Desorption electrospray ionisation mass spectrometry and tandem mass spectrometry of low molecular weight synthetic polymers

A range of low molecular weight synthetic polymers has been characterised by means of desorption electrospray ionisation (DESI) combined with both mass spectrometry (MS) and tandem mass spectrometry (MS/MS). Accurate mass experiments were used to aid the structural determination of some of the oligomeric materials. The polymers analysed were poly(ethylene glycol) (PEG), polypropylene glycol (PPG), poly(methyl methacrylate) (PMMA) and poly(alpha-methyl styrene). An application of the technique for characterisation of a polymer used as part of an active ingredient in a pharmaceutical tablet is described. The mass spectra and tandem mass spectra of all of the polymers were obtained in seconds, indicating the sensitivity of the technique.     

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.     

Analysis of different synthetic homopolymers by the use of a new calculation software for tandem mass spectra

The manual interpretation of tandem mass spectra of synthetic polymers is very time-consuming. Therefore, a new software tool was developed to accelerate the interpretation of spectra obtained without requiring any further knowledge about the polymer class or the fragmentation behavior under high-energy collision-induced dissociation (CID) conditions. The software only requires an alphabetical list of elements and a peak list of the measured substance as an xml file for the evaluation of the chosen mass spectrum. Tandem mass spectra of different homopolymers, like poly(2-oxazoline)s, poly(ethylene glycol) and poly(styrene), were interpreted by the new software tool. This contribution describes a fast and automated software tool for the rapid analysis of homopolymers.     

Simultaneous quantitative analysis of isobars by tandem mass spectrometry from unresolved chromatographic peaks

A method was developed for the simultaneous quantitation of isobars from unresolved chromatographic peaks. The method is based on differences in branching ratios of ion abundances in their tandem mass spectra and an assumption that the product ion mass spectra of a mixture can be considered as a linear combination of the spectra of individual constituents. We present analytical equations and a matrix-based approach for deconvoluting the concentration of individual components from the total peak intensity for two and three isobars and also a matrix-based generalization to any number of compounds. The feasibility of the simultaneous analysis of mixtures containing two compounds was assessed. The approach was evaluated for the analysis of structural isomers of methylmalonic and succinic acids in human plasma and urine samples for a group of 270 samples. The linear regression equation, standard error and correlation coefficient for the agreement with a traditional method utilizing chromatographic separation of the isomers were y = 0.999x - 0.005, 0.024 micro mol l(-1), and 0.985, respectively. The utility of a spectral contrast angle as a predictor of analysis feasibility was evaluated.     

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.     

Early synthetic dyes – a challenge for tandem mass spectrometry

The present study concerns identification of early yellow synthetic dyes from silk fibers taken from the 1930 spring color palette of the Lyon Dyers’ Guild (La Chambre Syndicale des Teinturiers). The identification was based mainly on the electrospray ionization tandem mass spectrometry spectra obtained in the positive and negative ion modes. This technique was combined with high‐performance liquid chromatography, which enabled separation of the analyzed compounds. Spectra registered for each of the examined synthetic dye allowed identification of their lost fragments. Moreover, isotopic profiles and exact measurements of m/z by using time of flight analyzer made possible to evaluate their elemental composition. In consequence, all obtained data, including UV–vis spectra, allowed to reconstruct molecular structures of examined colorants. Due to the lack of standards, the identification of the dyes was based only on the registration of fragment and quasi‐molecular ions, what is rather uncommon in such analysis and means groping for the correct structure rather than proving signal identity by comparison with standards. Depending on substituents present in dye molecules, the lost fragments of the examined compounds involved SO₂, NO^?, NO₂^?, CH₄, C₂H₄, C₂H₅^?, C₂H₆, CH₂ = N–CH₃, (CH₃)₂NH, CH₂ = NH, CH₃–NH₂, as well as CO and CO₂. The performed study led to identification of various colorants: rhodamine 6 G, rhodamine B, malachite green, quinoline yellow, picric acid and acetoquinone yellow 5JZ. Copyright © 2013 John Wiley & Sons, Ltd.     

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.     

Application of the StrOligo algorithm for the automated structure assignment of complex N-linked glycans from glycoproteins using tandem mass spectrometry

Oligosaccharides associated with proteins are known to give these molecules specific conformations and functions. Analysis of proteins would not be complete without studying the glycans. However, high-throughput techniques in proteomics will soon overwhelm the current capacity of methods if no automation is incorporated into glycomics. New capabilities of the StrOligo algorithm introduced for this purpose (Ethier et al., Rapid Commun. Mass Spectrom., 2002; 16: 1743) will be discussed here. Experimental tandem mass spectra were acquired to test the algorithm using a hybrid quadrupole-time-of-flight (QqTOF) instrument with a matrix-assisted laser desorption/ionization (MALDI) source. The samples were N-linked oligosaccharides from monoclonal antibody IgG, beta interferon and fetuin, detached by enzymatic deglycosylation and labeled at the reducing end. Improvements to the program were made in order to reduce the need for user intervention. StrOligo strips the spectra down to monoisotopic peaks only. The algorithm first builds a relationship tree, accounting for each observed loss of a monosaccharide moiety, and then analyzes the tree and proposes possible structures from combinations of adducts and fragment ion types. A score, which reflects agreement with experimental results, is then given to each proposed structure. The program then decides which combination is the best one and labels relevant peaks in the experimental mass spectrum using a modified nomenclature. The usefulness of the algorithm has been demonstrated by assigning structures to several glycans released from glycoproteins. The analysis was completed in less than 2 minutes for any glycan, which is a substantial improvement over manual interpretation.     

Hybrid mass spectrometers for tandem mass spectrometry

Mass spectrometers that use different types of analyzers for the first and second stages of mass analysis in tandem mass spectrometry (MS/MS) experiments are often referred to as "hybrid" mass spectrometers. The general goal in the design of a hybrid instrument is to combine different performance characteristics offered by various types of analyzers into one mass spectrometer. These performance characteristics may include mass resolving power, the ion kinetic energy for collision-induced dissociation, and speed of analysis. This paper provides a review of the development of hybrid instruments over the last 30 years for analytical applications.     

Improved mass accuracy for tandem mass spectrometry

With the emergence of top-down proteomics, the ability to achieve high mass measurement accuracy on tandem MS/MS data will be beneficial for protein identification and characterization. (FT-ICR) Fourier transform ion cyclotron resonance mass spectrometers are the ideal instruments to perform these experiments with their ability to provide high resolution and mass accuracy. A major limitation to mass measurement accuracy in FT-ICR instruments arises from the occurrence of space charge effects. These space charge effects shift the cyclotron frequency of the ions, which compromises the mass measurement accuracy. While several methods have been developed that correct these space charge effects, they have limitations when applied to MS/MS experiments. It has already been shown that additional information inherent in electrospray spectra can be used for improved mass measurement accuracy with the use of a computer algorithm called DeCAL (deconvolution of Coulombic affected linearity). This paper highlights a new application of the strategy for improved mass accuracy in tandem mass analysis. The results show a significant improvement in mass measurement accuracy on complex electron capture dissociation spectra of proteins. We also demonstrate how the improvement in mass accuracy can increase the confidence in protein identification from the fragment masses of proteins acquired in MS/MS experiments.     

PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry

A number of different approaches have been described to identify proteins from tandem mass spectrometry (MS/MS) data. The most common approaches rely on the available databases to match experimental MS/MS data. These methods suffer from several drawbacks and cannot be used for the identification of proteins from unknown genomes. In this communication, we describe a new de novo sequencing software package, PEAKS, to extract amino acid sequence information without the use of databases. PEAKS uses a new model and a new algorithm to efficiently compute the best peptide sequences whose fragment ions can best interpret the peaks in the MS/MS spectrum. The output of the software gives amino acid sequences with confidence scores for the entire sequences, as well as an additional novel positional scoring scheme for portions of the sequences. The performance of PEAKS is compared with Lutefisk, a well-known de novo sequencing software, using quadrupole-time-of-flight (Q-TOF) data obtained for several tryptic peptides from standard proteins.     

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.     

Structural studies on alkylisocyanate polymers by thermal degradation tandem mass spectrometry

Homopolymers and copolymers of alkylisocyanates having n-hexyl, 2,6-dimethylheptyl, 3,7-dimethyloctyl, and (2,2-dimethyl-1,3-dioxolan-4-yl)methyl substituents underwent thermal degradation in the course of desorption electron ionization to yield trimers and monomers that were characterized in situ by tandem mass spectrometry. The trimers were trisubstituted cyanuric acids, the protonated molecules displaying a characteristic series of alkene eliminations on collision-induced dissociation to yield protonated cyanuric acid, m/ z 130. Confirmation of the identity of the pyrolysates was obtained by using two types of MS3 experiments: the reaction intermediate scan and the two-dimensional familial scan. The ion chemistry of the trimers and of the protonated monomer, the alkylisocyanate, was elucidated. Among the many interesting fragmentation processes undergone by the ionized trimers were a and 3 C-C bond cleavages and charge-remote fragmentations, which provided information on branching in the alkyl substituent. The dioxolane-containing substituent showed unique ion chemistry. The monomer distribution in the copolymers was deduced from the abundances of the various protonated trimers. The distribution was found to be random in all copolymers except that containing the dioxolane substituent.     

Reproducible product-ion tandem mass spectra on various liquid chromatography/mass spectrometry instruments for the development of spectral libraries

The results of the comparison of product-ion tandem mass (MS/MS) spectra recorded on three ion trap mass spectrometers, a triple quadrupole mass spectrometer and a Fourier transform ion cyclotron resonance mass spectrometer are reported. The spectra were recorded in accordance with a simple experimental protocol, which involved the collision-induced dissociation (CID) attenuation of the abundance of the [M+H]+ ion to between 10 and 50% of its original abundance.The degree of similarity between the spectra from four of the mass spectrometers was calculated off-line by comparing the five most abundant ions from the spectrum on each instrument. A percentage fit value (20% for each ion that matches) was calculated by comparing each spectrum against the spectra recorded for the same compound on each instrument. The percentage of the inter-library pairwise comparisons (total = 434) that matched to > or = 60% ranged from 64-89%, depending on the instrument pair. A blind trial was also undertaken using five unknown compounds resulting in 1670 pairwise comparisons with the library entries. The blind trial produced no false positives and correct identifications in all cases. The results of the study have established the basis for the construction of a transferable product-ion MS/MS library.