ToF-SIMS Analysis of Adsorbed Proteins: Principal Component Analysis of the Primary Ion Species Effect on the Protein Fragmentation Patterns

In time-of-flight secondary ion mass spectrometry (ToF-SIMS), the choice of primary ion used for analysis can influence the resulting mass spectrum. This is because different primary ion types can produce different fragmentation pathways. In this study, analysis of single-component protein monolayers were performed using monatomic, tri-atomic, and polyatomic primary ion sources. Eight primary ions (Cs(+), Au(+), Au(3) (+), Bi(+), Bi(3) (+), Bi(3) (++), C(60) (+)) were used to examine to the low mass (m/z < 200) fragmentation patterns from five different proteins (bovine serum albumin, bovine serum fibrinogen, bovine immunoglobulin G and chicken egg white lysozyme) adsorbed onto mica surfaces. Principal component analysis (PCA) processing of the ToF-SIMS data showed that variation in peak intensity caused by the primary ions was greater than differences in protein composition. The spectra generated by Cs(+), Au(+) and Bi(+) primary ions were similar, but the spectra generated by monatomic, tri-atomic and polyatomic primary ion ions varied significantly. C(60) primary ions increased fragmentation of the adsorbed proteins in the m/z < 200 region, resulting in more intense low m/z peaks. Thus, comparison of data obtained by one primary ion species with that obtained by another primary ion species should be done with caution. However, for the spectra generated using a given primary ion beam, discrimination between the spectra of different proteins followed similar trends. Therefore, a PCA model of proteins created with a given ion source should only be applied to datasets obtained using the same ion source. The type of information obtained from PCA depended on the peak set used. When only amino acid peaks were used, PCA was able to identify the relationship between proteins by their amino acid composition. When all peaks from m/z 12-200 were used, PCA separated proteins based on a ratio of C(4)H(8)N(+) to K(+) peak intensities. This ratio correlated with the thickness of the protein films and Bi(1) (+) primary ions produced the most surface sensitive spectra.     

The analysis of biomedical poly(ortho esters) by near-IR Fourier transform Raman spectroscopy

In this paper near-IR Fourier transform Raman spectroscopy (FT-RS) has been applied to a series of homopolymer and copolymer biodegradable poly(ortho ester) systems, with the aim of establishing what further information it can furnish over and above conventional polymer characterization methods. The data suggest that the technique is able to provide reasonable information on diol content, furnishing semiquantitative data as a function of methylene number within the homopolymer and copolymer content in diethanolamines The complementary nature of FT-IR spectroscopy is briefly highlighted as a benchmark to which the FT-RS data can be compared.     

High-throughput approaches towards the definitive identification of pharmaceutical drug metabolites. 1. Evidence for an ortho effect on the fragmentation of 4-benzenesulfinyl-3-methylphenylamine using electrospray ionisation mass spectrometry

A 50 m/z unit loss from protonated 4-benzenesulfinyl-3-methylphenylamine has been observed and investigated using electrospray ionisation quadrupole ion trap mass spectrometry (ESI-QIT-MS). It was hypothesised that the specific fragmentation was affected by the presence of an ortho methyl group in relation to the sulfoxide functionality, i.e. an ortho effect influences the preferred dissociation pathway. This was because the des-methyl homologue did not display a 50 m/z unit loss. This fragmentation was shown to be a two-step process with sequential losses of a hydroxyl radical and a thiol radical. Molecular modelling calculations showed that the most favourable site of protonation for 4-benzenesulfinyl-3-methylphenylamine was the sulfoxide oxygen, which would facilitate the loss of a hydroxyl radical. Subsequent deuterium-exchange experiments confirmed that the loss was a hydroxyl radical and afforded definitive assignment of the site of protonation. Furthermore, the involvement of a single exchangeable hydrogen atom in the overall 50 m/z unit loss was demonstrated. Thus, supportive evidence was provided for the involvement of the ortho methyl group in the second stage of the fragmentation, leading to the loss of the thiol radical. Accurate mass measurements, performed using electrospray ionisation Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS), verified the elemental formulae of the individual losses. The ion structure following the 50 m/z unit loss was proposed to be a protonated aminofluorene and was supported by comparing the product ion spectrum of commercially available protonated 2-aminofluorene with the MS4 data of protonated 4-benzenesulfinyl-3-methylphenylamine. Fragmentation mechanisms are proposed. The relevance of the loss with regards to pharmaceutical drug metabolite identification is discussed.     

A facile approach to biodegradable poly(ε-caprolactone)-poly(ethylene glycol)-based polyurethanes containing pendant amino groups

A novel biodegradable poly(ε-caprolactone)-poly(ethylene glycol)-based polyurethanes (PCL-PEG-PU) with pendant amino groups was synthesized by direct coupling of PEG ester of NH₂-protected-(aspartic acid) (PEG-Asp-PEG diols) and poly(ε-caprolactone) (PCL) diols with hexamethylene dissocyanate (HDI) under mild reaction conditions and by subsequent deprotection of benzyloxycarbonyl (Cbz) groups. GPC, ¹H NMR, and ¹³C NMR studies confirmed the polymer structures and the complete deprotection. DSC and WXRD results indicated that the crystallinity of the copolymer was enhanced with increasing PCL diols in the copolymer. The content of amino group in the polymer could be adjusted by changing the molar ratio of PEG-Asp-PEG diols to PCL diols. Thus the results of this study provide a good way to prepare polyurethanes bearing hydrophilic PEG segments and reactive amino groups without complicated synthesis.     

o-(Pentafluorobenzyloxycarbonyl)benzoyl chloride: a novel electrophoric derivatisation reagent for amino compounds designed for negative ion chemical ionisation mass spectrometry

The synthesis of a novel electrophoric derivatisation reagent, o-(pentafluorobenzyloxycarbonyl)benzoyl chloride, is described. The reagent was tested against selected primary and secondary amino compounds as analytical targets. The derivatives exhibit excellent mass spectral properties under negative ion chemical ionisation (NICI), i.e. reduced fragmentation and thus high ion current for the targeted m/z during analysis. Since the reagent bears a pentafluorobenzyl ester group, resulting mass NICI mass spectra were expectedly dominated by dissociative resonance electron capture typically observed with these compounds. The reagent is suitable for detecting volatile primary and secondary amines with high sensitivity. Background is reduced by a shift in detected m/z and retention time, as demonstrated for the analysis of the drug methylphenidate from human plasma.     

Characterization of 4-Aryl-5-ethoxycarbonyl-6-methyl-3,4-dihydro- pyrimidin-2 （1H）-thiones by EI-TOF Mass Spectrometry

IntroductionIn1893,Pietro Biginelli reported the first synthe-sis(termed the Biginelli reaction)of3,4-dihydropyrim-idinone(denoted as“oxo-orO-Biginelli compound”in-cluding its derivatives,type A in Scheme1).In thelast decade,interest in these compounds …     

ToF-SIMS analysis of poly(l-lysine)-graft-poly(2-methyl-2-oxazoline) ultrathin adlayers

Understanding of the interfacial chemistry of ultrathin polymeric adlayers is fundamentally important in the context of establishing quantitative design rules for the fabrication of nonfouling surfaces in various applications such as biomaterials and medical devices. In this study, seven poly(l-lysine)-graft-poly(2-methyl-2-oxazoline) (PLL–PMOXA) copolymers with grafting density (number of PMOXA chains per lysine residue) 0.09, 0.14, 0.19, 0.33, 0.43, 0.56, and 0.77, respectively, were synthesized and characterized by means of nuclear magnetic resonance spectroscopy (NMR). The copolymers were then adsorbed on Nb₂O₅ surfaces. Optical waveguide lightmode spectroscopy method was used to monitor the surface adsorption in situ of these copolymers and provide information on adlayer masses that were then converted into PLL and PMOXA surface densities. To investigate the relationship between copolymer bulk architecture (as shown by NMR data) and surface coverage as well as surface architecture, time-of-flight secondary ion mass spectrometry (ToF-SIMS) analysis was performed. Furthermore, ToF-SIMS method combined with principal component analysis (PCA) was used to verify the protein resistant properties of PLL–PMOXA adlayers, by thorough characterization before and after adlayer exposure to human serum. ToF-SIMS analysis revealed that the chemical composition as well as the architecture of the different PLL–PMOXA adlayers indeed reflects the copolymer bulk composition. ToF-SIMS results also indicated a heterogeneous surface coverage of PLL–PMOXA adlayers with high grafting densities higher than 0.33. In the case of protein resistant surface, PCA results showed clear differences between protein resistant and nonprotein-resistant surfaces. Therefore, ToF-SIMS results combined with PCA confirmed that the PLL–PMOXA adlayer with brush architecture resists protein adsorption. However, low increases of some amino acid signals in ToF-SIMS spectra were detected after the adlayer has been exposed to human serum.

Comparison of Bi(1), Bi(3) and C(60) primary ion sources for ToF-SIMS imaging of patterned protein samples

Imaging time-of-flight secondary ion mass spectrometry (ToF-SIMS) has been used to study protein bound to a photolithographically-patterned, commercial poly(ethylene glycol) (PEG)-based polymer film. The effect of different ion sources on the fragmentation pattern from this sample was analyzed with respect to the surface sensitivity of characteristic protein fragments and contrast in the ion images. The method demonstrates that, under similar fluence (below the static limit), Bi(3) (+) provides better surface sensitivity for low mass fragments and the best image contrast as compared to Bi(1) (+) and C(60) (+) cluster sources. Principal component analysis (PCA) was utilized to process depth profiles for this sample and shows that a primary ion fluence of approximately 20 × 10(12) ions/cm(2) is required to etch through the adsorbed protein layer.     

Volatile evolution induced by energetic He++ ions in a poly(ester) based polyurethane

Irradiation of polymer samples using an accelerated beam of He⁺⁺ ions passed through a 10 μm thick window of havar foil has been performed. Such an irradiation simulates the effects of large α radiation doses. The experimental set up was designed so that the irradiated material was contained within a small sample chamber, which was isolated from the main vacuum chamber of the ion beam by means of the foil window. A mass spectrometer linked directly to the sample chamber facilitated analysis of gaseous products evolved from the materials as a consequence of irradiation. Samples of a poly(ester) based poly(urethane) polymer evolved mainly CO₂ along with a number of higher mass volatile species. Assignment of chemical structures to the main molecular ions has allowed deductions about the chemical processes underlying radiation induced change to be made. Furthermore, identification of trends in volatile production affords information about radiation induced crosslinking reactions, which do not directly result in the production of volatile species to be deduced.     

Quantifiable correlation of ToF-SIMS and XPS data from polymer surfaces with controlled amino acid and peptide content

Peptide-coated surfaces are widely employed in biomaterial design, but quantifiable correlation between surface composition and biological response is challenging due to, for example, instrumental limitations, a lack of suitable model surfaces or limitations in quantitatively correlating data from different surface analytical techniques. Here, we first establish a reference material that allows control over amino acid content. Reversible addition-fragmentation chain-transfer (RAFT) polymerisation is used to prepare a copolymer containing alkyne and furan units with well-defined chain length and composition. Huisgen Cu(I)-catalysed azide-alkyne cycloaddition reaction is used to attach the model azido-polyethyleneglycol-amide-modified pentafluoro-l -phenylalanine to the polymer. Different compositional ratios of the polymer provide a surface with varying amino acid content that is analysed by X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). Nitrogen-related signals are compared with fluorine signals from both techniques. Fluorine and nitrogen signals from both techniques are found to be related to the copolymer compositions, but the homopolymer data deviate from this trend. The approach is then translated to a heparin-binding peptide that supports cell adhesion. Human embryonic stem cells cultured on copolymer surfaces presenting different amounts of heparin-binding peptide show strong cell growth while maintaining pluripotency after 72 h of culture. The early cell adhesion at 24 h can be correlated to the logarithm of the normalised CH₄N⁺ ion intensity from ToF-SIMS data, which is established as a suitable and generalisable marker ion for amino acids and peptides. This work contributes to the ability to use ToF-SIMS in a more quantitative manner for the analysis of amino acid and peptide surfaces.     

Synthesis and Characterization of Poly(p-phenylene benzobisoxazole)/Poly(pyridobisimidazole) Block Copolymers

Poly(p-phenylene benzobisoxazole)/poly(pyridobisimidazole) block copolymers (PBO-b-PIPD) were prepared by introducing poly(pyridobisimidazole) (PIPD) moieties into the main chains of poly(p-phenylene benzobisoxazole) (PBO) in order to enhance its photostability. PBO and copolymer fibers were directly prepared from the polymerization solutions by dry-jet wet-spinning. Chemical structures and molecular chains arrangement of the block copolymers were characterized by Fourier transform infrared (FTIR) spectroscopy, solid-state ¹³C-NMR and wide angle X-ray diffraction (WAXD). Thermal stability of the copolymers was investigated by thermogravimetric analysis (TGA) in nitrogen. Thin films of PBO and copolymers were cast from methanesulfonic acid (MSA) solutions. Both the films and fibers were exposed to UV light to determine their photostability. Changes in the chemical structures and surface morphologies of the films were characterized by FTIR spectra and scanning electronic microscopy (SEM), respectively. After UV light exposure, the retention of strength for copolymer fibers is improved compared to PBO fibers. The results revealed that copolymers suffered less photodegradation in comparison with homopolymer. The mechanism for the improved photostability of the copolymers was discussed.     

Collision-induced dissociation mass spectra of positive ions derived from tetrahydropyranyl (THP) ethers of primary alcohols

Peaks for [M + H](+) are not observed when electrospray ionization mass spectra of tetrahydropyranyl (THP) ethers are recorded under acidic conditions. However, gaseous [M + H](+) ions can be generated from ammonium adducts of THP ethers of primary alcohols by in-source fragmentation. The product ion spectra of these proton adducts show two significant peaks at m/z 85 and 103. Tandem mass spectrometric data obtained from appropriately deuteriated derivatives and ab initio calculations indicate that the m/z 85 ion originates from more than one mechanism and represents two structurally different species. A charge-directed E1-elimination mechanism or an inductive cleavage mechanism can produce the 3,4,5,6-tetrahydropyrylium ion as one of the structures for the m/z 85 ion, whereas a charge-remote process with ring contraction can generate the 5-methyl-3,4-dihydro-2H-furylium ion as the other structure. A comparison of the relative abundances of product ions from different isotopologues showed that the charge-remote process is the preferred mechanism. This is congruent with the ab initio calculations, which showed that the dihydrofurylium ion bears the lowest energy structure. The less abundant m/z 103 ion, which represents a protonated tetrahydropyran-2-ol, is formed by a charge-remote process via a proton transfer from the alkyl substituent. This process involves the formation and rearrangement of a carbenium ion in close association with a hydroxypentanal molecule. A proton transfer from the carbenium ion to the aldehyde is followed by elimination of an alkene.     

Characterization of poly(2-oxazoline) homo- and copolymers by liquid chromatography at critical conditions

In this study liquid chromatography at critical conditions for poly(2-ethyl-2-oxazoline)s (PEtOx) has been performed for the first time in order to analyze functional PEtOx homopolymers and block copolymers. Besides the verification of the critical point of adsorption with two series of ester end group functionalized PEtOx homopolymers, to evaluate the effect of both the chain length dependence and the end group polarity, using a cyano column with a solvent combination of 2-propanol and water, also two-dimensional liquid chromatography (2D-LC) has been applied for a poly(2-oxazoline) block copolymer. The combined characterization techniques provided further information about the polymerization procedure with regard to the formation of side-products by separation of the block copolymer from the corresponding homopolymer impurities. In addition, hyphenation of LCCC with MALDI-TOF MS and ESI-Q-TOF tandem mass spectrometry verified the obtained results.     

Morphology-driven surface segregation in a blend of poly(epsilon-caprolactone) and poly(vinyl chloride)

A blend of poly(epsilon-caprolactone) (PCL) and poly(vinyl chloride) (PVC) with 90 wt % PCL was prepared. Two films of this blend, which were grown at 35 and 45 degrees C, showed the absence and presence of banded spherulites, respectively. A detailed examination conducted with time-of-flight secondary ion mass spectrometry (ToF-SIMS) found that the surface composition of the film grown at 45 degrees C was related to its structure, which was shown to contain ridges and valleys. Phase images obtained using atomic force microscopy (AFM) indicated that the ridges and valleys consisted of edge-on and flat-on lamellae, respectively. ToF-SIMS imaging revealed that PVC and PCL were located mainly on the surface of the valleys and ridges, respectively. This morphology-driven surface segregation was caused by the difference in the surface energy between the flat-on and edge-on lamellae.     

Gas chromatography-mass spectrometry analysis of regioisomeric ring substituted methoxy methyl phenylacetones

The methoxy methyl phenylacetones share an isobaric relationship (equivalent mass but different elemental composition) to the controlled precursor substance 3,4-methylenedioxyphenylacetone. The 10 methoxy methyl phenylacetones as well as the methylenedioxyphenylacetones show essentially equivalent mass spectra with major fragment ions at m/z 135 and 43. Those methoxy methyl phenylacetones with the methoxy group substituted ortho to the benzylic cation in the m/z 135 ion show a further fragmentation to lose formaldehyde (CH2O) and yield a significant ion at m/z 105. The loss of formaldehyde from the ortho methoxy benzyl cation was confirmed using commercially available regioisomeric 2-, 3-, and 4-methoxyphenylacetones. The 10 regioisomeric methoxy methyl phenylacetones were prepared from the appropriately substituted benzaldehydes. Complete gas chromatographic resolution of all ten regioisomeric ketones was obtained on a stationary phase containing modified beta-cyclodextrin. Using the cyclodextrin containing phase, the ortho methoxy-substituted ketones (K1-K4) eluted before the meta-methoxy-substituted ketones (K5-K8) and the para-methoxy-substituted ketones (K9-K10) showed the greatest affinity for the stationary liquid phase and eluted last. Complete separation of the 10 ketones was not obtained on Rtx-1 and Rtx-200 columns.     

2—羟基—4—邻苯二甲酰亚胺基丁酸的氢迁移反应

在甲烷为反应气的化学电离质谱条件下，质子化的２－羟基－４－邻苯二甲酰亚胺基丁酸的单分子质谱碎裂产生了ｍ／ｚ１４８的碎片离子，表明其碎裂过程发生了氢迁移反应，ＡＭ在分子轨道的理论计算结果为可能的质子化位置提供了理论依据；建立在氘代同位素标记和碰撞诱导解离实验的基础上，我们提出此离子的形成可能同时存在单氢迁移和双氢迁移，一些质谱图中的物征碎片中离子为可能的ＭｃＬａｆｆｅｒｔｙ重排和离子／中性（碎片）复     

Nitramine anion fragmentation: A mass spectrometric and Ab initio study

The fragment ion formation characteristics of the radical anions generated from hexahydro-1,3,5-trinitrotriazine (RDX) and its three nitroso metabolites were studied using GC/MS with negative chemical ionization (NCI) to understand the fragmentation mechanisms responsible for the formation of the most abundant ions observed in their NCI mass spectra. Ab initio and density functional theory calculations were used to calculate relative free energies for different fragment ion structures suggested by the m/z values of the most abundant ions observed in the NCI mass spectra. The NCI mass spectra of the four nitramines are dominated by ions formed by the cleavage of nitrogen-nitrogen and carbon-nitrogen bonds in the atrazine ring. The most abundant anions in the NCI mass spectra of these nitramines have the general formulas C(2)H(4)N(3)O (m/z 86) and C(2)H(4)N(3)O(2) (m/z 102). The analyses of isotope-labeled standards indicate that these two ions are formed by neutral losses that include two exocylic nitrogens and one atrazine ring nitrogen. Our calculations and observations of the nitramine mass spectra suggest that the m/z 86 and m/z 102 ions are formed from either the (M--NO)(-) or (M--NO(2))(-) fragment anions by a single fragmentation reaction producing neutral losses of CH(2)N(2)O or CH(2)N(2)O(2) rather than a set of sequential reactions involving neutral losses of HNO(2) or HNO and HCN.     

Unimolecular reactivity of uracil-Cu(2+) complexes in the gas phase.

The gas-phase interaction of copper(II) ions with uracil are studied by means of mass spectrometry and B3LYP/6-311+G(2df,2p)//B3LYP/6-31G(d) calculations. Positive-ion electrospray spectra show that the reaction of uracil with copper(II) gives rise to singly charged species, whereby the [Cu(uracil--H)](+) complex is the most intense ion in the spectra at low concentration. Mass spectrometry/mass spectrometry (MS/MS) experiments show that the loss of HNCO and NCO are the dominant fragmentation processes, accompanied by a minor loss of CO. A systematic study of the spectra obtained with different labeled species, namely, 2-(13)C- (m/z 175), 2-(13)C,1,3-(15)N(2)- (m/z 177) and 3-(15)N-uracil (m/z 175), concludes unambiguously that both the loss of HNCO and NCO involve exclusively C2 and N3, whereas only C4 is involved in the loss of CO. Suitable mechanisms for these fragmentation processes are proposed through a theoretical survey of the corresponding potential energy surface. In these mechanisms, pi complexes, which lie high in energy with respect to the global minimum, play a significant role in the loss of NCO; this explains why both products, HNCO and NCO involve the same atoms of the ring.     

Key fragments for identification of positional isomer pair in glucuronides from the hydroxylated metabolites of RT-3003 (Vintoperol) by liquid chromatography/electrospray ionization mass spectrometry.

The mass spectral properties of glucuronides of the 9- and 10-hydroxylated metabolites of RT-3003 (Vintoperol; (-)-1beta-ethyl-1alpha-hydroxymethyl-1,2,3,4,6,7, 12balpha-octahydroindolo[2,3-a]quinolizine), which were fractionated by high-performance liquid chromatography with fluorescence detection, were investigated using the positive ion electrospray ionization mode. These glucuronides showed predominantly the protonated molecular ion ([M + H](+) ion), and the [M + H](+) ion provided a characteristic product ion spectrum in which abundant ions were obtained at m/z 301, 160 and 142. The first ion, corresponding to the [aglycone + H](+) ion, was produced by neutral loss of the glucuronic acid moiety from the [M + H](+) ion. The product ion spectrum of the [M + H](+) ion of hydroxy-RT-3003 revealed a number of ions common to the glucuronide spectra, suggesting that other two ions observed most likely represent fragmentation of hydroxy-RT-3003. In turn, these glucuronides were positional isomers with respect to the binding site of glucuronic acid. The structures of the isomer pairs were discriminated by the presence of the ion of m/z 318 or 336 in the product ion spectrum. These ions were produced by fission of the C-ring, the same as for the formation of the ions of m/z 160 and 142, as were observed in the product ion spectrum from the [M + H](+) ion of hydroxy-RT-3003. For the formation of these ions, an unusual fragmentation process was proposed, and these ion structures were supported by evidence from the accurate mass measurement data. Additionally, in the sulfates of hydroxylated metabolites, a similar product ion corresponding to the ion of m/z 336 found in the phenolic glucuronides was observed, and was applied for identification of the sulfate metabolites.     

Trimethylsilyl transfer during electron ionization mass spectral fragmentation of some omega-hydroxycarboxylic and omega-dicarboxylic acid trimethylsilyl derivatives and the effect of chain length

The electron ionization (EI) mass spectral fragmentation of omega-hydroxycarboxylic and omega-dicarboxylic acid trimethylsilyl derivatives was investigated. The mass spectra of these compounds exhibited fragment ions resulting from classical fragmentation of the trimethylsilyl ether and ester groups, and others resulting from the interactions between the two functionalities (m/z 147, 204, 217, [M-31](+) and [M-105](+) in the case of omega-hydroxycarboxylic acid derivatives and m/z 147, 204, 217 and [M-131](+) in the case of omega-dicarboxylic acid derivatives). Several fragmentation pathways were proposed to explain the formation of these different fragment ions. It is proposed that the ions at m/z 204 and 217 are formed via an initial trimethylsilyl transfer between the ether and the ester group or between the two ester groups. This transfer appeared to be more favoured in the case of omega-dicarboxylic acid derivatives and to be dependent on the chain length. A more efficient transfer was in fact observed for compounds with a relatively long alkyl chain. In the case of shorter omega-hydroxycarboxylic and omega-dicarboxylic acid trimethylsilyl derivatives the formation of the ions at m/z 204 and 217 suffers strongly from competition from production of the ion at m/z 147.