Direct observation of bulk and surface chemical morphologies of Ginkgo biloba leaves by Fourier transform mid- and near-infrared microspectroscopic imaging

Fourier transform infrared microspectroscopy is a powerful tool to obtain knowledge about the spatial and/or temporal distributions of the chemical compositions of plants for better understanding of their biological properties. However, the chemical morphologies of plant leaves in the plane of the blade are barely studied, because sections in this plane for mid-infrared transmission measurements are difficult to obtain. Besides, native compositions may be changed by chemical reagents used when plant samples are microtomed. To improve methods for direct infrared microspectroscopic imaging of plant leaves in the plane of the blade, the bulk and surface chemical morphologies of nonmicrotomed Ginkgo biloba leaves were characterized by near-infrared transmission and mid-infrared attenuated total reflection microspectroscopic imaging. A new self-modeling curve resolution procedure was proposed to extract the spectral and concentration information of pure compounds. Primary and secondary metabolites of secretory cavities, veins, and mesophylls of Ginkgo biloba leaf blades were analyzed, and the distributions of cuticle, protein, calcium oxalate, cellulose, and ginkgolic acids on the adaxial surface were determined. By the integration of multiple infrared microspectroscopic imaging and chemometrics methods, it is possible to analyze nonmicrotomed leaves and other plant samples directly to understand their native chemical morphologies in detail.

Novel μ-membrane module for online determination of the free fatty acid content in the dispersed phase of oil-in-water emulsions

Monitoring the dispersed phase of an oil-in-water (O–W) emulsion by means of Fourier transform infrared (FTIR) spectroscopy is a challenging task, restricted to the continuous phase that is in contact with the FTIR probe. Nonetheless, real-time measurement and kinetic analysis by FTIR, including analysis of the dispersed, often non-polar phase containing substrates and/or products, is desirable. Enzymatic hydrolysis of sunflower oil was performed in an O–W emulsion. After separation of the oil phase by use of a newly developed μ-membrane module, infrared spectra were collected using an attenuated total reflectance (ATR) cell. Different chemometric models were calibrated using the partial least squares (PLS) algorithm. Online application of a chemometric model based on the FTIR spectra enabled real-time monitoring of free fatty acid concentrations in the oil phase.

Chemometric tool for identification of iron–gall inks by use of visible–near infrared fibre optic reflection spectroscopy

A method has been developed for identification of corrosive iron–gall inks in historical drawings and documents. The method is based on target-factor analysis of visible–near infrared fibre optic reflection spectra (VIS–NIR FORS). A set of reference spectra was obtained from model samples of laboratory-prepared inks covering a wide range of mixing ratios of basic ink components deposited on substrates and artificially aged. As criteria for correspondence of a studied spectrum with a reference spectrum, the apparent error in target (AET) and the empirical function SPOIL according to Malinowski were used. The capability of the proposed tool to distinguish corrosive iron–gall inks from bistre and sepia inks was evaluated by use of a set of control samples of bistre, sepia, and iron–gall inks. Examples are presented of analysis of historical drawings from the 15th and 16th centuries and written documents from the 19th century. The results of analysis based on the tool were confirmed by XRF analysis and colorimetric spot analysis.

Raman microspectroscopic chemical mapping and chemometric classification for the identification of gunshot residue on adhesive tape

A novel approach utilizing automated Raman microspectroscopic mapping for gunshot residue (GSR) detection was investigated. A well-established technique for GSR recovery (tape lifting) was utilized for GSR particle collection. Uncontaminated samples of the substrate (tape), organic GSR (OGSR), and inorganic GSR (IGSR) particles were characterized to generate three respective Raman spectroscopic training sets. Automated Raman mapping was used to rapidly collect spectra over areas of the tape substrate populated with GSR particles. Raman spectra collected from the maps were classified against the training sets via partial least squares discriminant analysis (PLS-DA) to determine if GSR was present. We report the application of Raman chemical mapping as a proof of concept for the positive detection of GSR particles of varying morphologies. The estimated size of GSR particles, which could be readily detected by this method, is about 3.4 μm. The efficiency of the classification was quantitated with rates of true positives and negatives. Validation studies scrutinizing the practicality of this approach as a viable tool for potential forensics investigations are currently in progress.

Charge Site Mass Spectra: Conformation-Sensitive Components of the Electron Capture Dissociation Spectrum of a Protein

A conventional electron capture dissociation (ECD) spectrum of a protein is uniquely characteristic of the first dimension of its linear structure. This sequence information is indicated by summing the primary c ^m+ and z ^m+? products of cleavage at each of its molecular ion’s inter-residue bonds. For example, the ECD spectra of ubiquitin (M?+?nH)ⁿ⁺ ions, n?=?7–13, provide sequence characterization of 72 of its 75 cleavage sites from 1843 ions in seven c ^(1–7)+ and eight z ^(1–8)+? spectra and their respective complements. Now we find that each of these c/z spectra is itself composed of “charge site (CS)” spectra, the c ^m+ or z ^m+? products of electron capture at a specific protonated basic residue. This charge site has been H-bonded to multiple other residues, producing multiple precursor ion forms; ECD at these residues yields the multiple products of that CS spectrum. Closely similar CS spectra are often formed from a range of charge states of ubiquitin and KIX ions; this indicates a common secondary conformation, but not the conventional α-helicity postulated previously. CS spectra should provide new capabilities for comparing regional conformations of gaseous protein ions and delineating ECD fragmentation pathways.

Identification and characterization of individual airborne volcanic ash particles by Raman microspectroscopy

We present for the first time the Raman microspectroscopic identification and characterization of individual airborne volcanic ash (VA) particles. The particles were collected in April/May 2010 during research aircraft flights, which were performed by Deutsches Zentrum für Luft- und Raumfahrt in the airspace near the Eyjafjallajökull volcano eruption and over Europe (between Iceland and Southern Germany). In addition, aerosol particles were sampled by an Electrical Low Pressure Impactor in Munich, Germany. As references for the Raman analysis, we used the spectra of VA collected at the ground near the place of eruption, of mineral basaltic rock, and of different minerals from a database. We found significant differences in the spectra of VA and other aerosol particles (e.g., soot, nitrates, sulfates, and clay minerals), which allowed us to identify VA among other atmospheric particulate matter. Furthermore, while the airborne VA shows a characteristic Raman pattern (with broad band from ca. 200 to ca. 700 cm^?1 typical for SiO₂ glasses and additional bands of ferric minerals), the differences between the spectra of aged and fresh particles were observed, suggesting differences in their chemical composition and/or structure. We also analyzed similarities between Eyjafjallajökull VA particles collected at different sampling sites and compared the particles with a large variety of glassy and crystalline minerals. This was done by applying cluster analysis, in order to get information on the composition and structure of volcanic ash.

Compressive Mass Analysis on Quadrupole Ion Trap Systems

Conventionally, quadrupole ion trap mass spectrometers eject ions of different mass-to-charge ratio (m/z) in a sequential fashion by performing a scan of the rf trapping voltage amplitude. Due to the inherent sparsity of most mass spectra, the detector measures no signal for much of the scan time. By exploiting this sparsity property, we propose a new compressive and multiplexed mass analysis approach—multi Resonant Frequency Excitation (mRFE) ejection. This new approach divides the mass spectrum into several mass subranges and detects all the subrange spectra in parallel for increased mass analysis speed. Mathematical estimation of standard mass spectrum is demonstrated while statistical classification on the parallel measurements remains viable because of the sparse nature of the mass spectra. This method can reduce mass analysis time by a factor of 3–6 and increase system duty cycle by 2×. The combination of reduced analysis time and accurate compound classification is demonstrated in a commercial quadrupole ion trap (QIT) system.

Spectroscopic analysis of bacterial biological warfare simulants and the effects of environmental conditioning on a bacterial spectrum

The ability to distinguish bacteria from mixed samples is of great interest, especially in the medical and defence arenas. This paper reports a step towards the aim of differentiating pathogenic endospores in situ, to aid any required response for hazard management using infrared spectroscopy combined with multivariate analysis. We describe a proof-of-principle study aimed at discriminating biological warfare simulants from common environmental bacteria. We also report an evaluation of multiple pre-processing techniques and subsequent differences in cross-validation of two pattern recognition models (Support Vector Machines and Principal Component–Linear Discriminant Analysis) for a six-class classification (bacterial classification). These classifications were possible with an average sensitivity of 88.0 and 86.9?%, and an average specificity of 97.6 and 97.5?% for the SVM and the PC-LDA models, respectively. Most spectroscopic models are built upon spectra from bacteria that have been specifically prepared for analysis by a particular method; this paper will comment upon the differences in the bacterial spectrum that occur between specific preparations when the bacteria have spent 30?days in the simulated weather conditions of a hot dry climate.

Structural characterization by infrared multiple photon dissociation spectroscopy of protonated gas-phase ions obtained by electrospray ionization of cysteine and dopamine

Structural characterization of protonated gas-phase ions of cysteine and dopamine by infrared multiple photon dissociation (IRMPD) spectroscopy using a free electron laser in combination with theory based on DFT calculations reveals the presence of two types of protonated dimer ions in the electrospray mass spectra of the metabolites. In addition to the proton-bound dimer of each species, the covalently bound dimer of cysteine (bound by a disulfide linkage) has been identified. The dimer ion of m/z 241 observed in the electrospray mass spectra of cysteine has been identified as protonated cystine by comparison of the experimental IRMPD spectrum to the IR absorption spectra predicted by theory and the IRMPD spectrum of a standard. Formation of the protonated covalently bound disulfide-linked dimer ions (i.e. protonated cystine) from electrospray of cysteine solution is consistent with the redox properties of cysteine. Both the IRMPD spectra and theory indicate that in protonated cystine the covalent disulfide bond is retained and the proton is involved in intramolecular hydrogen bonding between the amine groups of the two cysteine amino acid units. For cysteine, the protonated covalently bound dimer (m/z 241) dominated the mass spectrum relative to the proton-bound dimer (m/z 243), but this was not the case for dopamine, where the protonated monomer and the proton-bound dimer were both observed as major ions. An extended conformation of the ethylammonium side chain of gas-phase protonated dopamine monomer was verified from the correlation between the predicted IR absorption spectra and the experimental IRMPD spectrum. Dopamine has the same extended ethylamine side chain conformation in the proton-bound dopamine dimer identified in the mass spectra of electrosprayed dopamine. The structure of the proton-bound dimer of dopamine is confirmed by calculations and the presence of an IR band due to the shared proton. The presence of the shared proton in the protonated cystine ion can be inferred from the IRMPD spectrum.

Reinvestigation of the Structure of Protonated Lysine Dimer

To better understand inconsistencies between the predicted infrared (IR) spectra of previously suggested isomers of Lys₂H⁺ reported by Wu et al. (J. Am. Soc. Mass Spectrom. 22:1651–1659, 18) and the experimental IR photon dissociation (IRPD) spectrum obtained by Oh et al. (J. Am. Chem. Soc. 127:4076–4083, 4), the structure of Lys₂H⁺ was reinvestigated using IRPD spectroscopy in the extended region 2700–3700 cm^?1 and theoretical calculations. The new experimental IRPD spectrum is in good agreement with Oh’s spectrum in the corresponding wavelength range. Based on calculations at the MP2/6-311++G(d,p)//B3LYP/6-311++G(d,p) and MP2/6-31?+?G(d,p)//MP2/6-31?+?G(d,p) levels, a new salt-bridged isomer, ZW1, was found to be the most stable isomer; it is more energetically favored than the previously suggested charge-solvated isomer LL-CS01 by 10 or 26 kJ mol^?1. Although the calculated IR spectrum of ZW1 is in good agreement with the experimental one in the range 2700–3700 cm^?1, it is in poor agreement with the previous IRPD spectrum in the range 1000–1900 cm^?1. This investigation shows that the intermolecular interactions inside the dimer are more complex than previously supposed. It is possible that both salt-bridged and charge-solvated isomers of Lys₂H⁺ are stable in the gas phase, and the isomers generated during ionization are sensitive to the experimental conditions.

Absorption-Mode Fourier Transform Mass Spectrometry: The Effects of Apodization and Phasing on Modified Protein Spectra

The method of phasing broadband Fourier transform ion cyclotron resonance (FT-ICR) spectra allows plotting the spectra in the absorption-mode; this new approach significantly improves the quality of the data at no extra cost. Herein, an internal calibration method for calculating the phase function has been developed and successfully applied to the top-down spectra of modified proteins, where the peak intensities vary by 100×. The result shows that the use of absorption-mode spectra allows more peaks to be discerned within the recorded data, and this can reveal much greater information about the protein and modifications under investigation. In addition, noise and harmonic peaks can be assigned immediately in the absorption-mode.

Rapid screening of active ingredients in drugs by mass spectrometry with low-temperature plasma probe

A high-throughput method for rapid screening of active ingredients in drugs has been developed with mass spectrometry coupled to a low-temperature plasma (LTP) probe ion source. Without sample preparation or pretreatment, the active ingredients of 11 types of commercial pharmaceuticals, including hormones, antipyretic analgesics, cardiovascular, digestant, neuro-psychotherapeutic, diuretic, antithyroid, sulfa anti-inflammatory, antiparastic, sedative-hypnotics, and antibacterial, were directly desorbed/ionized and detected by a linear ion trap mass spectrometry (MS). The structures of these ingredients were elucidated by tandem MS. The analysis of 18 methyltestosterone tablets could be accomplished within 1.9 min, which allows fast detection with a speed of approximate 600 samples within 1 h. This work demonstrated that LTP probe ion source combined with MS is a high-throughput method for screening of pharmaceuticals and potentially applied to on-line quality control in pharmaceutical industry.

Local surface plasmon resonance of single silver nanorice particles in the near-infrared

We report on the synthesis and optical spectra of silver nanorice particles. Two strong absorption bands are resolved in the near UV and near-IR region, and the dark field scattering spectra are consistent with the absorption spectra. Finite-difference time-domain simulations reveal that the peak in the IR region can be attributed to the E field that is parallel to the long axis, while the peak in the UV can be attributed to the E field perpendicular to the short axis of the silver nanorice particles.

Spectroscopic studies on bilirubin aggregate at liquid/liquid interface

Bilirubin (BR) aggregating at liquid/liquid interface was firstly detected by Fourier transform infrared (FTIR) imaging/spectroscopy combining with ultraviolet-visible (UV/Vis) absorption spectra. In the UV/Vis absorption spectra of BR aggregate, a new shoulder appeared at 474 nm, and BR absorption maximum underwent red shift from 450 nm to a longer wavelength at 497 nm, which indicates that BR aggregate was formed at the interface. Meanwhile, the BR molecule structure changed or conformation torsion, that is, the increase in orbit overlap or dihedral angle and the enhancement of exciton coupling. In the study of FTIR imaging/spectroscopy, the hydrogen bond-sensitive infrared bands of BR aggregate showed remarkable changes in band shift and intensity compared with those of BR powder, suggesting that the intramolecular hydrogen bonds broke out and internal structure changed. These new findings will be helpful for understanding of the BR molecular interaction, transportation, complex with serum albumin and metal ions, and the effect of BR aggregating on biomembrane and human tissues.

Glycan Side Reaction May Compromise ETD-Based Glycopeptide Identification

Tris(hydroxymethyl)aminomethane (Tris) is one of the most frequently used buffer ingredients. Among other things, it is recommended and is usually used for lectin-based affinity enrichment of glycopeptides. Here we report that sialic acid, a common ‘capping’ unit in both N- and O-linked glycans may react with this chemical, and this side reaction may compromise glycopeptide identification when ETD spectra are the only MS/MS data used in the database search. We show that the modification may alter N- as well as O-linked glycans, the Tris-derivative is still prone to fragmentation both in ‘beam-type’ CID (HCD) and ETD experiments, at the same time—since the acidic carboxyl group was ‘neutralized’—it will display a different retention time than its unmodified counterpart. We also suggest solutions that—when incorporated into existing search engines—may significantly improve the reliability of glycopeptide assignments.

The effect of optical substrates on micro-FTIR analysis of single mammalian cells

The study of individual cells with infrared (IR) microspectroscopy often requires living cells to be cultured directly onto a suitable substrate. The surface effect of the specific substrates on the cell growth—viability and associated biochemistry—as well as on the IR analysis—spectral interference and optical artifacts—is all too often ignored. Using the IR beamline, MIRIAM (Diamond Light Source, UK), we show the importance of the substrate used for IR absorption spectroscopy by analyzing two different cell lines cultured on a range of seven optical substrates in both transmission and reflection modes. First, cell viability measurements are made to determine the preferable substrates for normal cell growth. Successively, synchrotron radiation IR microspectroscopy is performed on the two cell lines to determine any genuine biochemically induced changes or optical effect in the spectra due to the different substrates. Multivariate analysis of spectral data is applied on each cell line to visualize the spectral changes. The results confirm the advantage of transmission measurements over reflection due to the absence of a strong optical standing wave artifact which amplifies the absorbance spectrum in the high wavenumber regions with respect to low wavenumbers in the mid-IR range. The transmission spectra reveal interference from a more subtle but significant optical artifact related to the reflection losses of the different substrate materials. This means that, for comparative studies of cell biochemistry by IR microspectroscopy, it is crucial that all samples are measured on the same substrate type.

Quantifying silica in filter-deposited mine dusts using infrared spectra and partial least squares regression

The feasibility of measuring airborne crystalline silica (α-quartz) in noncoal mine dusts using a direct-on-filter method of analysis is demonstrated. Respirable α-quartz was quantified by applying a partial least squares (PLS) regression to the infrared transmission spectra of mine-dust samples deposited on porous polymeric filters. This direct-on-filter method deviates from the current regulatory determination of respirable α-quartz by refraining from ashing the sampling filter and redepositing the analyte prior to quantification using either infrared spectrometry for coal mines or x-ray diffraction (XRD) from noncoal mines. Since XRD is not field portable, this study evaluated the efficacy of Fourier transform infrared spectrometry for silica determination in noncoal mine dusts. PLS regressions were performed using select regions of the spectra from nonashed samples with important wavenumbers selected using a novel modification to the Monte Carlo unimportant variable elimination procedure. Wavenumber selection helped to improve PLS prediction, reduce the number of required PLS factors, and identify additional silica bands distinct from those currently used in regulatory enforcement. PLS regression appeared robust against the influence of residual filter and extraneous mineral absorptions while outperforming ordinary least squares calibration. These results support the quantification of respirable silica in noncoal mines using field-portable infrared spectrometers.

Application of a newly developed portable NIR imaging device to monitor the dissolution process of tablets

We have recently developed a novel portable NIR imaging device (D-NIRs), which has a high speed and high wavelength resolution. This NIR imaging approach has been developed by utilizing D-NIRs for studying the dissolution of a model tablet containing 20 % ascorbic acid (AsA) as an active pharmaceutical ingredient and 80 % hydroxypropyl methylcellulose, where the tablet is sealed by a special cell. Diffuse reflectance NIR spectra in the 1,000 to 1,600 nm region were measured during the dissolution of the tablet. A unique band at around 1,361 nm of AsA was identified by the second derivative spectra of tablet and used for AsA distribution NIR imaging. Two-dimensional change of AsA concentration of the tablet due to water penetration is clearly shown by using the band-based image at 1,361 nm in NIR spectra obtained with high speed. Moreover, it is significantly enhanced by using the intensity ratio of two bands at 1,361 and 1,354 nm corresponding to AsA and water absorption, respectively, showing the dissolution process. The imaging results suggest that the amount of AsA in the imaged area decreases with increasing water penetration. The proposed NIR imaging approach using the intensity of a specific band or the ratio of two bands combined with the developed portable NIR imaging instrument, is a potentially useful practical way to evaluate the tablet at every moment during dissolution and to monitor the concentration distribution of each drug component in the tablet.

Structural Investigation of Protonated Azidothymidine and Protonated Dimer

Infrared multiple photon dissociation (IRMPD) spectroscopy experiments and quantum chemical calculations have been used to explore the possible structures of protonated azidothymidine and the corresponding protonated dimer. Many interesting differences between the protonated and neutral forms of azidothymidine were found, particularly associated with keto-enol tautomerization. Comparison of computational vibrational and the experimental IMRPD spectra show good agreement and give confidence that the dominant protonated species has been identified. The protonated dimer of azidothymidine exhibits three intramolecular hydrogen bonds. The IRMPD spectrum of the protonated dimer is consistent with the spectrum of the most stable computational structure. This work brings to light interesting keto-enol tautomerization and exocyclic hydrogen bonding involving azidothymidine and its protonated dimer. The fact that one dominant protonated species is observed in the gas phase, despite both the keto and enol structures being similar in energy, is proposed to be the direct result of the electrospray ionization process in which the dominant protonated dimer structure dissociates in the most energetically favorable way.

A photoinduced electron transfer-based nanoprobe as a marker of acidic organelles in mammalian cells

Photoinduced electron transfer (PET)-based molecular probes have been successfully used for the intracellular imaging of the pH of acidic organelles. In this study, we describe the synthesis and characterization of a novel PET-based pH nanoprobe and its biological application for the signaling of acidic organelles in mammalian cells. A fluorescent ligand sensitive to pH via the PET mechanism that incorporates a thiolated moiety was synthesized and used to stabilize gold nanoparticles (2.4?±?0.6 nm), yielding a PET-based nanoprobe. The PET nanoprobe was unambiguously characterized by transmission electron microscopy, proton nuclear magnetic resonance, Fourier transform infrared, ultraviolet-visible absorption, and steady-state/time-resolved fluorescence spectroscopies which confirmed the functionalization of the gold nanoparticles with the PET-based ligand. Following a classic PET behavior, the fluorescence emission of the PET-based nanoprobe was quenched in alkaline conditions and enhanced in an acidic environment. The PET-based nanoprobe was used for the intracellular imaging of acidic environments within Chinese hamster ovary cells by confocal laser scanning microscopy. The internalization of the nanoparticles by the cells was confirmed by confocal fluorescence images and also by recording the fluorescence emission spectra of the intracellular PET-based nanoprobe from within the cells. Co-localization experiments using a marker of acidic organelles, LysoTracker Red DND-99, and a marker of autophagosomes, GFP-LC3, confirm that the PET-based nanoprobe acts as marker of acidic organelles and autophagosomes within mammalian cells.