Liquid chromatography—mass spectrometry — a new window for environmental analysis

A series of liquid chromatography methods using particle beam mass spectrometry has been developed to determine a broader range of organic pollutants. Results are presented on the determination of aromatic sulfonic acids in aqueous leachates; chlorinated phenoxy acid herbicides in soil and water; and of polyaromatic hydrocarbons from various matrices.     

lipID—a software tool for automated assignment of lipids in mass spectra

A new software tool called lipID is reported, which supports the identification of glycerophospholipids, glycosphingolipids, fatty acids and small oligosaccharides in mass spectra. The user‐extendable software is a Microsoft (MS) Excel Add‐In developed using Visual Basic for Applications and is compatible with all Versions of MS Excel since MS Excel 97. It processes singly given mass‐to‐charge values as well as mass lists considering a number of user‐defined options. The software's mode of operation, usage and options are explained and the benefits and limitations of the tool are illustrated by means of three typical analytical examples of lipid analyses. Copyright © 2009 John Wiley & Sons, Ltd.     

MASSyPup — an ‘Out of the Box’ solution for the analysis of mass spectrometry data

Mass spectrometry has evolved to a key technology in the areas of metabolomics and proteomics. Centralized facilities generate vast amount of data, which frequently need to be processed off‐site. Therefore, the distribution of data and software, as well as the training of personnel in the analysis of mass spectrometry data, becomes increasingly important. Thus, we created a comprehensive collection of mass spectrometry software which can be run directly from different media such as DVD or USB without local installation. MASSyPup is based on a Linux Live distribution and was complemented with programs for conversion, visualization and analysis of mass spectrometry (MS) data. A special emphasis was put on protein analysis and proteomics, encompassing the measurement of complete proteins, the identification of proteins based on Peptide Mass Fingerprints (PMF) or LC‐MS/MS data, and de novo sequencing. Another focus was directed to the study of metabolites and metabolomics, covering the detection, identification and quantification of compounds, as well as subsequent statistical analyses. Additionally, we added software for Mass Spectrometry Imaging (MSI), including hardware support for self‐made MSI devices. MASSyPup represents a ‘ready to work’ system for teaching or MS data analysis, but also represents an ideal platform for the distribution of MS data and the development of related software. The current Live DVD version can be downloaded free of charge from http://www.bioprocess.org/massypup . Copyright © 2014 John Wiley & Sons, Ltd.     

Simple modification of a protein database for mass spectral identification of N-linked glycopeptides

We describe an algorithm which modifies a protein database such that during a database search deamidation is limited to asparagines strictly contained within the N-glycosylation consensus sequence. The modified database was evaluated using a dataset created from the shotgun proteomic analysis of N-linked glycopeptides from human blood serum. We demonstrate that the application of the modified database eliminates incorrect glycopeptide assignments, reduces the peptide false-discovery rate, and eliminates the need for manual validation of glycopeptide identifications.     

Evaluation of the sensitivity of the ‘Wiley registry of tandem mass spectral data,MSforID’ with MS/MS data of the ‘NIST/NIH/EPA mass spectral library’

Tandem mass spectral libraries are versatile tools for small molecular identification finding application in forensic science, doping control, drug monitoring, food and environmental analysis, as well as metabolomics. Two important libraries are the ‘Wiley Registry of Tandem Mass Spectral Data, MSforID’ (Wiley Registry MSMS) and the collection of MS/MS spectra part of the 2011 edition of the ‘NIST/NIH/EPA Mass Spectral Library’ (NIST 11 MSMS). Herein, the sensitivity and robustness of the Wiley Registry MSMS were evaluated using spectra extracted from the NIST 11 MSMS library. The sample set was found to be heterogeneous in terms of mass spectral resolution, type of CID, as well as applied collision energies. Nevertheless, sensitive compound identification with a true positive identification rate ≥95% was possible using either the MSforID Search program or the NIST MS Search program 2.0g for matching. To rate the performance of the Wiley Registry MSMS, cross‐validation experiments were repeated using subcollections of NIST 11 MSMS as reference library and spectra extracted from the Wiley Registry MSMS as positive controls. Unexpectedly, with both search algorithms tested, correct results were obtained in less than 88% of cases. We examined possible causes for the results of the cross validation study. The large number of precursor ions represented by a single tandem mass spectrum only was identified as the basic cause for the comparably lower sensitivity of the NIST library. Copyright © 2013 John Wiley & Sons, Ltd.     

‘Fast atom bombardment’—A rediscovered method for mass spectrometry

In 1966, Devienne and co-workers studied extensively the sputtering of various target materials by a high energy molecular beam obtained by charge exchange. They obtained secondary ions that characterized for instance, organic and biological materials. These ions were analysed by mass spectrometry. This method was developed to be patented and many devices were studied. The principle of the apparatus constructed is very simple. An ion source produces an ion current of some microamperes. The ions are accelerated at some keV, and injected into a collision chamber in order to obtain a neutral beam by resonant charge exchange. The residual ions are deflected and this beam bombards the target. The target itself is surrounded by a small metal cylinder which is held at an appropriate potential to extract the positive or negative secondary ions formed. The ion beam is accelerated and focused into the entrance slit of a mass spectrometer. After the first devices, two types of apparatus were built in 1973 and 1975. With the first one, the analysis of the masses was obtained only by an electromagnet. The energy range of the secondary ions varied from 1 to 10 keV. The second apparatus was formed by an electromagnet, a dissociation chamber, and an electrostatic analyser. With this apparatus, it was possible to measure directly masses as large as 6000 daltons. With the first apparatus it was possible to study the adsorption of oxygen on silicon, and to obtain spectra, of many organics such as camphor, nitrodiphenylamine and, as in the earlier device, the spectrum of a non-volatile organic liquid diethylhexyl azelate, was obtained. After studies on different uranium compounds and their dissociations, the second apparatus was devoted to the formation and study of the chemical properties of clusters.     

Metastable ion studies. 4—mass spectral fragmentation and isomerization in the esters of chlorinated propenoic acids

Metastable peaks have been used to study the fragmentation pathways of the methyl and trideuteriomethyl chloropropenoates and chloromethyl propenoate. The molecular ion peaks of the unsaturated esters are more intense than those of the saturated esters, α-Cleavage, [M? OCH₃]⁺, produces the base peak in almost all compounds, the relative abundances of the additional peaks being low for chloromethyl propenoate. The losses of H₂O, CH₃^. and COOH^. indicate the isomerization of some ionized chloro esters to the chlorinated 2-butenoic acid molecular ions. An intense loss of H₂O observed for methyl 2-chloropropenoate indicates its most facile isomerization, [ester]^+˙ → [acid]^+˙, whereas the isomerization in methyl trichloropropenoate could not be observed. The molecular ion of chloromethyl propenoate, however, also seems to partly rearrange to the chlorinated 3-butenoic acid ion, since the first field free region metastable peak shows a weak loss of CO. The new reaction pathways, i.e. the losses of CHO^˙, CH₂O and CH₂CO from ionized chloromethyl propenoate, were detected.     

Rapid identification of microorganisms by mass spectrometry: improved performance by incorporation of in-house spectral data into a commercial database

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is increasingly used as a microbial diagnostic method for species identification of pathogens. However, MALDI-TOF identification of bacteria at the species level remains unsatisfactory, with the major problem being an incomplete database that still needs refinement and expansion. Augmentation of the original MALDI BioTyper 2.0 (Bruker) database by incorporating mass spectra obtained in-house from clinical isolates may increase the identification rate at the species level. We conducted a prospective study to assess whether the augmented database can improve the performance of MALDI-TOF MS for routine identification of species. Cluster analyses revealed distinct differences in MS spectral profiles of clinical isolates obtained in our hospital and those of ATCC strains in the Bruker database. In the first part of the study, which was performed over 3 weeks, 259 bacterial isolates were subjected to analysis by MALDI-TOF MS, and MS spectra of 229 successfully identified isolates (49 species) were incorporated into the original database to give the augmented Bruker-Chiba database. In a second separate analysis, the concordance of identification of 498 clinical isolates of the 49 species with conventional methods was 87.1% (434/498) with the commercial Bruker database and 98.0% (488/498) using the Bruker-Chiba database. These results indicate that refinement of a commercial database can be achieved relatively easy and effectively by incorporating MS spectra of clinical isolates obtained in a clinical laboratory.     

MassBank: a public repository for sharing mass spectral data for life sciences

MassBank is the first public repository of mass spectra of small chemical compounds for life sciences (<3000 Da). The database contains 605 electron‐ionization mass spectrometry(EI‐MS), 137 fast atom bombardment MS and 9276 electrospray ionization (ESI)‐MSⁿ data of 2337 authentic compounds of metabolites, 11 545 EI‐MS and 834 other‐MS data of 10 286 volatile natural and synthetic compounds, and 3045 ESI‐MS² data of 679 synthetic drugs contributed by 16 research groups (January 2010). ESI‐MS² data were analyzed under nonstandardized, independent experimental conditions. MassBank is a distributed database. Each research group provides data from its own MassBank data servers distributed on the Internet. MassBank users can access either all of the MassBank data or a subset of the data by specifying one or more experimental conditions. In a spectral search to retrieve mass spectra similar to a query mass spectrum, the similarity score is calculated by a weighted cosine correlation in which weighting exponents on peak intensity and the mass‐to‐charge ratio are optimized to the ESI‐MS² data. MassBank also provides a merged spectrum for each compound prepared by merging the analyzed ESI‐MS² data on an identical compound under different collision‐induced dissociation conditions. Data merging has significantly improved the precision of the identification of a chemical compound by 21–23% at a similarity score of 0.6. Thus, MassBank is useful for the identification of chemical compounds and the publication of experimental data. Copyright © 2010 John Wiley & Sons, Ltd.     

Computer processing and interpretation of mass spectral information. VIII—ariadna system

The structure of a laboratory system for processing and interpreting mass spectral data intended to solve a wide range of analytical problems (determination of the composition and structure of molecules, isotopic analysis, etc) and research problems (study of the structure and reactivity of ions in the gas phase) is described and its functional possibilities are discussed. The basic software of the system includes both methods for calculation of elemental compositions of ions with the use of masses and amplitudes of isotopic peaks and methods for establishing spectralstructural correlations based on information theory and molecular graph theory.     

An evaluation for cross-species proteomics research by publicly available expressed sequence tag database search using tandem mass spectral data

With 1383 tandem mass spectra derived from 120 individual protein spots separated by the two-dimensional (2-D) gel electrophoresis of protein samples from three different species, comparative analyses were performed by searching the Expressed Sequence Tag (EST) database (DB) and the NCBI non-redundant (nr) DB of green plants, respectively, which uses the Mascot search engine to establish a statistical basis. It was confirmed that the former could identify more peptides manually validated by de novo sequencing (DNS) from fewer species in more closely phylogenetic relationships than the latter in a statistically significant manner. Our data demonstrated that correct peptide identifications were given low Mascot scores (e.g. 6-14) and incorrect peptide identifications were given high Mascot scores (e.g. 68-83). Our data also showed that the current evaluation approaches to protein assignments are unsatisfactory because a few 'false-positive' proteins are recognized and several 'false-negative' proteins are rescued by manual validation.     

Multivariate analysis of time-resolved mass spectral data

Multvariate analysis of time-resolved pyrolysis/mass spectrometric data is described. The approach is based on the variance diagram (VARDIA), a recently developed technique that quantifies the clustering of variables in two-dimensional factor analysis (sub)-spaces in a rotational scanning procedure. A maximum in the VARDIA plot indicates a correlated behavior of the mass variables, indicating a common origin. This common origin is generally caused by a change in the concentration of a chemical component. With this information the “factor spectrum” and the scores of the component can be retrieved. For time-resolved serial data, consideration of the clustering behavior of the variables as a function of time is more appropriate than a rotational scanning procedure. Adaptation of the VARDIA for serial data, such as time-resolved data, is described. This approach has the advantage that all the factors can be used. It will be shown that the resolution of the obtained curve than the total ion current curve as a function of time. Examples will be given for time-resolved data of coal, rubber and wood samples.     

Computer processing and interpretation of mass spectral information. Part IX—generalized characteristics of mass spectra

The formation of numerical generalized characteristics (indices) of mass spectra by using one or two experimental parameters (mass numbers and/or ion peak amplitudes) is suggested. The influence of the measuring error of peak amplitudes on the statistical characteristics of indices was studied. It was ascertained by four classes of organometallic compounds that within an isolated class the value of each index is distributed by a normal law. The possibility of using mass spectral indices for the identification of unknown compounds is demonstrated.     

Doubly charged ion mass spectra 8—alkenes

Doubly charged ion mass spectra of 23 alkenes have been measured using a double focusing Hitachi RMU-7L mass spectrometer. Ion mass spectra were obtained using 100 eV electron energy and 3.2 kV ion accelerating voltage. Each 2E spectrum was determined using the olefinic compound under investigation as the target gas. In general, spectra are dominated by fragment ions which result from extensive hydrogen loss from the doubly charged molecular ion. Appearnce energies have been measured for intense fragment ions in each spectrum.     

Computer-based system for correlating molecular structures with mass spectral data

Algorithms are described for correlating a proposed molecular structure with a mass spectrum. All molecular substructures of a proposed structure are determined which have the same masses as the fragment ions. The most likely fragment ion structures are those molecular substructures formed with the fewest number of bond cleavages in the proposed structure. The algorithms, which incorporate methods for handling rearrangement and adduct ions, utilize either nominal or exact data originating from any ionization method. The algorithms are demonstrated using the mass spectra of a substituted azetidinyl ketone and the macrolide antibiotic avermectin A_1a.     

Electron ionisation mass spectral studies of bridgehead‐fused Δ2‐norbornanethiazolines

The electron ionisation (EI) mass spectra of a series of bridgehead‐fused Δ²‐norbornanethiazolines, a new class of bridgehead‐norbornane derivatives, have been studied and their cleavage mechanisms rationalised on the basis of the substituent shifts as well as on the identification of relevant peaks through accurate mass measurements and collision‐induced dissociation tandem mass spectrometric experiments. The fragmentation patterns of isomeric pairs of 6,6‐ and 10,10‐dimethylnorbornanethiazolines are almost identical, probably due to an initial isomerisation of molecular ion previous to the fragmentation. In general, the dominant peaks in the spectra of all the studied compounds originate from initial α‐cleavages of C(5)–C(6) or C(1)–C(10) bonds, followed by concomitant homolytic cleavage of C(1)–C(9) and C(7)–C(10) bonds. The driving force for this fragmentation pathway, directed by the gem‐dimethyl group, is the formation of a highly stabilised thiazolilmethyl cation which constitutes the base peak in all the spectra and allows the identification of these interesting ligands. Copyright © 2009 John Wiley & Sons, Ltd.     

Evaluation of synthetic liquid chromatography—diode array detection—mass spectrometry data for the determination of enzyme kinetics

In this paper, we investigate the accuracy and precision of the results from diode array detector (DAD) data and mass spectrometry (MS) data as obtained subsequent to chromatographic separations using computer simulations. Special attention was given to simulations of multiple injections from a developing enzymatic reaction. These simulations result in three-way LC–DAD–MS kinetic data; LC–DAD and LC–MS data were also evaluated independently in this investigation. The noise characteristics of the MS detector prevent accurate determination of the individual reaction rate constants by the analysis method. Using the data from the DAD in combination with the MS detector results in improved estimation of the rate constants. The results also indicate that the higher resolving power of the MS information compensates for the lower signal-to-noise ratio in these data, compared to DAD data.