Observation of pronounced b*,y cleavages in the electron capture dissociation mass spectrometry of polyamidoamine (PAMAM) dendrimer ions with amide functionalities

Mass spectrometry of dendrimers

Mass spectrometry (MS) has become an essential technique to characterize dendrimers as it proved efficient at tackling analytical challenges raised by their peculiar onion-like structure. Owing to their chemical diversity, this review covers benefits of MS methods as a function of dendrimer classes, discussing advantages and limitations of ionization techniques, tandem mass spectrometry (MS/MS) strategies to determine the structure of defective species, as well as most recently demonstrated capabilities of ion mobility spectrometry (IMS) in the field. Complementarily, the well-defined structure of these macromolecules offers major advantages in the development of MS-based method, as reported in a second section reviewing uses of dendrimers as MS and IMS calibration standards and as multifunctional charge inversion reagents in gas phase ion/ion reactions.

Chimera Spectrum Diagnostics for Peptides Using Two-Dimensional Partial Covariance Mass Spectrometry

The rate of successful identification of peptide sequences by tandem mass spectrometry (MS/MS) is adversely affected by the common occurrence of co-isolation and co-fragmentation of two or more isobaric or isomeric parent ions. This results in so-called `chimera spectra', which feature peaks of the fragment ions from more than a single precursor ion. The totality of the fragment ion peaks in chimera spectra cannot be assigned to a single peptide sequence, which contradicts a fundamental assumption of the standard automated MS/MS spectra analysis tools, such as protein database search engines. This calls for a diagnostic method able to identify chimera spectra to single out the cases where this assumption is not valid. Here, we demonstrate that, within the recently developed two-dimensional partial covariance mass spectrometry (2D-PC-MS), it is possible to reliably identify chimera spectra directly from the two-dimensional fragment ion spectrum, irrespective of whether the co-isolated peptide ions are isobaric up to a finite mass accuracy or isomeric. We introduce '3-57 chimera tag' technique for chimera spectrum diagnostics based on 2D-PC-MS and perform numerical simulations to examine its efficiency. We experimentally demonstrate the detection of a mixture of two isomeric parent ions, even under conditions when one isomeric peptide is at one five-hundredth of the molar concentration of the second isomer.

Infrared multiple photon dissociation spectroscopy and density functional theory (DFT) studies of protonated permethylated β-cyclodextrin-water non-covalent complexes

We present infrared multiple photon dissociation (IRMPD) spectroscopy and quantum chemical calculation results for the protonated permethylated β-cyclodextrin (CD)-water non-covalent complex, the simplest β-CD non-covalent complex, in the gas-phase. The IRMPD spectrum in the region 2700-3750 cm(-1) consisted of three strong peaks at 3096, 3315, and 3490 cm(-1). These spectral features in the experimental IRMPD spectrum were compared with a large set of infrared absorption spectra predicted using density functional theory (DFT) calculations for the protonated β-CD-water complex. Complex III (see ), in which the water molecule (at the primary rim) and the proton (at the secondary rim) were separated, was found to suitably reflect the main spectral characteristics found in the experimental IRMPD spectrum. The absence of the homodromic hydrogen bond ring, due to replacement of hydroxyl groups with methoxy groups in permethylated β-CD, rendered the primary rim open compared with the unmodified β-CD 'one-gate-closed' lowest energy conformer. This study demonstrates that IRMPD studies combined with DFT theoretical calculations can be a good method for studying molecular interactions of large host-guest pairs.

Radical-driven peptide backbone dissociation tandem mass spectrometry

In recent years, a number of novel tandem mass spectrometry approaches utilizing radical-driven peptide gas-phase fragmentation chemistry have been developed. These approaches show a peptide fragmentation pattern quite different from that of collision-induced dissociation (CID). The peptide fragmentation features of these approaches share some in common with electron capture dissociation (ECD) or electron transfer dissociation (ETD) without the use of sophisticated equipment such as a Fourier-transform mass spectrometer. For example, Siu and coworkers showed that CID of transition metal (ligand)-peptide ternary complexes led to the formation of peptide radical ions through dissociative electron transfer (Chu et al., 2000. J Phys Chem B 104:3393-3397). The subsequent collisional activation of the generated radical ions resulted in a number of characteristic product ions, including a, c, x, z-type fragments and notable side-chain losses. Another example is the free radical initiated peptide sequencing (FRIPS) approach, in which Porter et al. and Beauchamp et al. independently introduced a free radical initiator to the primary amine group of the lysine side chain or N-terminus of peptides (Masterson et al., 2004. J Am Chem Soc 126:720-721; Hodyss et al., 2005 J Am Chem Soc 127: 12436-12437). Photodetachment of gaseous multiply charged peptide anions (Joly et al., 2008. J Am Chem Soc 130:13832-13833) and UV photodissociation of photolabile radical precursors including a C-I bond (Ly & Julian, 2008. J Am Chem Soc 130:351-358; Ly & Julian, 2009. J Am Soc Mass Spectrom 20:1148-1158) also provide another route to generate radical ions. In this review, we provide a brief summary of recent results obtained through the radical-driven peptide backbone dissociation tandem mass spectrometry approach.

Quantitative determination of poly(amidoamine) dendrimers in urine by liquid chromatography/electrospray ionization hybrid quadrupole linear ion trap mass spectrometry

RATIONALE

Dendrimer nanocarriers have become of increasing interest in the field of biomedicine for their drug delivery potential. Surface modifications and optimized nanosize control are the strategies being followed to enhance drug delivery efficacy and renal clearance, especially for dendrimers of a lower generation number. The aim of this study was the development and performance evaluation of an analytical method for the quantitative determination of polyamidoamine (PAMAM) dendrimers in urine.

METHODS

PAMAM dendrimers (generations G0 to G3) were analyzed using liquid chromatography/electrospray ionization hybrid quadrupole linear ion trap mass spectrometry (LC/ESI-QqLIT-MS). Quantitative analysis was performed in selected reaction monitoring (SRM) mode. To confer a higher degree of confidence on the identification of PAMAM dendrimers, an SRM scan and collision-induced dissociation (CID), as a dependent scan, were performed in one single run using the information-dependent acquisition (IDA) mode.

RESULTS

The LC/ESI-QqLIT-MS method, in SRM mode, allowed quantitative determination in urine matrix with good repeatability and reproducibility (relative standard deviation (R.S.D.) from 2 to 15%), linearity (R >0.99) over the concentration range (6∙10^-4 to 5∙10^-2  mmol.L^-1 ), and sensitivity within the micromolar range. The detection limit values were above 1∙10^-4  mmol.L^-1 in both solvent and urine, for the generations studied.

CONCLUSIONS

The developed method has demonstrated a capability for the identification and quantification of PAMAM dendrimer nanoparticles in a complex liquid matrix. The use of an LC/ESI-QqLIT-MS system, of modest m/z range and unit resolution, offers an alternative in the analysis of lower generation PAMAM dendrimers between mass analyzers of higher resolution and the conventional LC-UV method that is commonly applied for dendrimer quantification, but which lacks sufficient identification capacity. Copyright © 2013 John Wiley & Sons, Ltd.

Tandem mass spectrometric analysis of isosorbide-1,4-cyclohexane-dicarboxylic acid polyester oligomer cations using ion-trap mass spectrometry

RATIONALE

Isosorbide is a promising biomass-derived molecule that can be used as a replacement for fossil resource-derived diol monomers used in polyester synthesis. Due to its increased use in sustainable development, it is useful to understand the tandem mass spectrometric (MS/MS) fragmentation pathways of the isosorbide-based copolymer as an aid to interpreting the MS/MS spectra of other isosorbide-containing copolymers.

METHODS

Collision-activated dissociation (CAD) experiments were performed on the sodiated/protonated molecules, [(AB)(n)A+Na(or H)](+), n = 2-5, of isosorbide (A)-1,4-cyclohexanedicarboxylic acid (B) oligomers formed by ion-trap electrospray ionization (ESI).

RESULTS

Product ions arose from cleavage of the bonds between isosorbide and 1,4-cyclohexanedicarboxylic acid. In the MS/MS spectra, f(n)'' product ions were most abundant, followed by e(n) ions. McLafferty rearrangement appeared to provide the most facile pathway to yield the abundant f(n)'' and e(n) ions. In addition, a(n), b(n)'', f(n)''u(n)'', and en (+) ions were observed. Inductive cleavage and β-elimination were suggested to be the pathways involved in generating e(n)(+)- and e(n)/b(n)''-type ions, respectively.

CONCLUSIONS

Based on the obtained CAD spectra, the alternating sequences of two copolymer building blocks, A and B, were unambiguously determined. The fragmentation pathways leading to the observed product ion types were also established.

MALDI in-source decay mass spectrometry of polyamidoamine dendrimers

We report using MALDI-ISD (in-source decay) mass spectrometry (MS) to characterize highly branched synthetic polymers of polyamidoamine (PAMAM) dendrimer. This inherently monodisperse polymer possesses dendritic branches networked by tertiary amines and an amide functionality in each repeating unit. Among various ISD matrices examined, 2,5-DHB was the most efficient, yielding 33 fragments produced by single- or multiple-bond cleavages. Detailed analysis revealed that cleavages at tertiary amine sites (S- and E-type fragments) were the most pronounced, with various other cleavages around amide groups. The fragmentation mechanism appeared to follow the radical-induced dissociation pathway. In addition, the matrix dependence of PAMAM MALDI-ISD differed from that of peptides/proteins. The observed fragments provided rich structural information, which was suitable to characterize dendritic polymers.

Defining intact protein primary structures from saliva: a step toward the human proteome project

Top-down mass spectrometry has been used to investigate structural diversity within some abundant salivary protein families. In this study, we report the identification of two isoforms of protein II-2 which differed in mass by less than 1 Da, the determination of a sequence for protein IB8a that was best satisfied by including a mutation and a covalent modification in the C-terminal part, and the assignment of a sequence of a previously unreported protein of mass 10433 Da. The final characterization of Peptide P-J was achieved, and the discovery of a truncated form of this peptide was reported. The first sequence assignment was done at low resolution using a hybrid quadrupole time-of-flight instrument to quickly identify and characterize proteins, and data acquisition was switched to Fourier-transform ion cyclotron resonance (FTICR) for proteins that required additional sequence coverage and certainty of assignment. High-resolution and high mass accuracy mass spectrometry on a FTICR-mass spectrometry (MS) instrument combined with electron-capture dissociation (ECD) provided the most informative data sets, with the more frequent presence of "unique" ions that unambiguously define the primary structure. A mixture of predictable and unusual post-translational modifications in the protein sequence precluded the use of shotgun-annotated databases at this stage, requiring manual iterations of sequence refinement in many cases. This led us to propose guidelines for an iterative processing workflow of MS and MSMS data sets that allow researchers to completely assign the identity and the structure of a protein.

Fragmentation pathways of polymer ions

Tandem mass spectrometry (MS/MS) is increasingly applied to synthetic polymers to characterize chain-end or in-chain substituents, distinguish isobaric and isomeric species, and determine macromolecular connectivities and architectures. For confident structural assignments, the fragmentation mechanisms of polymer ions must be understood, as they provide guidelines on how to deduce the desired information from the fragments observed in MS/MS spectra. This article reviews the fragmentation pathways of synthetic polymer ions that have been energized to decompose via collisionally activated dissociation (CAD), the most widely used activation method in polymer analysis. The compounds discussed encompass polystyrenes, poly(2-vinyl pyridine), polyacrylates, poly(vinyl acetate), aliphatic polyester copolymers, polyethers, and poly(dimethylsiloxane). For a number of these polymers, several substitution patterns and architectures are considered, and questions regarding the ionization agent and internal energy of the dissociating precursor ions are also addressed. Competing and consecutive dissociations are evaluated in terms of the structural insight they provide about the macromolecular structure. The fragmentation pathways of the diverse array of polymer ions examined fall into three categories, viz. (1) charge-directed fragmentations, (2) charge-remote rearrangements, and (3) charge-remote fragmentations via radical intermediates. Charge-remote processes predominate. Depending on the ionizing agent and the functional groups in the polymer, the incipient fragments arising by pathways (1)-(3) may form ion-molecule complexes that survive long enough to permit inter-fragment hydrogen atom, proton, or hydride transfers.

Peptide fragmentation by corona discharge induced electrochemical ionization

Fundamental studies have greatly improved our understanding of electrospray, including the underlying electrochemical reactions. Generally regarded as disadvantageous, we have recently shown that corona discharge (CD) can be used as an effective method to create a radical cation species [M](+·), thus optimizing the electrochemical reactions that occur on the surface of the stainless steel (SS) electrospray capillary tip. This technique is known as CD initiated electrochemical ionization (CD-ECI). Here, we report on the fundamental studies using CD-ECI to induce analytically useful in-source fragmentation of a range of molecules that complex transition metals. Compounds that have been selectively fragmented using CD-ECI include enolate forming phenylglycine containing peptides, glycopeptides, nucleosides, and phosphopeptides. Collision induced dissociation (CID) or other activation techniques were not necessary for CD-ECI fragmentation. A four step mechanism was proposed: (1) complexation using either Fe in the SS capillary tip material or Cu(II) as an offline complexation reagent; (2) electrochemical oxidation of the complexed metal and thus formation of a radical cation (e.g.; Fe - e(-) → Fe(+·)); (3) radical fragmentation of the complexed compound; (4) electrospray ionization of the fragmented neutrals. Fragmentation patterns resembling b- and y-type ions were observed and allowed the localization of the phosphorylation sites.

Electron capture dissociation mass spectrometry of metallo-supramolecular complexes

The electron capture dissociation (ECD) of metallo-supramolecular dinuclear triple-stranded helicate Fe(2)L(3)(4+) ions was determined by Fourier transform ion cyclotron resonance mass spectrometry. Initial electron capture by the di-iron(II) triple helicate ions produces dinuclear double-stranded complexes analogous to those seen in solution with the monocationic metal centers Cu(I) or Ag(I). The gas-phase fragmentation behavior [ECD, collision-induced dissociation (CID), and infrared multiphoton dissociation (IRMPD)] of the di-iron double-stranded complexes, (i.e., MS(3) of the ECD product) was compared with the ECD, CID, and IRMPD of the Cu(I) and Ag(I) complexes generated from solution. The results suggest that iron-bound dimers may be of the form Fe(I)(2)L(2)(2+) and that ECD by metallo-complexes allows access, in the gas phase, to oxidation states and coordination chemistry that cannot be accessed in solution.

Ultraviolet photodissociation at 266 nm of phosphorylated peptide cations

Ultraviolet (UV) photodissociation (PD) experiments using 266 nm light were performed for a series of phosphopeptide cations in a Fourier transform mass spectrometer. The objective of the experiments was to determine whether 266 nm UV irradiation on the phosphopeptide cations would induce unique peptide backbone dissociation. In addition, the general behavior of the phosphate loss (-80 or -98 Da) was monitored, particularly for those phosphopeptides with a phosphotyrosine residue that itself is a UV chromophore. For phosphopeptides with a UV chromophore, their photodissociation behavior was very similar to that of low-energy sustained off-resonance irradiation collisionally activated dissociation (SORI-CAD), with a few exceptions. For example, b- and y-type peptide backbone fragments were prevalent, and their dephosphorylation behavior was consistent with that of the SORI-CAD results. For phosphoserine peptides, the loss of a phosphate group was always observed. On the other hand, for phosphotyrosine peptides, the phosphate loss was found to be dependent on the presence of a basic amino group in the sequence and the charge state of the precursor ions, in agreement with the CAD results in the literature. However, hydrogen atom loss or aromatic side chain loss, which is known to be the excited state specific fragmentation pathway, was rarely observed in our 266 nm UV PD experiments, in contrast to the previous UV PD literature (particularly at 220 nm). The mechanism for these observations is described in terms of dominant internal conversion followed by intramolecular vibrational energy redistribution (IVR).

Characterization of polyphosphoesters by Fourier transform ion cyclotron resonance mass spectrometry

FT-ICR mass spectrometry, together with collision-induced dissociation and electron capture dissociation, has been used to characterize the polyphosphoester poly[1,4-bis(hydroxyethyl)terephthalate-alt-ethyloxyphosphate] and its degradation products. Three degradation pathways were elucidated: hydrolysis of the phosphate-[1,4-bis(hydroxyethyl)terephthalate] bonds; hydrolysis of the phosphate-ethoxy bonds; and hydrolysis of the ethyl-terephthalate bonds. The dominant degradation reactions were those that involved the phosphate groups. This work constitutes the first application of mass spectrometry to the characterization of polyphosphoesters and demonstrates the suitability of high mass accuracy FT-ICR mass spectrometry, with CID and ECD, for the structural analysis of polyphosphoesters and their degradation products.

Electron capture dissociation and collision-induced dissociation of metal ion (Ag(+), Cu(2+), Zn(2+), Fe(2+), and Fe(3+)) complexes of polyamidoamine (PAMAM) dendrimers

The electron capture dissociation (ECD) and collision-induced dissociation (CID) of complexes of polyamidoamine (PAMAM) dendrimers with metal ions Ag(+), Cu(2+), Zn(2+), Fe(2+), and Fe(3+) were determined by Fourier transform ion cyclotron resonance mass spectrometry. Complexes were of the form [PD + M + mH](5+) where PD = generation two PAMAM dendrimer with amidoethanol surface groups, M = metal ion, m = 2-4. Complementary information regarding the site and coordination chemistry of the metal ions can be obtained from the two techniques. The results suggest that complexes of Fe(3+) and Cu(2+) are coordinated via both core tertiary amines, whereas coordination of Ag(+) involves a single core tertiary amine. The Zn(2+) and Fe(2+) complexes do not appear to involve coordination by the dendrimer core.

Electron capture dissociation, electron detachment dissociation, and collision-induced dissociation of polyamidoamine (PAMAM) dendrimer ions with amino, amidoethanol, and sodium carboxylate surface groups

Here, we investigate the effect of the structure (generation) and nature of the surface groups of different polyamidoamine (PAMAM) dendrimers on electron-mediated dissociation, either electron capture dissociation (ECD) or electron detachment dissociation (EDD), and compare the fragmentation with that observed in collision-induced dissociation (CID). ECD and EDD of the PAMAM dendrimers resulted in simple mass spectra, which are straightforward to interpret, whereas CID produced complex mass spectra. The results show that electron-mediated dissociation (ECD and EDD) of PAMAM dendrimers does not depend on the nature of the surface group but tends to occur within the innermost generations. CID of the PAMAM dendrimers showed a strong dependence on the nature of the surface group and occurred mostly in the outer generation. The results demonstrate the potential utility of ECD and EDD as a tool for the structural analysis of PAMAM dendrimers.

Gas-phase fragmentation of half- and first-generation polyamidoamine dendrimers by electrospray mass spectrometry using a quadrupole ion trap

Polyamidoamine (PAMAM) dendrimers are nanopolymers that can bind with biomolecules such as DNA, drugs or proteins. In order to study these complexes, we first fragmented half- and first-generation PAMAM, G0.5 and G1, respectively, using a quadrupole ion trap (QIT) equipped with an electrospray ionisation source. For both G0.5 and G1 we observed a series of impurities that only can stem from synthesis defects and that are principally due to missing branches and intramolecular cyclisations. Fragmentations of G1 showed regularity in the product ions. These ions result from the loss of 60 Da, obtained by an intramolecular cyclisation, and from the loss of 114 Da, obtained by a four-centred hydrogen transfer or a retro-Michael reaction. The fragmentations stemmed either from competitive or from consecutive reactions, even though resonant fragmentation QIT was used. It is shown that the principal fragmentation reaction is a retro-Michael rearrangement for both G1 and G0.5. In addition, by fragmenting totally deuterated [G1-d28]Na+ we were able to establish fragmentation pathways.

Current literature in mass spectrometry

In order to keep subscribers up‐to‐date with the latest developments in their field, John Wiley & Sons are providing a current awareness service in each issue of the journal. The bibliography contains newly published material in the field of mass spectrometry. Each bibliography is divided into 11 sections: 1 Books, Reviews & Symposia; 2 Instrumental Techniques & Methods; 3 Gas Phase Ion Chemistry; 4 Biology/Biochemistry: Amino Acids, Peptides & Proteins; Carbohydrates; Lipids; Nucleic Acids; 5 Pharmacology/Toxicology; 6 Natural Products; 7 Analysis of Organic Compounds; 8 Analysis of Inorganics/Organometallics; 9 Surface Analysis; 10 Environmental Analysis; 11 Elemental Analysis. Within each section, articles are listed in alphabetical order with respect to author (6 Weeks journals ‐ Search completed at 4th. Oct. 2006)

Electron capture dissociation mass spectrometry of peptide cations containing a lysine homologue: a mobile proton model for explaining the observation of b-type product ions

Eleven doubly protonated peptides with a residue homologous to lysine were investigated by electron capture dissociation mass spectrometry (ECD-MS). Lysine homologues provide the unique opportunity to examine the ECD fragmentation behavior by allowing us to vary the length of the lysine side chain, with minimal structural change. The lysine homologue has a primary amine side chain with a length that successively decreases by one methylene (CH(2)) unit from the --CH(2)CH(2)CH(2)CH(2)NH(2) of lysine and the accompanying decrease of its proton affinities: lysine (K), 1006.5(+/-7.2) kJ/mol; ornithine (K(*)), 1001.1(+/-6.6) kJ/mol; 2,4-diaminobutanoic acid (K(**)), 975.8(+/-7.4) kJ/mol; 2,3-diaminopropanoic acid (K(***)), 950.2(+/-7.2) kJ/mol. In general, the lysine-homologous peptides exhibited overall ECD fragmentation patterns similar to that of the lysine-containing peptides in terms of the locations, abundances, and ion types of products, such as yielding c(+) and z(+.) ions as the dominant product ions. However, a close inspection of product ion mass spectra showed that ECD-MS for the alanine-rich peptides with an ornithinyl or 2,4-diaminobutanoyl residue gave rise to b ions, while the lysinyl-residue-containing peptides did not, in most cases, produce any b ions. The peptide selectivity in the generation of b(+) ions could be understood from within the framework of the mobile proton model in ECD-MS, previously proposed by Cooper (Ref. 29). The exact mass analysis of the resultant b ions reveals that these b ions are not radical species but rather the cationic species with R-CO(+) structure (or protonated oxozalone ion), that is, b(+) ions. The absence of [M+2H](+.) species in the ECD mass spectra and the selective b(+)-ion formation are evidence that the peptides underwent H-atom loss upon electron capture, and then the resulting reduced species dissociated following typical MS/MS fragmentation pathways. This explanation was further supported by extensive b(+) ions generated in the ECD of alanine-based peptides with extended conformations.