Automated charge state determination of complex isotope-resolved mass spectra by peak-target Fourier transform

This study describes a new algorithm for charge state determination of complex isotope-resolved mass spectra. This algorithm is based on peak-target Fourier transform (PTFT) of isotope packets. It is modified from the widely used Fourier transform method because Fourier transform may give ambiguous charge state assignment for low signal-to-noise ratio (S/N) or overlapping isotopic clusters. The PTFT algorithm applies a novel "folding" strategy to enhance peaks that are symmetrically spaced about the targeted peak before applying the FT. The "folding" strategy multiplies each point to the high-m/z side of the targeted peak by its counterpart on the low-m/z side. A Fourier transform of this "folded" spectrum is thus simplified, emphasizing the charge state of the "chosen" ion, whereas ions of other charge states contribute less to the transformed data. An intensity-dependent technique is also proposed for charge state determination from frequency signals. The performance of PTFT is demonstrated using experimental electrospray ionization Fourier transform ion cyclotron resonance mass spectra. The results show that PTFT is robust for charge state determination of low S/N and overlapping isotopic clusters, and also useful for manual verification of potential hidden isotopic clusters that may be missed by the current analysis algorithms, i.e., AID-MS or THRASH.     

Computer-aided interpretation of mass spectra

A system is described in which computer techniques are used to carry out major steps in the procedure for interpretation of high-resolution mass spectral data. These steps include identification and evaluation of the molecular ion, neutral fragments lost from the molecular ion, and characteristic ion series, followed by elucidation of specific structural details using a sub-routine for the particular compound class selected. The technique shows promise of not only increasing the interpreter's efficiency, but of providing more specific and detailed structural information from the spectral data.     

Probability based matching of mass spectra. Rapid identification of specific compounds in mixtures

An automated system is described for computer examination of the mass spectrum of an unknown mixture for the presence of a specific compound. The probability that the compound is present is indicated as a ‘confidence index’ K; 2^K should signify the average number of compounds, selected at random, whose mass spectra would have to be examined to find data which match the target spectrum to the same degree as does the unknown. The value of K is determined by the uniqueness U of the m/e value, the abundance A, and the criterion of abundance agreement W of the matching peaks, and of the compound concentration D in the sample. Application to spectra from a variety of compounds, including illicit drugs, indicates that the system has high sensitivity and selectivity, and that the value of K is a useful index of the reliability of the identification. Initial testing of this system has utilized an automated quadrupole mass spectrometer under control of a dedicated microcomputer with sample introduction through a flash evaporator and membrane separator.     

Automated structural assignment of derivatized complex N-linked oligosaccharides from tandem mass spectra

Glycoprotein function is controlled by several biological factors, one of them being the structure of carbohydrate chains (glycans) attached to specific amino acids of the protein backbone. Changes in glycan structures have been shown to modify the secondary and tertiary conformation of glycoproteins, thus their function. Powerful analytical tools are available for the characterization of sugar structures, and recently mass spectrometry (MS) has been increasingly useful for this purpose. Manual interpretation of tandem mass spectrum is possible but tedious. Automated interpretation should speed the analysis and enhance the results obtained. A new computer program for automated interpretation of tandem MS spectra of complex N-linked glycans oligosaccharides from mammals will be described. N-Linked oligosaccharides standards were derivatized with 1-phenyl-3-methyl-5-pyrazolone (PMP) and analyzed by matrix-assisted laser desorption/ionization (MALDI)-tandem MS. Simulated tandem mass spectra of other common glycans were also generated to test the algorithm. The MALDI-MS/MS spectra featured resolved isotopic distributions for the [M + H](+) and fragment ions of oligosaccharides. These isotopic distributions complicated the automated analysis of the spectra and were removed to leave only monoisotopic peaks. An algorithm was written for this purpose, yielding simplified tandem mass spectra. Another algorithm is then used to determine the structure of the oligosaccharide. A score is then given to each structure, depending on agreement with experimental results. The program successfully assigned the true structure in 24 out of the 28 cases (86%) and the true structure was among the three top scoring structures in all cases.     

Automated interpretation of low-energy collision-induced dissociation spectra by SeqMS, a software aid for de novo sequencing by tandem mass spectrometry

SeqMS, a software aid for de novo sequencing by tandem mass spectrometry (MS/MS), which was initially developed for the automated interpretation of high-energy collision-induced dissociation (CID) MS/MS spectra of peptides, has been applied to the interpretation of low-energy CID and post-source decay (PSD) spectra of peptides. Based on peptide backbone fragmented ions and their related ions, which are the dominant ions observed in the latter two techniques, the types of ions and their propensities to be observed have been optimized for efficient interpretation of the spectra. In a typical example, the modified SeqMS allowed the complete sequencing of a 31-amino acid synthetic peptide, except for the isobaric amino acids (Leu or Ile, and Lys or Gln), based on only the low-energy CID-MS/MS spectrum.     

Processing and interpretation of core-electron XPS spectra of complex plasma-treated polyethylene-based surfaces using a theoretical peak model

Interpretation of X-ray photoelectron spectroscopy (XPS) spectra of complex material surfaces, such as those obtained after surface plasma treatment of polymers, is confined by the available references. The limited understanding of the chemical surface composition may impact the ability to determine suitable coupling chemistries used for surface decoration or assess surface-related properties like biocompatibility. In this work, XPS is used to investigate the chemical composition of various ultra-high-molecular-weight polyethylene (UHMWPE) surfaces. UHMWPE doped with α-tocopherol or functionalised by active screen plasma nitriding (ASPN) was investigated as a model system. Subsequently, a more complex combined system obtained by ASPN treatment of α-tocopherol doped UHMWPE was investigated. Through ab initio orbital calculations and by employing Koopmans' theorem, the core-electron binding energies (CEBEs) were evaluated for a substantial number of possible chemical functionalities positioned on PE-based model structures. The calculated ΔCEBEs showed to be in reasonable agreement with experimental reference data. The calculated ΔCEBEs were used to develop a material-specific peak model suitable for the interpretation of merged high-resolution C 1 s, N 1 s and O 1 s XPS spectra of PE-based materials. In contrast to conventional peak fitting, the presented approach allowed the distinction of functionality positioning (i.e. centred or end-chain) and evaluation of the long-range effects of the chemical functionalities on the PE carbon backbone. Altogether, a more detailed interpretation of the modified UHMWPE surfaces was achieved whilst reducing the need for manual input and personal bias introduced by the spectral analyst.     

The computer-assisted interpretation of copolymer mass spectra

A computer program called MSCOPOL has been developed to aid in the interpretation of copolymer mass spectra. The program reads the mass spectrum, calculates the most likely monomer masses via correlation or Fourier transform methods, determines possible end group masses based on the monomer masses, and can then search monomer and end group data bases for likely chemical moieties. Refinement of the end group result is possible by calculation of the monomer ratio and degree of polymerization as a function of end group mass. The program is written in Microsoft Visual Basic and runs on an IBM compatible PC. Applications are shown for polystyrene, poly(N-vinyl pyrrolidone/vinyl acetate), and poly(ethylene oxide/propylene oxide).     

Chemical interpretation of differences in pyrolysis—mass spectra of simulated mixtures of biopolymers by factor analysis with graphical rotation

A method is described for the separation of a set of pyrolysis-mass spectra of simulated mixtures into subspectra for each of the components and for calculation of their relative concentrations. The technique is based on factor analysis and graphical rotation and is evaluated on a data set, constructed by linear combination of pyrolysis-mass spectra of three biopolymers.     

Automated deconvolution and deisotoping of electrospray mass spectra

Electrospray ionization (ESI) of peptides and proteins produces a series of multiply charged ions with a mass/charge (m/z) ratio between 500 and 2000. The resulting mass spectra are crowded by these multiple charge values for each molecular mass and an isotopic cluster for each nominal m/z value. Here, we report a new algorithm simultaneously to deconvolute and deisotope ESI mass spectra from complex peptide samples based on their mass-dependent isotopic mean pattern. All signals corresponding to one peptide in the sample were reduced to one singly charged monoisotopic peak, thereby significantly reducing the number of signals, increasing the signal intensity and improving the signal-to-noise ratio. The mass list produced could be used directly for database searching. The developed algorithm also simplified interpretation of fragment ion spectra of multiply charged parent ions.     

Automated evaluation of photographically recorded spark-source mass spectra

A computer routine was developed for qualitative and quantitative analysis of photographically recorded spark-source mass spectra. Particular attention is given to the case of a graphite matrix. The program starts from the line intensities (expressed as Seidel values) and isotope masses calculated from the densitometer readings by a commercially available routine. From the intensities in the different exposures (typically 15 stages), it computes the parameters for the linear parts of the density curves for each ion. Taking into account mutual interferences of multivalent ions, isotope or C-clusters, oxide, carbide and dicarbide ions, the program automatically identifies and then quantifies the elements present. The precision of the results is around 5%. Reading and complete processing of one photoplate is achieved within 2–3 h.     

Dynamic,computer-assisted interpretation of infrared spectra of condensed-phase mixtures

A knowledge-based system, MIXIR, designed to assist researchers in interpreting the infrared spectra of condensed-phase mixtures is described. This system overcomes many of the inherent limitations of static-rule-based systems. An iterative problem-solving approach is permitted, making use of information gained during the interpretation process. The dynamic rule selection and significance evaluation alos allow the user to provide information on the sample matrix, or to select a subset of the compounds for rule derivation. The MIXIR system was evaluated with a knowledge base compiled using IRBASE, a complementary program, and a test set of 20 mixtures.     

Quantitative mass spectrometry by internal standardisation using a single focusing mass spectrometer and the peak switching facilities of a peak matching device

A quantitative mass spectrometric method for the determination of small sample sizes is described. This method is applicable to both single and double focusing mass spectrometers, if a conventional peak matching device or any other suitable peak switching facility is attached to the instrument. In the conventional integrated ion current technique a constant pressure of the vapour of hepta-cosafluoro-tri-n-butylamine or a comparable standard is maintained in the analyser. By contrast to this in our method the calibrating substance is evaporated together with the sample from the same capillary of the probe. Substances with a similar chemical structure (in most cases higher or lower homologues) can be used as internal standards. Since thermal effects in the probe and sensitivity changes of the mass spectrometer during the flash evaporation of the substances affect the integrated ion current curves of both sample and standard equally, the ratio of the curves is largely independent of these parameters. With a single focusing mass spectrometer (CH-5 Varian, MAT) reproducibilities of the determinations were within ±10%, with substance amounts in the range between 10^?10 to 10^?11 mole.     

Use of decomposition of ion charge-state distributions for the interpretation of electrospray ionization mass spectra of bioorganic compound

The application of our method of the decomposition of mass spectral peak series due to independent unique modifications at a number of molecular sites to the analysis of electrospray ionization mass spectra containing multiply charged ions peaks of biopolymer solutions is considered. The capabilities and limitations of this approach are discussed. Data on the results mass spectrum decomposition of the chicken eggs lysozyme and pepsin at different acquisition conditions are presented. Based on these data, at least partial unfolding of the initially native lisozyme biomolecule in solution in the electrospray ion source can be supposed. The presence of pepsin positive ions with the number of charges significantly exceeding five basic amino acid residues can be explained by the localization of two positive solvent ions close to some initially negatively charged groups of acidic amino acid residues in the ion source.     

Enhanced spectrum matching of mixed mass spectra by means of quality factors

A system of computer programs for recognizing impure or mixed spectra was assembled that provided automatic subtraction of reference mass spectra from a mixed spectrum. The software was 99% successful in recognizing pure spectra for the cases tested. Subtractions were done on mixed spectra in 70% of the cases tested. Spectrum subtraction enhanced the ability of the matching program to match components of a multicomponent mixture correctly, whereas quality factors were a great aid in the evaluation of the overall match validity.     

Expert system for interpretation of the infrared spectra of environmental mixtures

A program for the identification of the principal components of mixtures through interpretation of the infrared mixture spectrum (IntIRpret) was developed. This program, which was developed as a preliminary screening tool for unknown organic mixtures, has five main subroutines: the interferogram processing and peak-selection subroutine (PUSHSUB), the automated knowledge-acquisition subroutine (AUTOGEN), the system optimization subroutine (STO), the interpretation subroutine (PAIRS), and final processing subroutine to subtract spectral similarity (PAIRSPLUS). Principal advantages of this system compared to earlier systems are speed, flexibility and accuracy.     

Intensity of molecular ion peak in electron ionization mass spectra

Compounds from NIST??08 and Wiley 8th databases were considered as a representative subset of the general population of organic compounds which can be analyzed using mass spectrometry with electron ionization. The percentage of organic compounds as a function of intensity of molecular ion (M^+?) peak normalized to the base peak was determined for the first time. It was shown that only 26% compounds have high-intensity M^+? peaks (greater than 50% of base peak). Intensity of M^+? peak is less than or equal to 1 or 5% of base peak for 24 or 37% compounds respectively. It means that in case of trace-level analysis M^+? peak may not be registered for quarter (or even more) of organic compounds. It is well-known that the absence of M^+? peaks in electron ionization mass spectra reduces reliability of unknown compound identification based on library search. Therefore determination of molecular mass by independent technique (e.g., mass spectrometry with chemical ionization) is necessary for increasing the identification reliability.     

Algorithms for automatic interpretation of high resolution mass spectra

Automated interpretation of high-resolution mass spectra in a reliable and efficient manner represents a highly challenging computational problem. This work aims at developing methods for reducing a high-resolution mass spectrum into its monoisotopic peak list, and automatically assigning observed masses to known fragment ion masses if the protein sequence is available. The methods are compiled into a suite of data reduction algorithms which is called MasSPIKE (Mass Spectrum Interpretation and Kernel Extraction). MasSPIKE includes modules for modeling noise across the spectrum, isotopic cluster identification, charge state determination, separation of overlapping isotopic distributions, picking isotopic peaks, aligning experimental and theoretical isotopic distributions for estimating a monoisotopic peak's location, generating the monoisotopic mass list, and assigning the observed monoisotopic masses to possible protein fragments. The method is tested against a complex top-down spectrum of bovine carbonic anhydrase. Results of each of the individual modules are compared with previously published work.     

A new matching algorithm for high resolution mass spectra

We present a new matching algorithm designed to compare high-resolution spectra. Whereas existing methods are bound to compare fixed intervals of ion masses, the accurate mass spectrum (AMS) distance method presented here is independent of any alignment. Based on the Jeffreys-Matusitas (JM) distance, a difference between observed peaks across pairs of spectra can be calculated, and used to find a unique correspondence between the peaks. The method takes into account that there may be differences in resolution of the spectra. The algorithm is used for indexing in a database containing 80 accurate mass spectra from an analysis of extracts of 80 isolates representing the nine closely related species in the Penicillium series Viridicata. Using this algorithm we can obtain a retrieval performance of approximately 97-98% that is comparable with the best of the existing methods (e.g., the dot-product distance). Furthermore, the presented method is independent of any variable alignment procedures or binning.     

Determination of hydroxyaromatic compounds in complex mixtures by tandem mass spectrometry

Derivatization of alkylated hydroxyaromatics with N-methyl-bis(trifluoracetamide) is used for a rapid screening for alkylated hydroxyaromatic compounds in complex mixtures by tandem mass spectrometry. Applications are based on a detailed investigation of the fragmentation reactions of derivatized alkylated phenols, 2,3-dihydroindenols, indenols, 1,2,3,4-terrahydronaphtbols and naphthols. As shown by daughter-ion mass spectra obtained in different field-free regions of a BEQQ-instrument, the loss of CF₃COOH, CF₃CO˙ or CF₃COO^˙, respectively, is common for the compounds studied and can be used for their detection by means of neutral mass loss scans.