Automatic analysis of mixed spectra : Generalised spectral subtraction applied to electron spin resonance spectroscopy

A new technique is described for estimating the pure component spectra from a set of linearly independent spectra. The process is one of generalised spectral subtraction in which an iterative combination of multivariate linear least-squares analysis and matrix transformation is applied to the input data to give estimates of the number of independent components in the original mixed spectra. This technique is applicable to bipolar data (e.g. from e.p.r. spectra) as well as absorption spectra determined by any spectroscopic technique, provided that the spectra may be reasonably assumed to be an additive mixture of unknown pure components. Numerical model examples are given together with an experimental application to electron spin resonance.     

A full multiple scattering model for the analysis of time-resolved X-ray difference absorption spectra

A full multiple theoretical model (MXAN) is applied to fit picosecond difference X-ray absorption spectra at the ruthenium L(3) edge upon photoexcitation of aqueous [RuII(bpy)3]2+. We show that fitting difference spectra allows an increase in sensitivity, such that slight structural changes can be retrieved, which are not detected in fitting full spectra. The Ru-N bond distances of the excited complex in the (3)MLCT state are in good agreement with recently published values. The implementation of the present approach to L-edge spectra and its high sensitivity opens opportunities for its extension to a large class of experiments where difference X-ray absorption spectra are recorded.     

Attenuated total reflection Fourier transform infrared spectroscopy of redox transitions in photosynthetic reaction centers: comparison of perfusion- and light-induced difference spectra

Chemically induced Fourier transform infrared difference spectra associated with redox transitions of several primary electron donors and acceptors in photosynthetic reaction centers (RCs) have been compared with the light-induced FTIR difference spectra involving the same cofactors. The RCs are deposited on an attenuated total reflection (ATR) prism and form a film that is enclosed in a flow cell. Redox transitions in the film of RCs can be repetitively induced either by perfusion of buffers poised at different redox potentials or by illumination. The perfusion-induced ATR-FTIR difference spectra for the oxidation of the primary electron donor P in the RCs of the purple bacteria Rb. sphaeroides and Rp. viridis and P700 in the photosystem 1 of Synechocystis 6803, as well as the Q(A)/Q(A) transition of the quinone acceptor (Q(A)) in Rb. sphaeroides RCs are reported for the first time. They are compared with the light-induced ATR-FTIR difference spectra P+Q(A)/PQ(A) for the RCs of Rb. sphaeroides and P700+/P700 for photosystem 1. It is shown that the perfusion-induced and light-induced ATR-FTIR difference spectra recorded on the same RC film display identical signal to noise ratios when they are measured under comparable conditions. The ATR-FTIR difference spectra are very similar to the equivalent FTIR difference spectra previously recorded upon photochemical or electrochemical excitation of these RCs in the more conventional transmission mode. The ATR-FTIR technique requires a smaller amount of sample compared with transmission FTIR and allows precise control of the aqueous environment of the RC films.     

Quantitative Auger electron spectroscopic analysis of carbides,nitrides and carbonitrides

A novel method for the quantitative evaluation of Auger electron spectra based on peak areas is presented. Sample and reference spectra in integral mode are filtered by an area conserving digital filter. This transforms the peak shapes influenced by chemical effects into standard peak shapes. After filtering a linear combination of reference spectra, differentiated spectra accounting for peak shifts and some low order polynomials to account for variations in the background is fitted to the sample spectrum by a least squares method. The need to approximate the spectrum of the secondary electron background explicitly for direct calculation of peak areas is thus eliminated. Filters of different widths are applied to reduce errors by chemical effects. The composition of the sample is computed from the composition of the reference samples and the coefficients obtained from the fit.To demonstrate the validity of this technique it has been applied to both, Gaussian model peaks and spectra of titanium carbonitrides. A further test on an alloy series is under investigation. The results show that the method works as predicted and gives accurate quantification.     

Multistep correlations via covariance processing of COSY/GCOSY spectra: opportunities and artifacts

Long-range homonuclear coupling pathways can be observed in COSY or GCOSY spectra by the acquisition of spectra with larger numbers of increments of the evolution period, t(1), than would normally be used. Alternatively, covariance processing of COSY-type spectra acquired with modest numbers of t(1) increments, allows the observation of multistage correlations. In this work results obtained from covariance-processed GCOSY spectra are fully analyzed and compared to normally processed COSY and 80 ms TOCSY spectra. Multistage or 'RCOSY-type' correlations are observed when remote protons both exhibit correlations to the same coupling partner e.g. A --> B and B --> C gives rise to an A --> C correlation. In the strict sense, RCOSY-type responses are artifacts albeit providing useful information. Nonbeneficial artifact correlations are observed when protons couple to other protons that overlap or partially overlap. The origin of artifact responses is also analyzed.     

A new fast and fault-tolerant identification algorithm for spectral databases

A new method for an automatic, computer and database driven identification of UV/VIS spectra is described. It is shown that an identification algorithm must consider the spectral differences as well as their common features. The described identification method allows identifications, even if the spectra are distorted or shifted.     

Continuous wavelet transform applied to removing the fluctuating background in near-infrared spectra

A novel method based on continuous wavelet transform (CWT) was proposed as a preprocessing tool for the near-infrared (NIR) spectra. Due to the property of the vanishing moments of the wavelet, the fluctuating background of the NIR spectra can be successfully removed through convolution of the spectra with an appropriate wavelet function. The vanishing moments of a wavelet and the scale parameter are two key factors that govern the result of the background elimination. The result of its application to both the simulated spectra and the NIR spectra of tobacco samples demonstrates that CWT is a competitive tool for removing fluctuating background in spectra.     

Classification of single-molecule surface-enhanced resonance Raman spectra of Rhodamine 6G from isolated Ag colloidal particles by principal component analysis

Surface enhanced resonance Raman (SERR) spectra of Rhodamine 6G are measured from single isolated Ag particles and analyzed by using a chemometrics technique, principal component analysis (PCA). The Ag particles are incubated with various amounts of R6G yielding the ratio of Ag particles to R6G molecules from 1:1 to 1:1000. Acquired SERR spectra are considered due to a single or very few R6G molecules. PCA is used to determine the number of chemically distinguishable species that contribute to the measured SERR spectra. A simple clustering tool, score bi-plot, is then inspected on grouping of the SERR spectra. The spectra are found to be largely similar except for the variability in the intensity and position of the bands that is believed to be correlated with the lifetime of the strong enhancement at specific places on an Ag surface. The spectra from four different Ag particles carrying more than 1000 R6G molecules are, however, unambiguously separated. Different aspects of the applied data analysis method and physicochemical perspective of the results are discussed.     

Gas phase spectra of all-benzenoid polycyclic aromatic hydrocarbons: triphenylene

The jet-cooled laser-induced fluorescence and dispersed fluorescence spectra of the S1(A1')<--S0(A1') transition of triphenylene are reported. The spectra exhibit false origins of e' symmetry which are modeled by performing calculations of Herzberg-Teller coupling using time-dependent density functional theory. It is found that this level of theory reproduces the main features of the observed spectra. The oscillator strength of the strongest band is calculated to be f=7x10(-4). From a combination of theory and the observed upper state lifetime of 41 ns, an estimate of the fluorescence yield is made of PhiF=0.084, in agreement with previous studies in the condensed phase.     

Parallels between multiple population-period transient spectroscopy and multidimensional coherence spectroscopies

We have recently shown that homogeneous and heterogeneous kinetics can be distinguished by experiments that compare the evolution of the population of a state over two time intervals [E. van Veldhoven et al., ChemPhysChem 8, 1761 (2007)]. This paper elaborates on the analogy between these multiple population-period transient spectroscopy (MUPPETS) experiments and more familiar spectroscopies based on the evolution of coherences. Using a modified inverse-Laplace transform, a standard kinetics decay is re-expressed as a "rate spectrum." A nonexponential decay creates a linewidth in this spectrum. Mechanisms for line broadening in rate spectra are compared to those for line broadening in frequency-domain spectra. Homogeneous and heterogeneous kinetics are defined precisely and are shown to be the counterparts of homogeneous and inhomogeneous line broadenings in frequency-domain spectra. Homogeneous line broadening mechanisms are further divided into equilibrium and nonequilibrium mechanisms, with equilibrium mechanisms more prevalent in frequency spectra and nonequilibrium mechanisms more prevalent in rate spectra. Spectral representations of two-dimensional MUPPETS experiments are developed that are equivalent to two-dimensional coherence spectroscopies. In particular, spectra equivalent to hole-burning and to correlation spectra are defined. Frequency-domain spectra are often modeled as an inhomogeneous distribution of identical homogeneous line shapes. A parallel homogeneous-heterogeneous model for kinetics is defined. Within this model, MUPPETS has sufficient information to completely separate the homogeneous and heterogeneous contributions to a nonexponential decay, even when the homogeneous contribution is nonexponential.     

A quantitative measure of the reliability of searches of spectral libraries

A quantitative measure of library search reliability has been developed. Applications of the quantitative reliability metric (QRM) for evaluating the reliability of library searches for unknown target spectra and the use of this measure to detect the failure of a library search caused by noise, contaminant peaks and missing library spectra are discussed. The effects of noise and composite infrared spectra of mixtures on the QRM are examined for test sets of 561 infrared spectra. The QRM is also used to evaluate the performance of a search of an infrared library compressed by eigenvector projection.     

Thermal denaturation of polyalanine peptide in water by molecular dynamics simulations and theoretical prediction of infrared spectra: helix-coil transition kinetics

Perspectives in the helix-coil transition kinetics of secondary structures are examined by temperature-jump molecular dynamics (T-jump MD) simulations and theoretically calculated infrared (IR) spectra. Homopolymeric polyalanine, Ac-(A)(21)-NHMe (A21), is unfolded in water by T-jumps from 273 to 300 K approximately 450 K using AMBER ff99 and ff03 force fields. MD simulation results provide in silico evidence that 3(10)-helix and type I beta-turn motifs are highly probable in both ff99 and ff03 results. Temperature-dependent difference IR spectra of A21 do not possess an isosbestic point in both results, and isotope-labeled difference IR spectra in ff03 results predict characteristic profiles observed in experiments. Unfolding rates obtained from simulated time-resoled IR spectra are in good agreement with those estimated by helical contents, but they are still an order of magnitude smaller than experimental values. We demonstrate that the conventional criteria such as single-exponential fit of transient amide I absorbance, sigmoidal fit of temperature-dependent amide I absorbance, and Arrhenius plot of relaxation rates cannot guarantee the validity of assuming a two-state mechanism. We suggest a way of determining T(m) by the temperature dependence of center frequency and full width at half-maximum of amide I band. Overall, both ff99 and ff03 force fields give consistent results in reproducing key aspects concerned experimentally, but are not predominantly satisfactory in quantitative aspects.     

Monitoring the melt-extrusion transesterification of ethylene-vinylacetate copolymer by self-modeling curve resolution analysis of on-line near-infrared spectra

The transesterification of molten ethylene-vinylacetate (EVA) copolymers by octanol with sodium methoxide as catalyst in an extruder has been monitored by on-line near infrared (NIR) spectroscopy. A total of 60 NIR spectra were acquired for 37 min with the last spectrum recorded 31 min after the addition of octanol and catalyst was stopped. The experimental spectra show strong baseline fluctuations which are corrected for by multiplicative scatter correction (MSC). The chemometric methods of the orthogonal projection approach (OPA) and multivariate curve resolution (MCR) were used to resolve the spectra and to derive concentration profiles of the species. The detailed analysis reveals the absence of completely pure variables which leads to small errors in the calculation of pure spectra. The initial estimation of a concentration that is necessary as an input parameter for MCR also presents a non-trivial task. We obtained results that were not ideal but applicable for practical concentration control. They enable a fast monitoring of the process in real-time and resolve the spectra of the EVA copolymer and the ethylene-vinyl alcohol (EVAL) copolymer to be very close to the reference spectra. The chemometric methods used and the decomposed spectra are discussed in detail.     

Peptide conformation in gas phase probed by collision-induced dissociation and its correlation to conformation in condensed phases

A kinetic peptide fragmentation model for quantitative prediction of peptide CID spectra in an ion trap mass spectrometer has been reported recently. When applying the model to predict the CID spectra of large peptides, it was often found that the predicted spectra differed significantly from their experimental spectra, presumably due to noncovalent interactions in these large polypeptides, which are not considered in the fragmentation model. As a result, site-specific quantitative information correlated to the secondary/tertiary structure of an ionized peptide may be extracted from its CID spectrum. To extract this information, the kinetic peptide fragmentation model was modified by incorporating conformation-related parameters. These parameters are optimized for best fit between the predicted and the experimental spectrum. A conformational stability map is then generated from these conformation-related parameters. Analysis of a few bioactive alpha-helical peptides including melittin, glucagon and neuropeptide Y by this technique demonstrated that their stability maps in the gas phase correlate strongly to their secondary structures in the condensed phases.     

Some aspects of the scope and limitations of derivative spectroscopy

Synthesised spectra are used to illustrate discussion of some relationships between recorded absorption profiles and their second and fourth derivative spectra. Limitations arising from the fortuitous overlap of a derivative peak with a neighbouring wing, and the possibilities of resolving spectra into their overlapping bands are also considered. The combined use of second and fourth derivative spectra to ascertain the correct number of bands within an observed profile is described. It is suggested that the practice of computing a least-squares fit of overlapping bands to a spectral profile be changed, because the minimisation achieved often produces a result involving excessive or negative absorbances: the spectral profile should be regarded as a boundary limit and any unaccounted (positive) absorbance then assessed as possible evidence for an additional band. An example is given, concerning the resolution of the spectrum of a thin, single crystal of uranium(IV) oxide at 77 K superimposed on an absorption edge. A comparison of the difference between the observed spectrum and the sum of its resolution into twelve overlapping bands, plus a similar comparison of their fourth derivative spectra, reveals a thirteenth band.     

On the extraction of spectra of components from spectra of mixtures. A development in factor theory—I

The theory of factor analysis is extended to permit the computer based extraction of the spectra of pure components from spectra of mixtures. A simultaneous linear, non-orthogonal transformation of the eigenspectra and eigenvectors is used to generate all positive absorbances and concentrations within noise level. Applications to actual spectra of mixtures of: (A) ethyl ethanoate, butan-2-one and oct-1-ene; (B) ethyl ethanoate, butan-2-one and cyclohexane; and (C) butan-2-one, cyclohexane and 2-methylpentane are presented. The effects of changes in signs of the constrained diagonal elements of the transformation matrix is investigated. To explore the ability of the software to cope with component spectra in which there are no wavenumbers at which one component dominates an artificial set of mixtures is examined. Recognizable spectra are extracted. It appears that, even when there are no wavenumbers at which one component dominates, the condition of finding “the sum of squares of negative absorbances/concentrations” near zero is adequate to yield useful spectra for library searches.     

Probing the non-analytic properties of exciton band structures by reflection spectroscopy

A method of probing the exciton band structure about the centre of the Brillouin zone is developed. Oblique angle reflectance spectra at angles of incidence up to 80° for a (001) face of an anthracene crystal have been obtained for both an air-crystal and a silica-crystal interface. A method for transforming the reflectance data to optical constants is developed and used. From this method the direction of propagation of radiation k? at any frequency inside the crystal for any incident angle can be determined. For a model of an isotropic crystal consisting of anisotropic molecules, dipole-dipole theory for an arbitrary k? is developed, exciton band structures from this theory are calculated and theoretical spectra based on these calculated band structures are presented. The theoretical spectra are in very good agreement with the experimental data. Information about the exciton density of states is deduced from the results.     

MS2Grouper: Group assessment and synthetic replacement of duplicate proteomic tandem mass spectra

Shotgun proteomics experiments require the collection of thousands of tandem mass spectra; these sets of data will continue to grow as new instruments become available that can scan at even higher rates. Such data contain substantial amounts of redundancy with spectra from a particular peptide being acquired many times during a single LC-MS/MS experiment. In this article, we present MS2Grouper, an algorithm that detects spectral duplication, assesses groups of related spectra, and replaces these groups with synthetic representative spectra. Errors in detecting spectral similarity are corrected using a paraclique criterion-spectra are only assessed as groups if they are part of a clique of at least three completely interrelated spectra or are subsequently added to such cliques by being similar to all but one of the clique members. A greedy algorithm constructs a representative spectrum for each group by iteratively removing the tallest peaks from the spectral collection and matching to peaks in the other spectra. This strategy is shown to be effective in reducing spectral counts by up to 20% in LC-MS/MS datasets from protein standard mixtures and proteomes, reducing database search times without a concomitant reduction in identified peptides.     

Automatic recalibration and processing of tandem mass spectra using formula annotation

High accuracy, high resolution tandem mass spectrometry (MS/MS) is becoming more common in analytical applications, yet databases of these spectra remain limited. Databases require good quality spectra with sufficient compound information, but processing, calibration, noise reduction and retrieval of compound information are time‐consuming tasks that prevent many contributions. We present a comprehensive workflow for the automatic processing of MS/MS using formula annotation for recalibration and cleanup to generate high quality spectra of standard compounds for upload to MassBank ( www.massbank.jp ). Compound information is retrieved via Internet services. Reference standards of 70 pesticides were measured at various collision energies on an LTQ‐Orbitrap XL to develop and evaluate the workflow. A total of 944 resulting spectra are now available on MassBank. Evidence of nitrogen adduct formation during MS/MS fragmentation processes was found, highlighting the benefits high accuracy MS/MS offers for spectral interpretation. A database of recalibrated, cleaned‐up spectra resulted in the most correct spectra ranked in first place, regardless of whether the search spectra were recalibrated or not, whereas the average rank of the correct molecular formula was improved from 2.55 (uncalibrated) to 1.53 when using recalibrated MS/MS data. The workflow is available as an R package RMassBank capable of generating MassBank records from raw MS and MS/MS data and can be adjusted to process data acquired with different settings and instruments. This workflow is a vital step towards addressing the need for more high quality, high accuracy MS/MS spectra in spectral databases and provides important information for spectral interpretation. Copyright © 2012 John Wiley & Sons, Ltd.     

Calculating the vibrational spectra of molecules: An introduction for experimentalists with contemporary examples

The theoretical evaluation of vibrational spectra has, in the past, played a crucial role regarding assignment of vibrational spectra, an aspect that might be largely forgotten. This, however, is actually ever so true today, where despite the presence of data bases of spectra (atlas of spectra) there is still a large number of species including, though certainly not exclusively, less stable species which have spectra lacking appropriate interpretation. In recent years the capabilities to calculate vibrational spectra have greatly improved. In this review the basic various approaches are introduced. For practical use, the use of comparatively simple tools including Hartree–Fock level or standard DFT type calculations often already do a very good job at the comparative level. An important recent development includes the observation that differences between experimental and calculated frequencies are largely due to neglect of anharmonicity rather than the theoretical method employed. Methods to include anharmonicity are becoming available for users. The introduction of methods allowing for periodic calculations, involving full 3D molecular structures, lead to new opportunities and final answers to long-standing issues. A number of examples are provided showing where calculated spectra have provided unique added value to experimental work.