Software algorithm for automatic interpretation of mass spectra of glycerolipids

A new software algorithm for automatic interpretation of mass spectra of glycerolipids has been developed. The algorithm utilizes a user-specified list of parameters needed to process the spectra. The compounds in mass spectra are identified according to range of measured m/z values, after which the spectra are automatically corrected by the content of naturally occurring isotopes and ion intensities of identified compounds by response correction factors. Automatic processing of the spectra was shown to be accurate and reliable by testing with numerous spectra of glycerophospholipids obtained by liquid chromatography/electrospray ionization mass spectrometry and by comparing the results with manual interpretation of the spectra. If quantitative analysis using internal standards is performed, all the identified compounds in the sample are quantified automatically. A dilution factor may be defined for each sample and is applied to correct the alterations in sample concentration during sample preparation. Processing of several replicate spectra simultaneously produces mean results with standard deviations. The software may also be used to subtract the results of two analyses and to calculate the mean result of replicate subtractions. The algorithm was shown to save time and labor in repetitive processing of mass spectra of similar type. It may be applied to processing of spectra obtained by various mass spectrometric methods.     

The rapid characterisation of poly(ethylene glycol) oligomers using desorption electrospray ionisation tandem mass spectrometry combined with novel product ion peak assignment software

A rapid method for the characterisation of polyglycol esters and ethers is described which uses accurate mass desorption electrospray ionisation (DESI) quadrupole time-of-flight mass spectrometry (Q-ToFMS). The results are combined with newly developed software which aids the interpretation of product ions produced using collision-induced dissociation (CID) of selected precursor ions. The poly(ethylene glycol) (PEG) samples analysed were PEG dibenzoate, PEG monooleate, PEG butyl ether, PEG bis(2-ethyl hexanoate) and PEG diacrylate. Lithium metal was used for cationisation of the PEG oligomers since it yielded the most useful structural information compared with other group I metals. The full scan mass spectra and product ion mass spectra were all obtained in <5 s. Interpretation of the MS/MS product ion spectra, using the product ion interpretation software which incorporates previously developed fragmentation rules, was carried out in <1 s.     

Characterization of poly[(R)-3-hydroxybutyrate-co-epsilon-caprolactone] copolymers by matrix-assisted laser desorption/ionization time-of-flight and electrospray ionization mass spectrometry

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) of narrowly dispersed molecular weight gel permeation chromatography (GPC) fractions was used to characterize random and microblock poly[(R)-3-hydroxybutyrate-co-epsilon-caprolactone] [P(HB-co-CL)] copolymers obtained via the acid-catalyzed transesterification of the corresponding homopolymers, poly([(R)-3-hydroxybutyrate] (PHB) and poly(epsilon-caprolactone) (PCL). High-quality mass spectra were obtained, which made it possible to establish the nature of the polymer end groups. Besides the carboxylic termination, two other moieties were found: alcoholic and tosyl end groups. MALDI mass spectra of CL-rich samples possessed mostly tosyl end groups, while HB-rich samples possessed mostly alcoholic end groups, showing that the tosyl moiety is linked prevalently to CL terminal units. The higher resolution of electrospray ionization (ESI) mass spectra of lower molecular weight GPC fractions permitted the identification of the different oligomer species hypothesized in the assignment of the corresponding MALDI mass spectra. Partial methanolysis of these copolymers was explored as a method of producing mixed HB-CL oligomers to be utilized as new synthons, possessing a minor number of chiral centers from those obtained from hydrolysis of biotechnologically synthesized poly(hydroxyalkanoates) (PHAs).     

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.     

New tools and resources in metabolomics: 2016–2017

Rapid advances in mass spectrometry (MS) and nuclear magnetic resonance (NMR)‐based platforms for metabolomics have led to an upsurge of data every single year. Newer high‐throughput platforms, hyphenated technologies, miniaturization, and tool kits in data acquisition efforts in metabolomics have led to additional challenges in metabolomics data pre‐processing, analysis, interpretation, and integration. Thanks to the informatics, statistics, and computational community, new resources continue to develop for metabolomics researchers. The purpose of this review is to provide a summary of the metabolomics tools, software, and databases that were developed or improved during 2016–2017, thus, enabling readers, developers, and researchers access to a succinct but thorough list of resources for further improvisation, implementation, and application in due course of time.     

Comparison of ribonucleic acid homopolymer ionization energies and charge injection barriers

Thin films of guanosine and uridine ribonucleic acid (RNA) homopolymers (poly rG, poly rU) were grown in high vacuum in several steps on highly oriented pyrolytic graphite (HOPG) using electrospray deposition. Between deposition steps, the sample surface was characterized with X-ray and ultraviolet photoemission spectroscopy (XPS, UPS). The resulting spectra series allowed the determination of the orbital alignment at the HOPG interface, as well as the ionization energies of the homopolymer thin films. Comparison with earlier results on cytidine and adenosine RNA homopolymers (poly rC, poly rA) indicates significant ionization energy and charge injection barrier differences between purines and pyrimidines.     

A comparison of the static SIMS and G‐SIMS spectra of biodegradable homo‐polyesters

Static SIMS (SSIMS) is a surface analytical technique capable of providing molecular chemical information from solids. A major barrier to the wider take‐up of the technique is the complexity associated with the interpretation of SSIMS spectra. Quality of the interpretation depends on the expertise of analysts and making references to the limited mass spectral libraries. For many materials, there are no SSIMS library spectra. A new library‐independent method, G‐SIMS, is capable of facilitating the interpretation of SSIMS data. G‐SIMS spectra contain parent fragments, which are formed without substantial degradation or rearrangements, and highlight molecular fragments, which are directly related to the surface. In our study, G‐SIMS has been tested on medically relevant biodegradable polyester series, including poly (glycolic acid) (PGA), poly‐l‐(lactic acid) (PLA), poly‐β‐(hydroxybutyrate) (PHB) and poly‐ε‐(caprolactone) (PCL). The polyester series chosen here have closely related structures, which allow us to explore the capabilities of G‐SIMS. The G‐SIMS spectra have facilitated the identification of different polyesters by exhibiting mainly characteristic ions, representative of the polymers' molecular structures. The results also indicated that for the chosen polyester series, the larger the repeating monomer structures, the smaller the maximum number of repeat units were seen in the G‐SIMS spectra. The G‐SIMS spectra for the homologous polyester series have provided an insight into the fragmentation mechanisms as a function of repeating monomer molecular weights and structures. Copyright © 2008 John Wiley & Sons, Ltd.     

Liquid-crystalline polysiloxanes with fluoro-substituted side chains

Sixteen new side chain liquid polysiloxanes, either homopolymers derived from poly(hydrogenmethyl)siloxane or copolymers derived from poly(hydrogenmethyl-dimethylsiloxane), are reported with side chains carrying fluoro-substituents. The known effects of fluoro-substitution in low molar mass liquid crystals are strongly echoed in the polymeric analogues and interesting comparisons are made between homo- and co-polymers carrying the same fluorinated side chains.     

Tandem mass spectrometry of synthetic polymers

The detailed characterization of macromolecules plays an important role for synthetic chemists to define and specify the structure and properties of the successfully synthesized polymers. The search for new characterization techniques for polymers is essential for the continuation of the development of improved synthesis methods. The application of tandem mass spectrometry for the detailed characterization of synthetic polymers using the soft ionization techniques matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS) and electrospray ionization mass spectrometry (ESI‐MS), which became the basic tools in proteomics, has greatly been increased in recent years and is summarized in this perspective. Examples of a variety of homopolymers, such as poly(methyl methacrylate), poly(ethylene glycol), as well as copolymers, e.g. copolyesters, are given. The advanced mass spectrometric techniques described in this review will presumably become one of the basic tools in polymer chemistry in the near future. Copyright © 2009 John Wiley & Sons, Ltd.     

ESIprot: a universal tool for charge state determination and molecular weight calculation of proteins from electrospray ionization mass spectrometry data

Electrospray ionization (ESI) ion trap mass spectrometers with relatively low resolution are frequently used for the analysis of natural products and peptides. Although ESI spectra of multiply charged protein molecules also can be measured on this type of devices, only average spectra are produced for the majority of naturally occurring proteins. Evaluating such ESI protein spectra would provide valuable information about the native state of investigated proteins. However, no suitable and freely available software could be found which allows the charge state determination and molecular weight calculation of single proteins from average ESI‐MS data. Therefore, an algorithm based on standard deviation optimization (scatter minimization) was implemented for the analysis of protein ESI‐MS data. The resulting software ESIprot was tested with ESI‐MS data of six intact reference proteins between 12.4 and 66.7 kDa. In all cases, the correct charge states could be determined. The obtained absolute mass errors were in a range between ?0.2 and 1.2 Da, the relative errors below 30 ppm. The possible mass accuracy allows for valid conclusions about the actual condition of proteins. Moreover, the ESIprot algorithm demonstrates an extraordinary robustness and allows spectral interpretation from as little as two peaks, given sufficient quality of the provided m/z data, without the necessity for peak intensity data. ESIprot is independent from the raw data format and the computer platform, making it a versatile tool for mass spectrometrists. The program code was released under the open‐source GPLv3 license to support future developments of mass spectrometry software. Copyright © 2010 John Wiley & Sons, Ltd.     

Comparison of different search engines using validated MS/MS test datasets

Massive amounts of tandem mass spectra are produced in high-throughput proteomics studies. The manual interpretation of these spectra is not feasible. Instead, search engines are used to match the tandem mass spectra with sequence information contained in proteomics and genomics databases. Typically, these search engines provide a list of the best matching peptide sequences for an individual tandem mass spectrum. As well, they provide scores that are somewhat related to the confidence level in the match. Many peptide tandem mass spectra search engines have been reported. These search engines provide very different results depending on the type of mass spectrometers used and their input parameters. Here we describe a comparative analysis of different search engines using validated test sets of tandem mass spectra. We have defined test sets of MS/MS spectra derived from high throughput proteomics experiments performed by HPLC-ESI-MS/MS on ion trap (LCQ) and tandem quadrupole time-of-flight instruments with a pulsar functionality (Qstar Pulsar) mass spectrometers. We analyzed the ability of the different search engines to identify the correct peptides, and the cross-validations of the different search engines.     

Screening for anabolic steroids and related compounds in illegal cocktails by liquid chromatography/time-of-flight mass spectrometry and liquid chromatography/quadrupole time-of-flight tandem mass spectrometry with accurate mass measurement.

Findings of illegal hormone preparations such as syringes, bottles, cocktails, and so on, are an important information source for the nature of the current abuse of anabolic steroids and related compounds as growth-promoting agents in cattle. A new screening method for steroids in cocktails is presented based on liquid chromatography (LC) with diode-array UV-absorbance detection and electrospray ionization time-of-flight mass spectrometry (ESI-TOFMS). Accurate mass measurements were performed at a mass resolution of 4000 using continuous introduction of a lock mass through a second (electro)sprayer. Similar experiments were carried out using dual-sprayer quadrupole time-of-flight mass spectrometry (ESI-QTOFMS/MS) at a mass resolution of 10 000 with data-dependent MS/MS acquisition; i.e. beyond an intensity threshold for the [M + H](+) ions, MS/MS spectra were automatically acquired at three different collision energies. Elemental compositions were calculated for precursor and product ions and it is shown that the combined information from LC retention behavior, UV spectra, elemental compositions, and accurate mass MS/MS spectra yield a fast impression of the steroids present in the complex mixture. Using a new software tool for structure elucidation of MS/MS spectra, an additional non-steroidal additive was identified as well.     

Collision-induced dissociation pathways of anabolic steroids by electrospray ionization tandem mass spectrometry

Anabolic steroids are structurally similar compounds, and their product-ion spectra obtained by tandem mass spectrometry under electrospray ionization conditions are quite difficult to interpret because of poly-ring structures and lack of a charge-retaining center in their chemical structures. In the present study, the fragmentation of nine anabolic steroids of interest to the racing industry was investigated by using triple quadrupole mass spectrometer, Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer, and a linear ion trap instrument. With the aid of an expert system software (Mass Frontier version 3.0), accurate mass measurements, and multiple stage tandem mass spectrometric (MS(n)) experiments, fragmentation pathways were elucidated for boldenone, methandrostenolone, tetrahydrogestrinone (THG), trenbolone, normethandrolone and mibolerone. Small differences in the chemical structures of the steroids, such as an additional double-bond or a methyl group, result in significantly different fragmentation pathways. The fragmentation pathways proposed in this paper allow interpretation of major product ions of other anabolic steroids reported by other researchers in a recent publication. The proposed fragmentation pathways are helpful for characterization of new steroids. The approach used in this study for elucidation of the fragmentation pathways is helpful in interpretation of complicated product-ion spectra of other compounds, drugs and their metabolites.     

A new technique (COMSPARI) to facilitate the identification of minor compounds in complex mixtures by GC/MS and LC/MS: tools for the visualization of matched datasets

In the rapidly growing field of metabolomics, it is common to analyze complex biological samples by chromatography coupled to mass spectrometry. While several techniques are available for the detection of significant peaks in individual samples, it is still difficult to determine small differences between similar samples. Using conventional software, visual inspections of individual chromatograms or individual mass spectra are often of little use because the differences in the composition of small molecules are too small to be recognizable. Thus, we developed a new approach to visualizing mass spectral datasets using a tool that allows one to easily detect these small differences between mass spectra and chromatograms derived from matched samples. Using these tools on extracts from wild-type and methyltransferase knockout strains of the yeast Saccharomyces cerevisiae, we were able to readily identify those mass spectra in our data sets that were different between the wild-type and the knockout extracts and to identify the molecules involved. The software was also successfully applied to a set of LC/MS data from peptide digests that were performed with identical substrates but different enzymes. We have named this visualization tool COMSPARI (COMparision of SPectrAl Retention Information) and are making the software publicly available via Internet at.     

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry with size-exclusion chromatographic fractionation for structural characterization of synthetic aliphatic copolyesters

We report matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) and off-line coupling of size-exclusion chromatography with MALDI-TOFMS analysis (SEC/MALDI-TOFMS) methods for the detailed characterization of poly[(R,S)-3-hydroxybutyrate-co-L-lactic acid], P[(R,S)-3HB-co-LA], and poly[(R,S)-3-hydroxybutyrate-co-epsilon-caprolactone], P[(R,S)-3HB-co-CL], copolymer samples which are expected to be used in special medical application as scaffolds for cartilage and soft tissue engineering. The novel copolyesters contained randomly distributed (R,S)-3-hydroxybutyrate structural units, were synthesized by transesterification of the corresponding homopolymers, i.e. atactic poly[(R,S)-3-hydroxybutyrate], a-PHB, and poly(L-Lactide) (PLLA) or poly(epsilon-caprolactone) (PCL), respectively. The MS methods used for the characterization of the resulting polydisperse copolyester samples were supported by classical methods (NMR, SEC). The structures of individual copolyester macromolecules, including end-group chemical structures, were established using initially MALDI-TOFMS and then SEC/MALDI-TOFMS. The compositions of the copolyesters were determined by two methods, namely based on 1H NMR and MALDI-TOF spectra. The two sets of values showed good agreement. The sequence distribution was determined using the signal intensities of individual copolyester macromolecules, which appeared in MALDI-TOF mass spectra. Furthermore, sequence analysis gave information about the degree of transesterification. The copolyesters synthesized, with only one exception, were demonstrated to be almost random, which implies that the ester-ester exchange was close to completion.     

Chromatographic characterization of amphiphilic di‐ and tri‐block copolymers of poly(ethylene oxide) and poly(ε‐caprolactone)

Amphiphilic di‐ and tri‐block copolymers based on poly(ethylene oxide) as a hydrophilic segment and poly(ε‐caprolactone) as a hydrophobic part are synthesized by the ring‐opening polymerization of ε‐caprolactone while using poly(ethylene glycol)s and methoxy poly(ethylene glycol)s of varying molar masses as macro‐initiators. The synthesized block copolymers are characterized with respect to their total relative molar mass and its distribution by size exclusion chromatography. Liquid chromatography at critical conditions of both blocks is established for the analysis of individual block lengths and tracking presence of unwanted homopolymers of both types in the block copolymer samples. New critical conditions of polycaprolactone on reversed phase column are reported using organic mobile phase. The established critical conditions of polycaprolactone extended the applicable molar mass range significantly compared to already reported critical conditions of polycaprolactone in aqueous mobile phase. Block copolymers are also analyzed at critical conditions of poly(ethylene glycol). Complete analysis of the di‐ and tri‐block copolymers at corresponding critical conditions provided a fair estimate of molar mass of non‐critical block besides information regarding presence of homopolymers of both types in the samples.     

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.     

Photolysis and emission spectra of substituted polyacrylophenones

Poly-[3′,4′-dimethoxyacrylophenone], poly-4′-phenylacrylophenone, poly-2′-acrylonaphthone and copolymers of acrylophenone monomers with styrene and methyl methacrylate were prepared. Quantum yields of main chain scission in chlorobenzene by 313 nm radiation were 10³ times lower for all homopolymers and copolymers studied than for polyacrylophenone. The emission spectra of the polymers, copolymers and model compounds were taken for films at 77 K. The 3′,4′-dimethoxyacrylophenone, 4′-phenylacrylophenone and 2′-acrylonaphthone structural units exhibited poorly resolved emission spectra in homopolymer, copolymer and model compound. No difference in the emission spectra of films and dispersed homopolymer or copolymer in a poly(methyl methacrylate) matrix was observed. The decay of the emission of all homopolymers and copolymers under study was exponential, the life-time exceeding 0.20 sec.     

Target list building for volatile metabolite profiling of fruit

Fruit flavour is the combination of numerous biochemicals: sugars for sweetness, acids for sourness and volatile metabolites for aroma. The objective of this study was to establish a method to develop a target list of statistically relevant compounds for the characterization of melon from non-targeted data, while preserving the profile information. Five different varieties were sampled (sampling 12 biological replicates from 12 plants) using dynamic headspace extraction, then analysed by gas chromatography–mass spectrometry in full scan mode. Using Metalign and SIMCA-P software the raw data was spectrally aligned and then subjected to principal component analysis (PCA). The principal component analysis plot showed good separation of the five varieties based on their full scan GC–MS profile. Mass spectral data points responsible for the differences between varieties were highlighted by further statistical analysis. The mass spectra were then reconstructed and the corresponding chemicals identified using library search or reference standards were available to create a new target component list. To validate the new target list, the initial data set was re-processed using the targeted approach and the results subjected again to principal component analysis. The two representations showed excellent agreement on the separation of the five varieties. The new target list obtained from this study can be applied to differentiate and characterize the volatile profile of melon varieties using a list of statistically significant compounds.     

Design and development of a new program for data processing of mass spectra acquired by means of a high-resolution double-focusing glow-discharge mass spectrometer

An new program has been developed and implemented for data analysis of mass spectra obtained by use of the VG9000 glow-discharge mass spectrometer. The program, designed to run in a Windows 9X environment includes several tools for import and export of data, cluster generators, etc. An automated technique for the interpretation of mass spectra is also built into the program; this enables faster and operator-independent interpretation. When major interferences or not-well defined signals are involved, the automated technique might fail to find the correct result. Therefore, a manual, VG9000 software-like, bypass is at hand. A comparison of the different techniques and programs shows, in general, comparable results. An installable version of the software is available on the university FTP-server (ftp://PLASMA-FTP.uia.ac.be/ private/imsas/).