimal increase occurred for glycine. Time-resolved fluorescence intensity was employed to investigate how analytes affected the energy pooling of the matrix. No detectable energy pooling was observed for pure THAP and THAP/analyte mixtures. The results can be described by using a thermal proton transfer model, which suggested that thermally induced proton transfer is crucial in the primary ion generation in UV-MALDI.

Thermal Proton Transfer Reactions in Ultraviolet Matrix-Assisted Laser Desorption/Ionization

One of the reasons that thermally induced reactions are not considered a crucial mechanism in ultraviolet matrix-assisted laser desorption ionization (UV-MALDI) is the low ion-to-neutral ratios. Large ion-to-neutral ratios (10(-4)) have been used to justify the unimportance of thermally induced reactions in UV-MALDI. Recent experimental measurements have shown that the upper limit of the total ion-to-neutral ratio is approximately 10(-7) at a high laser fluence and less than 10(-7) at a low laser fluence. Therefore, reexamining the possible contributions of thermally induced reactions in MALDI may be worthwhile. In this study, the concept of polar fluid was employed to explain the generation of primary ions in MALDI. A simple model, namely thermal proton transfer, was used to estimate the ion-to-neutral ratios in MALDI. We demonstrated that the theoretical calculations of ion-to-neutral ratios exhibit the same trend and similar orders of magnitude compared with those of experimental measurements. Although thermal proton transfer may not generate all of the ions observed in MALDI, the calculations demonstrated that thermally induced reactions play a crucial role in UV-MALDI.

Is energy pooling necessary in ultraviolet matrix‐assisted laser desorption/ionization?

Energy pooling has been suggested as the key process for generating the primary ions during ultraviolet matrix-assisted laser desorption/ionization (UV-MALDI). In previous studies, decreases in fluorescence quantum yields as laser fluence increased for 2-aminobenzoic acid, 2,5-dihydroxybenzoic acid (2,5-DHB), and 3-hydroxypicolinic acid were used as evidence of energy pooling. This work extends the research to other matrices and addresses whether energy pooling is a universal property in UV-MALDI. Energy pooling was investigated in a time-resolved fluorescence experiment by using a short laser pulse (355 nm, 20 ps pulse width) for excitation and a streak camera (1 ps time resolution) for fluorescence detection. The excited-state lifetime of 2,5-DHB decreased with increases in laser fluence. This suggests that a reaction occurs between two excited molecules, and that energy pooling may be one of the possible reactions. However, the excited-state lifetime of 2,4,6-trihydroxyacetophenone (THAP) did not change with increases in laser fluence. The upper limit of the energy pooling rate constant for THAP is estimated to be approximately 100-500 times smaller than that of 2,5-DHB. The small energy pooling rate constant for THAP indicates that the potential contribution of the energy pooling mechanism to the generation of THAP matrix primary ions should be reconsidered.

Matching the laser wavelength to the absorption properties of matrices increases the ion yield in UV-MALDI mass spectrometry

A high analytical sensitivity in ultraviolet matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) is only achieved if the laser wavelength corresponds to a high optical absorption of the matrix. Laser fluence and the physicochemical properties of the compounds, e.g., the proton affinity, also influence analytical sensitivity significantly. In combination, these parameters determine the amount of material ejected per laser pulse and the ion yield, i.e., the fraction of ionized biomolecules. Here, we recorded peptide ion signal intensities as a function of these parameters. Three cinnamic acid matrices were investigated: α-cyano-4-hydroxycinnamic acid, α-cyano-4-chlorocinnamic acid, and α-cyano-2,4-difluorocinnamic acid. In addition, 2,5-dihydroxybenzoic acid was used in comparison experiments. Ion signal intensities "per laser shot" and integrated ion signal intensities were acquired over 900 consecutive laser pulses applied on distinct positions on the dried-droplet sample preparations. With respect to laser wavelength, the two standard MALDI wavelengths of 337/355 nm were investigated. Also, 305 or 320 nm was selected to account for the blue-shifted absorption profiles of the halogenated derivatives. Maximal peptide ion intensities were obtained if the laser wavelength fell within the peak of the absorption profile of the compound and for fluences two to three times the corresponding ion detection threshold. The results indicate ways for improving the analytical sensitivity in MALDI-MS, and in particular for MALDI-MS imaging applications where a limited amount of material is available per irradiated pixel.

Potential of radical scavenging reagents as a matrix additive in the direct detection of S-nitrosylated peptides with UV-MALDI MS

Nitric oxide (NO) exerts a ubiquitous influence on cellular signaling, largely through S-nitrosylation/denitrosylation of cysteines in proteins. The ability to analyze S-nitrosylation directly by mass spectrometry (MS) would be highly useful in understanding the action of NO in various biological processes. However, S-nitrosylation has never been detected by ultraviolet matrix-assisted laser desorption/ionization (UV-MALDI) MS because the NO group completely dissociates during the ionization process.In this study, tetraphenylporphyrin (TPP) was used as matrix additive with 2,5-dihydroxybenzoic acid (DHB) to evaluate its suppressive effect on the NO group dissociation of S-nitrosylated peptides. Samples were subjected to MS and MS/MS analysis by MALDI-TOF MS and MALDI-QIT-TOF MS, respectively. In MS analysis using TPP as a matrix additive, the presumably intact molecular ion [M+H]+ peak was also observed, although the NO-dissociated ions [M−NO+H]+ were mainly detected. In contrast, in the absence of TPP, this [M+H]+ peak was not observed. MS/MS analysis of this ion indicated that the peptides contained S-nitrosylated cysteines. Furthermore, other reagents with radical scavenging activity (retinoic acid, α-tocopherol, ascorbic acid, naringenin, and 3,5-di-tert-butyl-4-hydroxytoluene) were tested to examine the possibility of their use as matrix additives for S-nitrosylation detection. As with TPP, these additives showed a suppressive effect on NO group dissociation. In conclusion, radical scavenging reagents are effective additive candidates for detecting S-nitrosylation directly with UV-MALDI MS.

Selective Screening of Tyrosine-Nitrated Peptides in Tryptic Mixtures by In-Source Photodissociation at 355 nm in Matrix-Assisted Laser Desorption Ionization

Nitration of tyrosine residues in proteins is an important post-translational modification related to various diseases such as Alzheimer's. In this work, efficient and selective photodissociation (PD) at 355 nm was observed for [M + H](+), [M + H - 16](+), and [M + H - 32](+) generated by matrix-assisted ultraviolet laser desorption ionization (UV-MALDI) of tyrosine-nitrated peptides (nitropeptides). Product ion spectra obtained by post-source PD at this wavelength contained useful information on the amino acid sequence. The spectra for nitropeptides obtained with 355 nm irradiation inside the ion source (MALDI/in-source PD) displayed characteristic triplet patterns due to PD of the above ions. For peptides displaying prominent signal in a MALDI mass map of a tryptic mixture, which are mostly those with arginine at the C-terminus, in-source PD allowed positive identification of their tyrosine-nitrated forms. Identification of such nitropeptides was possible at the 10 fmol level (in tryptic digest of 100 fmol BSA).

Negative ion ultraviolet matrix-assisted laser desorption ionization mass spectrometry and post source decay of glycosyl esters of nucleoside pyrophosphates.

Six different glycosyl esters of nucleoside pyrophosphates (monosaccharide nucleotides) were analyzed by means of matrix-assisted laser desorption/ionisation reflectron time-of-flight mass spectrometry (MALDI/RToF MS) in the negative ion mode. Several matrices were evaluated and 3-hydroxypicolinic acid as well as alpha-cyano-4- hydroxycinnamic acid (CHCA) turned out to be the matrices of choice applying the thin layer technique to obtain maximum sensitivity for deprotonated molecular ion detection and maximal fragmentation particular with CHCA. The determination of the molecular mass with a mass accuracy below 0.1% was feasible with sample amounts in the lower femtomole range applying a MALDI desk-top mass spectrometer. A further important refinement of this technique was the use of post source decay (PSD) fragment ion analysis with a curved field reflector (which means no stepping of the reflector voltage). Detailed structural information of the six selected monosaccharide nucleotides could be obtained with PSD and differences in the fragmentation pattern were used to distinguish them. This method (based on molecular mass and PSD fragment ion analysis) has been applied to verify the presence of a glycosyl ester of nucleoside pyrophosphate in samples from Saccharomyces cerevisiae.

Cyanogen Bromide Peptides of the Fibrillar Collagens I, III, and V and Their Mass Spectrometric Characterization: Detection of Linear Peptides, Peptide Glycosylation, and Cross-Linking Peptides Involved in Formation of Homo- and Heterotypic Fibrils

The network of the fibrillar collagens I, III, and V, extracted from fetal calf skin and cleaved with cyanogen bromide, was studied by means of ultraviolet matrix-assisted laser desorption ionization time-of-flight mass spectrometry (UV-MALDI MS). Nearly all of the expected cyanogen bromide peptides of the different alpha chains were detected. Distinct peptides are identified that can serve as a reference signal for the individual alpha-chains. Homo- and heterotypic cross-linking patterns, some of which have not been described before for bovine collagen, are indicated by comparison of the mass spectrometric data with documented amino acid sequences. Potential cross-linking mechanisms are discussed. For example, the mass spectrometric data suggest that the formation of heterotypic I/III and I/V fibrils is substantially determined by the telo-regions of type I collagen, which are covalently connected to the corresponding helical and nonhelical cross-linking domains of adjacent molecules either by 4D or 0D-stagger bonds. The chemical nature of the cross-links can be concluded. The data also indicate a disturbed formation of heterotypic fibrils. Finally, collagen glycosylation can also be identified.

Effects of silsesquioxane coating structure on mechanical interfacial properties of carbon fibre/polyarylacetylene composites

Carbon fibres (CF) were treated with different coatings, including [3-(methacryloxy)propyl]trimethoxylsilane (MPMS), [3-(methacryloxy)propyl]silsesquioxane (MPMS-SSO), and (methacryloxy)propyl polyhedral oligomeric silsesquioxane (Methacryl-POSS), to improve the interfacial properties of carbon fibre reinforced polyarylacetylene (PAA) matrix composites. MPMS-SSO was obtained from the hydrolytic condensation of MPMS. The complicated structure, including cage and ladder one, of MPMS-SSO may be assigned by Fourier transforms infrared (FT-IR) spectra, 1H, 13C and 29Si nuclear magnetic resonance (NMR) and ultraviolet matrix-assisted laser desorption ionization time-of-flight mass spectrometry (UV-MALDI-TOF MS). Interlaminar shear strength (ILSS) was tested to investigate the effect of coating structure on the interfacial bonding. The values of ILSS of untreated and treated CF/PAA composites with different coatings (MPMS, MPMS-SSO and Methacryl-POSS) show that the treatment effect of Methacryl-POSS coating is the best one and the MPMS-SSO coating is better than that of MPMS coating. SEM micrographs of shear fracture of CF/PAA composites also suggested the different coating treatment effects. The differences of increasing degrees of ILSS indicate that the structure of coating is important when silsesquioxanes are used as coatings to treat fibre surface for building up the adhesion and improving interfacial properties of fibre reinforced polymer matrix composites.

Ionic liquid matrix for direct UV-MALDI-TOF-MS analysis of dermatan sulfate and chondroitin sulfate oligosaccharides.

Polyanionic oligosaccharides such as dermatan sulfate (DS) and chondroitin sulfate (CS) exhibit poor ionization efficiencies and tend to undergo thermal fragmentation through the loss of SO(3) under conventional ultraviolet matrix-assisted laser desorption/ionization (UV-MALDI) conditions. A new ionic liquid matrix (ILM), a guanidinium salt of alpha-cyano-4-hydroxycinnamic acid, facilitates direct UV-MALDI mass spectrometric (MS) analysis of underivatized DS and CS oligosaccharides up to a decasaccharide in their common form as sodium salts. The resulting mass spectra show very low extent of fragmentation through an SO(3) loss. The new ILM is suitable for MALDI-MS analysis of mixtures containing oligosaccharides with different numbers of sulfo groups.

Antioxidant activity and hepatoprotective potential of agaro-oligosaccharides in vitro and in vivo

BackgroundAgaro-oligosaccharides derived from red seaweed polysaccharide have been reported to possess antioxidant activity. In order to assess the live protective effects of agar-oligosaccharides, we did both in vitro and in vivo studies based on own-made agaro-oligosaccharides, and the structural information of this oligosaccharide was also determined.MethodStructure of agaro-oligosaccharides prepared with acid hydrolysis on agar was confirmed by matrix-assisted ultraviolet laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) and NMR. The antioxidant effect of agaro-oligosaccharides on intracellular reactive oxygen species (ROS) was assessed by 2', 7'-dichlorofluorescin diacetate. Carbon tetrachloride was used to induce liver injury, some index including SOD, GSH-Px, MDA, AST, ALT were examined to determine the hepatoprotective effect of agaro-oligosaccharides.ResultsAgaro-oligosaccharides we got were composed of odd polymerizations with molecular weights ranged from 500 to 2500. Results from intracellular test indicated that agaro-oligosaccharides could significantly scavenge the level of oxidants in the hepatocytes, more beneficially, also associated with the improvement of cell viability In vivo studies of the antioxidant effects on tissue peroxidative damage induced by carbon tetrachloride in rat model indicated that agaro-oligosaccharides could elevate the activity of superoxide dismutase (SOD), glutathione peroxidase (GSH-Px) and decrease the level of malondialdehyde (MDA), glutamate oxaloacetate transaminase (AST), glutamic pyruvic transaminase (ALT) significantly. At 400 mg/kg, MDA level reduced 44 % and 21 % in liver and heart, SOD and GSH-Px increased to highest in liver and serum, while ALT level decreased 22.16 % in serum.ConclusionOverall, the results of the present study indicate that agaro-oligosaccharides can exert their in vitro and in vivo hepatoprotective effect through scavenging oxidative damage induced by ROS.

Matrix-assisted ultraviolet laser-desorption ionization and electrospray-ionization time-of-flight mass spectrometry of sulfated neocarrabiose oligosaccharides

Several commercial sulfated neocarrabiose oligosaccharides were analyzed by matrix-assisted ultraviolet laser-desorption ionization time-of-flight mass spectrometry (UV-MALDI-TOF-MS). UV-MALDI-TOF-MS was carried out in the linear and reflectron modes and, as routine, in both the positive- and negative-ion modes. 2,5-Dihydroxybenzoic acid and nor-harmane were used as matrices. In the positive- and negative-ion modes, with both matrices, peaks corresponding to (M+Na) + and (M−Na) − ions, respectively, were obtained, with only some signals due to glycosidic linkage cleavages (prompt fragmentation). With 2,5-dihydroxybenzoic acid abundant matrix signals were observed; nor-harmane afforded very few matrix signals in both ion modes, but more desulfation (prompt fragmentation) of the compounds occurred. When the desorption/ionization process was highly efficient, the post-source decay (PSD) fragmentation patterns were also investigated; most of the fragments detected derived from glycosidic linkage cleavages. Electrospray-ionization time-of-flight mass spectrometry (ESI-TOF-MS) in the negative-ion mode confirmed, with the observation of the (M−Na) − and the multiply charged anions, the identity and the purity of the samples.

A quantitative model of ultraviolet matrix-assisted laser desorption/ionization.

A quantitative model of primary ionization in ultraviolet matrix-assisted laser desorption/ionization (UV-MALDI) is presented. It includes not only photochemical processes such as exciton pooling, but also the effects of the desorption event. The interplay of these two is found to be a crucial aspect of the MALDI process. The desorbing plume is modeled as an adiabatic expansion with entrained clusters. The parameters in the model are defined as much as possible via experiment or by analogy with known effects. The model was applied to the matrix 2,5-dihydroxybenzoic acid and found to reproduce the fluence dependence of the fluorescence yield and key features of the picosecond two-pulse ion generation efficiency curves. In addition, the model correctly predicts a fluence rather than irradiance threshold, the magnitude of the threshold, the magnitude of the ion yield, laser wavelength effects, plume temperatures, plume expansion velocities and the spot size effect.

Modeling the cluster formation during infrared and ultraviolet matrix-assisted laser desorption ionization of oligonucleotides in succinic acid matrix with molecular mechanics

A large succinic acid (HOOC(CH2)2COOH) matrix containing 7 × 7 × 7 unit cells with guest oligonucleotide AGCAGCT was modeled with molecular dynamics simulation for infrared matrix-assisted laser desorption ionization. We simulated the laser heating of the succinic acid (this data is still missing from the literature) with λ=2.94 μm infrared laser pulses and compared it to ultraviolet excitation. We did this in order to elucidate the cluster formation of succinic acid in the gas phase in itself and around the analyte. At this wavelength, the laser energy is coupled into the matrix through the OH vibrations of the carboxyl groups. The most pronounced difference we observed at 1,500 K simulation is that infrared heating generates about 10–15 more succinic acid molecules bound to the analyte in noncovalent complex form than the ultraviolet mode, which generates about 2 molecules thus bound. We report energy redistribution within the matrix between the host and guest species as well as other dynamical properties. The parameter and topology data for succinic acid that we used are reported and ready for use in CHARMM computer code environment for simulation.