Collisionally activated dissociation and infrared multiphoton dissociation of oligonucleotides in a quadrupole ion trap

Unveiling the intricacy of gapmer oligonucleotides through advanced tandem mass spectrometry approaches and scan accumulation for 2DMS

Antisense oligonucleotides (ASOs) are crucial for biological applications as they bind to complementary RNA sequences, modulating protein expression. ASOs undergo synthetic modifications like phosphorothioate (PS) backbone and locked nucleic acid (LNA) to enhance stability and specificity. Tandem mass spectrometry (MS) techniques were employed to study gapmer ASOs, which feature a DNA chain within RNA segments at both termini, revealing enhanced cleavages with ultraviolet photodissociation (UVPD) and complementary fragment ions from collision-induced dissociation (CID) and electron detachment dissociation (EDD). 2DMS, a data-independent analysis technique, allowed for comprehensive coverage and identification of shared fragments across multiple precursor ions. EDD fragmentation efficiency correlated with precursor ion charge states, with higher charges facilitating dissociation due to intramolecular repulsions. An electron energy of 22.8 eV enabled electron capture and radical-based cleavage. Accumulating multiple scans and generating average spectra improved signal intensity, aided by denoising algorithms. Data analysis utilised a custom Python script capable of handling modifications and generating unique mass lists.

Analyzing RNA posttranscriptional modifications to decipher the epitranscriptomic code

The discovery of RNA silencing has revealed that non-protein-coding sequences (ncRNAs) can cover essential roles in regulatory networks and their malfunction may result in severe consequences on human health. These findings have prompted a general reassessment of the significance of RNA as a key player in cellular processes. This reassessment, however, will not be complete without a greater understanding of the distribution and function of the over 170 variants of the canonical ribonucleotides, which contribute to the breathtaking structural diversity of natural RNA. This review surveys the analytical approaches employed for the identification, characterization, and detection of RNA posttranscriptional modifications (rPTMs). The merits of analyzing individual units after exhaustive hydrolysis of the initial biopolymer are outlined together with those of identifying their position in the sequence of parent strands. Approaches based on next generation sequencing and mass spectrometry technologies are covered in depth to provide a comprehensive view of their respective merits. Deciphering the epitranscriptomic code will require not only mapping the location of rPTMs in the various classes of RNAs, but also assessing the variations of expression levels under different experimental conditions. The fact that no individual platform is currently capable of meeting all such demands implies that it will be essential to capitalize on complementary approaches to obtain the desired information. For this reason, the review strived to cover the broadest possible range of techniques to provide readers with the fundamental elements necessary to make informed choices and design the most effective possible strategy to accomplish the task at hand.

Review of fragmentation of synthetic single-stranded oligonucleotides by tandem mass spectrometry from 2014 to 2022

The fragmentation of oligonucleotides by mass spectrometry allows for the determination of their sequences. It is necessary to understand how oligonucleotides dissociate in the gas phase, which allows interpretation of data to obtain sequence information. Since 2014, a range of fragmentation mechanisms, including a novel internal rearrangement, have been proposed using different ion dissociation techniques. The recent publications have focused on the fragmentation of modified oligonucleotides such as locked nucleic acids, modified nucleobases (methylated, spacer, nebularine and aminopurine) and modification to the carbon 2'-position on the sugar ring; these modified oligonucleotides are of great interest as therapeutics. Comparisons of different dissociation techniques have been reported, including novel approaches such as plasma electron detachment dissociation and radical transfer dissociation. This review covers the period 2014-2022 and details the new knowledge gained with respect to oligonucleotide dissociation using tandem mass spectrometry (without priori sample digestion) during that time, with a specific focus on synthetic single-stranded oligonucleotides.

THERAPEUTIC OLIGONUCLEOTIDES, IMPURITIES, DEGRADANTS, AND THEIR CHARACTERIZATION BY MASS SPECTROMETRY

Oligonucleotides are an emerging class of drugs that are manufactured by solid-phase synthesis. As a chemical class, they have unique product-related impurities and degradants, characterization of which is an essential step in drug development. The synthesis cycle, impurities produced during the synthesis and degradation products are presented and discussed. The use of liquid chromatography combined with mass spectrometry for characterization and quantification of product-related impurities and degradants is reviewed. In addition, sequence determination of oligonucleotides by gas-phase fragmentation and indirect mass spectrometric methods is discussed. © 2019 John Wiley & Sons Ltd. Mass Spec Rev.

Ribonucleic Acid Sequence Characterization by Negative Electron Transfer Dissociation Mass Spectrometry

Modified oligonucleotides represent a promising avenue for drug development, with small interfering RNAs (siRNA) and microRNAs gaining traction in the therapeutic market. Mass spectrometry (MS)-based analysis offers many benefits for characterizing modified nucleic acids. Negative electron transfer dissociation (NETD) has proven valuable in sequencing oligonucleotide anions, particularly because it can retain modifications while generating sequence-informative fragments. We show that NETD can be successfully implemented on a widely available quadrupole-Orbitrap-linear ion trap mass spectrometer that uses a front-end glow discharge source to generate radical fluoranthene reagent cations. We characterize both unmodified and modified ribonucleic acids and present the first application of activated-ion negative electron transfer dissociation (AI-NETD) to nucleic acids. AI-NETD achieved 100% sequence coverage for both a 6-mer (5'-rGmUrArCmUrG-3') with 2'-O-methyl modifications and a 21-mer (5'-rCrArUrCrCrUrCrUrArGrArGrGrArUrArGrArArUrG-3'), the luciferase antisense siRNA. Both NETD and AI-NETD afforded complete sequence coverage of these molecules while maintaining a relatively low degree of undesired base-loss products and internal products relative to collision-based methods.

Comparison of the fragmentation behavior of DNA and LNA single strands and duplexes

DNA and locked nucleic acid (LNA) were characterized as single strands, as well as double stranded DNA-DNA duplexes and DNA-LNA hybrids using tandem mass spectrometry with collision-induced dissociation. Additionally, ion mobility spectrometry was carried out on selected species. Oligonucleotide duplexes of different sequences-bearing mismatch positions and abasic sites of complementary DNA 15-mers-were investigated to unravel general trends in their stability in the gas phase. Single-stranded LNA oligonucleotides were also investigated with respect to their gas phase behavior and fragmentation upon collision-induced dissociation. In contrast to the collision-induced dissociation of DNA, almost no base loss was observed for LNAs. Here, backbone cleavages were the dominant dissociation pathways. This finding was further underlined by the need for higher activation energies. Base losses from the LNA strand were also absent in fragmentation experiments of the investigated DNA-LNA hybrid duplexes. While DNA-DNA duplexes dissociated easily into single stranded fragments, the high stability of DNA-LNA hybrids resulted in predominant fragmentation of the DNA part rather than the LNA, while base losses were only observed from the DNA single strand of the hybrid.

DNA Oligonucleotide Fragment Ion Rearrangements Upon Collision-Induced Dissociation

Collision-induced dissociation (CID) of m/z-isolated w type fragment ions and an intact 5' phosphorylated DNA oligonucleotide generated rearranged product ions. Of the 21 studied w ions of various nucleotide sequences, fragment ion sizes, and charge states, 18 (~86%) generated rearranged product ions upon CID in a Synapt G2-S HDMS (Waters Corporation, Manchester, England, UK) ion mobility-mass spectrometer. Mass spectrometry (MS), ion mobility spectrometry (IMS), and theoretical modeling data suggest that purine bases can attack the free 5' phosphate group in w type ions and 5' phosphorylated DNA to generate sequence permuted [phosphopurine](-) fragment ions. We propose and discuss a potential mechanism for generation of rearranged [phosphopurine](-) and complementary y-B type product ions.

Photodissociation mass spectrometry: new tools for characterization of biological molecules

Photodissociation mass spectrometry combines the ability to activate and fragment ions using photons with the sensitive detection of the resulting product ions by mass spectrometry. This combination affords a versatile tool for characterization of biological molecules. The scope and breadth of photodissociation mass spectrometry have increased substantially over the past decade as new research groups have entered the field and developed a number of innovative applications that illustrate the ability of photodissociation to produce rich fragmentation patterns, to cleave bonds selectively, and to target specific molecules based on incorporation of chromophores. This review focuses on many of the key developments in photodissociation mass spectrometry over the past decade with a particular emphasis on its applications to biological molecules.

Electron transfer followed by collision-induced dissociation (NET-CID) for generating sequence information from backbone-modified oligonucleotide anions

RATIONALE

Oligonucleotides with 2'-modifications and/or phosphorothioate (PS) backbones are prone to undergo limited backbone fragmentation upon ion trap collision-induced dissociation (CID). For better identification and characterization of chemically modified oligonucleotides, a more universal fragmentation method is desirable.

METHODS

Gas-phase dissociation of various 2'-position-modified oligonucleotides and mixed-backbone oligonucleotides (MBOs) has been studied by ion trap CID of the radical anion species formed via electron transfer ion/ion reactions.

RESULTS

For 2'-modified mix-mer radical anions, complete sequence information was generated with non-complementary d/w-ion series, while a/z-ions were observed randomly with relatively low intensity. The 2'-position modification, which has been observed to affect CID patterns of oligonucleotide anions, did not exhibit any observable influence on the dissociation patterns of oligonucleotide radical anions. For MBOs comprised of DNA nucleotides, ion trap CID of even-electron species generated complementary a-B/w-type ions and multiple fragment types at the phosphorothioate (PS) linkages. For MBOs comprised of 2'-OMe-modified nucleotides, only PS bond cleavage was observed for ion trap CID of doubly deprotonated precursor ions. Negative electron transfer reaction with or without supplemental activation of MBOs gave rise to a/d/w-type fragments similar to those of the 2'-modified mix-mers. PS bonds were observed to be more fragile under the electron detachment process, and phosphodiester (PO) bond cleavages were noted upon further collisional activation.

CONCLUSIONS

NET-CID proved to be an efficient method of generating full sequence information for 2'-modifications and/or mixed-backbone oligonucleotides.

Fragmentation of singly, doubly, and triply charged hydrogen deficient peptide radical cations in infrared multiphoton dissociation and electron induced dissociation

Gas phase fragmentation of hydrogen deficient peptide radical cations continues to be an active area of research. While collision induced dissociation (CID) of singly charged species is widely examined, dissociation channels of singly and multiply charged radical cations in infrared multiphoton dissociation (IRMPD) and electron induced dissociation (EID) have not been, so far, investigated. Here, we report on the gas phase dissociation of singly, doubly and triply charged hydrogen deficient peptide radicals, [M + nH]((n+1)+·) (n=0, 1, 2), in MS(3) IRMPD and EID and compare the observed fragmentation pathways to those obtained in MS(3) CID. Backbone fragmentation in MS(3) IRMPD and EID was highly dependent on the charge state of the radical precursor ions, whereas amino acid side chain cleavages were largely independent of the charge state selected for fragmentation. Cleavages at aromatic amino acids, either through side chain loss or backbone fragmentation, were significantly enhanced over other dissociation channels. For singly charged species, the MS(3) IRMPD and EID spectra were mainly governed by radical-driven dissociation. Fragmentation of doubly and triply charged radical cations proceeded through both radical- and charge-driven processes, resulting in the formation of a wide range of backbone product ions including, a-, b-, c-, y-, x-, and z-type. While similarities existed between MS(3) CID, IRMPD, and EID of the same species, several backbone product ions and side chain losses were unique for each activation method. Furthermore, dominant dissociation pathways in each spectrum were dependent on ion activation method, amino acid composition, and charge state selected for fragmentation.

Shedding light on the frontier of photodissociation

The development of new ion activation/dissociation methods is motivated by the need for more versatile ways to characterize structures of ions, especially in the growing arena of biological mass spectrometry in which better tools for determining sequences, modifications, interactions, and conformations of biopolymers are essential. Although most agree that collision-induced dissociation (CID) remains the gold standard for ion activation/dissociation, recent inroads in electron- and photon-based activation methods have cemented their role as outstanding alternatives. This article will focus on the impact of photodissociation, including its strengths and drawbacks as an analytical tool, and its potential for further development in the next decade. Moreover, the discussion will emphasize photodissociation in quadrupole ion traps, because that platform has been used for one of the greatest arrays of new applications over the past decade.

A new approach to IRMPD using selective ion dissociation in a quadrupole ion trap

Infrared multiphoton photodissociation (IRMPD) in a quadrupole ion trap is not selective for a parent ion. Product ions are decreased in abundance by continuous sequential dissociation and may be lost below the low mass cut-off. The IRMPD process is made selective by resonantly exciting trapped ions into an axially offset laser path. Product ions form and collisionally relax out of the laser path to accumulate in the center of the trap. The technique, termed selective broadband (SB) IRMPD, limits sequential dissociation to preserve first generation product ion abundance. The abundances of larger product ions are maximized by completely dissociating the parent ion, but continuous sequential dissociation does not form small product ions below the low mass cut-off associated with conventional IRMPD. Smaller product ions are further increased in abundance in another tandem mass spectrum by performing sequential stages of SB-IRMPD, adjusting the trapping rf amplitude to dissociate larger product ions at the same q(z) range. Thermal assistance is used to perform SB-IRMPD at higher bath gas pressures for increased sensitivity.

Characterization of oligodeoxynucleotides and modifications by 193 nm photodissociation and electron photodetachment dissociation

Ultraviolet photodissociation (UVPD) at 193 nm is compared to collision induced dissociation (CID) for sequencing and determination of modifications of multideprotonated 6-20-mer oligodeoxynucleotides. UVPD at 193 nm causes efficient charge reduction of the deprotonated oligodeoxynucleotides via electron detachment, in addition to extensive backbone cleavages to yield sequence ions of relatively low abundance, including w, x, y, z, a, a-B, b, c, and d ions. Although internal ions populate UVPD spectra, base loss ions from the precursor are absent. Subsequent CID of the charge-reduced oligodeoxynucleotides formed upon electron detachment, in a net process called electron photodetachment dissociation (EPD), results in abundant sequence ions in terms of w, z, a, a-B, and d products, with a marked decrease in the abundance of precursor base loss ions and internal fragments. Complete sequencing was possible for virtually all oligodeoxynucleotides studied. EPD of three modified oligodeoxynucleotides, a methylated oligodeoxynucleotide, a phosphorothioate-modified oligodeoxynucleotide, and an ethylated-oligodeoxynucleotide, resulted in specific and extensive backbone cleavages, specifically, w, z, a, a-B, and d products, which allowed the modification site(s) to be pinpointed to a more specific location than by conventional CID.

Hybrid activation methods for elucidating nucleic acid modifications

Hybrid tandem mass spectrometry (MS/MS) techniques combining electron transfer (ET) and collision activated dissociation (CAD), infrared multiphoton dissociation (IRMPD), or ultraviolet photodissociation (UVPD) were implemented and evaluated for the characterization of a series of oligonucleotides and oligoribonucleotides, including both native single strands and single strands containing platinated, phosphorothioated, and 2'-O-methylated modification sites. ET-IRMPD and ET-UVPD of oligodeoxynucleotides and oligoribonucleotides resulted in rich fragmentation with respect to production of w, a, z, and d ions for DNA, and c, y, w, a-B, d, and z ions for RNA, with many product ions retaining the modification and thus allowing site specific identification. ET-IRMPD caused more extensive secondary dissociation of the ions, in addition to a broader distribution of detectable sequence ions attributed to using a lower mass cutoff. ET-UVPD promoted higher energy fragmentation pathways and created the most diverse MS/MS spectra. The numerous products generated by the hybrid MS/MS techniques resulted in specific and extensive backbone cleavages which allowed the modification sites of multiply modified oligonucleotides to be elucidated.

Increased sequence coverage of thymine-rich oligodeoxynucleotides by infrared multiphoton dissociation compared to collision-induced dissociation

Infrared multiphoton dissociation (IRMPD) of thymine-rich oligodeoxynucleotides in a linear ion-trap mass spectrometer affords far more extensive fragmentation than conventional collision-induced dissociation (CID). For oligodeoxynucleotides containing one non-thymine base, CID results primarily in cleavage on the 3' side of the non-thymine nucleobase, whereas IRMPD results in cleavages between all the nucleobases and thus provides complete sequence coverage. Furthermore, for oligodeoxynucleotides containing a single non-thymine base, it is shown that the full series of diagnostic sequence ions observed in the IRMPD mass spectra arise from secondary dissociation of the two primary products formed from the initial cleavage site located next to the non-thymine base.

Mass spectrometric studies of alkali metal ion binding on thrombin-binding aptamer DNA

The binding sites and consecutive binding constants of alkali metal ions, (M(+) = Na(+), K(+), Rb(+), and Cs(+)), to thrombin-binding aptamer (TBA) DNA were studied by Fourier-transform ion cyclotron resonance spectrometry. TBA-metal complexes were produced by electrospray ionization (ESI) and the ions of interest were mass-selected for further characterization. The structural motif of TBA in an ESI solution was checked by circular dichroism. The metal-binding constants and sites were determined by the titration method and infrared multiphoton dissociation (IRMPD), respectively. The binding constant of potassium is 5-8 times greater than those of other alkali metal ions, and the potassium binding site is different from other metal binding sites. In the 1:1 TBA-metal complex, potassium is coordinated between the bottom G-quartet and two adjacent TT loops of TBA. In the 1:2 TBA-metal complex, the second potassium ion binds at the TGT loop of TBA, which is in line with the antiparallel G-quadruplex structure of TBA. On the other hand, other alkali metal ions bind at the lateral TGT loop in both 1:1 and 1:2 complexes, presumably due to the formation of ion-pair adducts. IRMPD studies of the binding sites in combination with measurements of the consecutive binding constants help elucidate the binding modes of alkali metal ions on DNA aptamer at the molecular level.

Infrared multiphoton dissociation of small-interfering RNA anions and cations

Infrared multiphoton dissociation (IRMPD) on a linear ion trap mass spectrometer is applied for the sequencing of small interfering RNA (siRNA). Both single-strand siRNAs and duplex siRNA were characterized by IRMPD, and the results were compared with that obtained by traditional ion trap-based collision induced dissociation (CID). The single-strand siRNA anions were observed to dissociate via cleavage of the 5' P-O bonds yielding c- and y-type product ions as well as undergo neutral base loss. Full sequence coverage of the siRNA anions was obtained by both IRMPD and CID. While the CID mass spectra were dominated by base loss ions, accounting for approximately 25% to 40% of the product ion current, these ions were eliminated through secondary dissociation by increasing the irradiation time in the IRMPD mass spectra to produce higher abundances of informative sequence ions. With longer irradiation times, however, internal ions corresponding to cleavage of two 5' P-O bonds began to populate the product ion mass spectra as well as higher abundances of [a - Base] and w-type ions. IRMPD of siRNA cations predominantly produced c- and y-type ions with minimal contributions of [a - Base] and w-type ions to the product ion current; the presence of only two complementary series of product ions in the IRMPD mass spectra simplified spectral interpretation. In addition, IRMPD produced high abundances of protonated nucleobases, [G + H](+), [A + H](+), and [C + H](+), which were not detected in the CID mass spectra due to the low-mass cut-off associated with conventional CID in ion traps. CID and IRMPD using short irradiation times of duplex siRNA resulted in strand separation, similar to the dissociation trends observed for duplex DNA. With longer irradiation times, however, the individual single-strands underwent secondary dissociation to yield informative sequence ions not obtained by CID.

Gas-phase chemistry of multiply charged bioions in analytical mass spectrometry

Ion chemistry has long played an important role in molecular mass spectrometry (MS), as it is central to the use of MS as a structural characterization tool. With the advent of ionization methods capable of producing gaseous ions from large biomolecules, the chemistry of gaseous bioions has become a highly active area of research. Gas-phase biomolecule-ion reactions are usually driven by interactions with neutral molecules, photons, electrons, ions, or surfaces. Ion dissociation or transformation into different ion types can be achieved. The types of reaction products observed depend on the characteristics of the ions, the transformation methods, and the time frame of observation. This review focuses on the gas-phase chemistries of ions derived from the electrospray ionization of peptides, proteins, and oligonucleotides, with particular emphasis on their utility in bioanalysis. Various ion-transformation strategies, which further facilitate structural interrogation by converting ions from one type to another, are also summarized.

Identification of fragmentation channels of dinucleotides using deuterium labeling

The fragmentation of the totally deuterated dinucleotide dAT(-) in labile positions (heteroatom-bound hydrogens) was compared for different MS/MS methods: CID, IRMPD, and EID. These experiments allowed us to affirm the coexistence of several fragmentation channels. They can be classified according to the involvement of nonlabile or labile protons in the fragmentation process. Moreover, double resonance experiments were performed in IRMPD and EID. They demonstrated the existence of consecutive fragmentation processes. The probability with which each channel is taken depends on the fragmentation technique used, i.e., the energy and the time scale of the method. The fragmentation channels that involve labile protons requiring peculiar three-dimensional structures are entropically unfavorable and enthalpically favorable. They are more observed in IRMPD and EID. The involvement of labile and, therefore, exchangeable protons in the fragmentation mechanism casts doubt on the use of tandem mass spectrometry to localize incorporated deuteriums in oligonucleotides.

Interactions of sulfur-containing acridine ligands with DNA by ESI-MS

The alkylating proficiency of sulfur-containing mustards may be increased by using an acridine moiety to guide the sulfur mustard to its cellular target. In this study, the interactions of a new series of sulfur-containing acridine ligands, some that also function as alkylating mustards, with DNA were evaluated by electrospray ionization mass spectrometry (ESI-MS). Relative binding affinities were estimated from the ESI-MS data based on the fraction of bound DNA for DNA/acridine mixtures. The extent of binding observed for the series of sulfur-containing acridines was similar, presumably because the intercalating acridine moiety was identical. Upon infrared multi-photon dissociation (IRMPD) of the resulting oligonucleotide/sulfur-containing acridine complexes, ejection of the ligand was the dominant pathway for most of the complexes. However, for AS4, an acridine sulfide mustard, and AN1, an acridine nitrogen mustard, strand separation with the ligand remaining on one of the single strands was observed. At higher irradiation times, a variety of sequence ions were observed, some retaining the AS4/AN1 ligand, which was indicative of covalent binding.

Infrared multiphoton dissociation of peptide cations in a dual pressure linear ion trap mass spectrometer

A dual pressure linear ion trap mass spectrometer was modified to permit infrared multiphoton dissociation (IRMPD) in each of the two cells-the first a high pressure cell operated at nominally 5 x 10(-3) Torr and the second a low pressure cell operated at nominally 3 x 10(-4) Torr. When IRMPD was performed in the high pressure cell, most peptide ions did not undergo significant photodissociation; however, in the low pressure cell peptide cations were efficiently dissociated with less than 25 ms of IR irradiation regardless of charge state. IRMPD of peptide cations allowed the detection of low m/z product ions including the y(1) fragments and immonium ions which are not typically observed by ion trap collision induced dissociation (CID). Photodissociation efficiencies of approximately 100% and MS/MS (tandem mass spectrometry) efficiencies of greater than 60% were observed for both multiply and singly protonated peptides. In general, higher sequence coverage of peptides was obtained using IRMPD over CID. Further, greater than 90% of the product ion current in the IRMPD mass spectra of doubly charged peptide ions was composed of singly charged product ions compared to the CID mass spectra in which the abundances of the multiply and singly charged product ions were equally divided. Highly charged primary product ions also underwent efficient photodissociation to yield singly charged secondary product ions, thus simplifying the IRMPD product ion mass spectra.

Electron Transfer Dissociation of Oligonucleotide Cations

Electron transfer dissociation (ETD) of multi-protonated 6 - 20-mer oligonucleotides and 12- and 14-mer duplexes is compared to collision activated dissociation (CAD). ETD causes efficient charge reduction of the multi-protonated oligonucleotides in addition to limited backbone cleavages to yield sequence ions of low abundance. Subsequent CAD of the charge-reduced oligonucleotides formed upon electron transfer, in a net process termed electron transfer collision activated dissociation (ETcaD), results in rich fragmentation in terms of w, a, z, and d products, with a marked decrease in the abundance of base loss ions and internal fragments. Complete sequencing was possible for nearly all oligonucleotides studied. ETcaD of an oligonucleotide duplex resulted in specific backbone cleavages, with conservation of weaker non-covalent bonds.

Improving IRMPD in a quadrupole ion trap

A focused laser is used to make infrared multiphoton photodissociation (IRMPD) more efficient in a quadrupole ion trap mass spectrometer. Efficient (up to 100%) dissociation at the standard operating pressure of 1 x 10(-3) Torr can be achieved without any supplemental ion activation and with shorter irradiation times. The axial amplitudes of trapped ion clouds are measured using laser tomography. Laser flux on the ion cloud is increased six times by focusing the laser so that the beam waist approximates the ion cloud size. Unmodified peptide ions from 200 Da to 3 kDa are completely dissociated in 2.5-10 ms at a bath gas pressure of 3.3 x 10(-4) Torr and in 3-25 ms at 1.0 x 10(-3) Torr. Sequential dissociation of product ions is increased by focusing the laser and by operating at an increased bath gas pressure to minimize the size of the ion cloud.

Infrared multiphoton dissociation in quadrupole ion traps

The development of new ion activation techniques continues to be a dynamic area of scientific discovery, in part to complement the tremendous innovations in ionization methods that have allowed the mass spectrometric analysis of an enormous array of molecules. Ion activation/dissociation provides key information about ion structures, binding energies, and differentiation of isomers, as well as affording a primary means of identifying compounds in mixtures. Numerous new activation methods have emerged over the past two decades in an effort to develop alternatives to collisional activated dissociation, the gold standard for providing structurally diagnostic fragmentation patterns. Collisional activated dissociation does not always offer sufficiently high or controllable energy deposition, thus rendering it less useful for certain classes of molecules, such as large proteins or macromolecular complexes. Photodissociation is one of the most promising alternatives and is readily implemented in ion trapping and time-of-flight mass spectrometers. Photodissociation generally entails using a laser to irradiate ions with UV, visible, or IR photons, thus resulting in internal energy deposition based on the number and wavelengths of the photons. The activation process can be extremely rapid and efficient, as well as having the potential for high total energy deposition. This review describes infrared multiphoton dissociation in quadrupole ion trap mass spectrometry. A comparison of photodissociation and collisional activated dissociation is covered, in addition to some of the methods to increase photodissociation efficiency. Numerous applications of IRMPD are discussed as well, including ones related to the analysis of drugs, peptides, nucleic acids, and oligosaccharides.

Improved infrared multiphoton dissociation of peptides through N-terminal phosphonite derivatization

A strategy for improving the sequencing of peptides by infrared multiphoton dissociation (IRMPD) in a linear ion trap mass spectrometer is described. We have developed an N-terminal derivatization reagent, 4-methylphosphonophenylisothiocyanate (PPITC), which allows the attachment of an IR-chromogenic phosphonite group to the N-terminus of peptides, thus enhancing their IRMPD efficiencies. After the facile derivatization process, the PPITC-modified peptides require shorter irradiation times for efficient IRMPD and yield extensive series of y ions, including those of low m/z that are not detected upon traditional CID. The resulting IRMPD mass spectra afford more complete sequence coverage for both model peptides and tryptic peptides from cytochrome c. We compare the effectiveness of this derivatization/IRMPD approach to that of a common N-terminal sulfonation reaction that utilizes 4-sulfophenylisothiocyanate (SPITC) in conjunction with CID and IRMPD.

Characterization of oligodeoxynucleotide fragmentation pathways in infrared multiphoton dissociation and electron detachment dissociation by Fourier transform ion cyclotron double resonance

Infrared multiphoton dissociation (IRMPD) is a vibrational excitation tandem mass spectrometric fragmentation method valuable for sequencing of oligonucleotides. For oligodeoxynucleotides, typical product ions correspond to sequence-specific 5' (a-base) and their complementary 3' w-type ions from carbon-oxygen bond cleavage at the 3' position of the deoxyribose from which a nucleobase is lost. Such fragmentation patterns are also observed in collision activated dissociation (CAD). The CAD oligodeoxynucleotide fragmentation mechanism has been characterized in detail. By contrast, fragmentation schemes in IRMPD have not been rigorously established. In this paper, we apply, for the first time, Fourier transform ion cyclotron double resonance (DR) experiments to characterize IRMPD fragmentation pathways of oligodeoxynucleotide anions. Our results suggest that neutral base loss precedes backbone fragmentation but that T-rich oligodeoxynucleotides fragment via a different mechanism, similar to the mechanisms proposed for CAD. We also extend the DR approach to characterize intermediates in electron detachment dissociation of hexamer oligodeoxynucleotides. Here, we found that charge reduced radical precursor ions constitute major intermediates for dT(6), d(GCATAC) and d(GCATGC). Furthermore, (a/z-T) ions (z ions correspond to C-O bond cleavage on the other side of a backbone phosphate group as compared to the formation of a ions) mainly originate from secondary fragmentation of a/z radical ions for the oligodeoxynucleotide dT(6).

Ultraviolet photodissociation at 355 nm of fluorescently labeled oligosaccharides

Ultraviolet photodissociation (UVPD) produces complementary fragmentation to collision-induced dissociation (CID) when implemented for activation of fluorescently labeled oligosaccharide and glycan ions. Reductive amination of oligosaccharides with fluorophore reagents results in efficient photon absorption at 355 nm, producing fragment ions from the nonreducing end that do not contain the appended fluorophore. In contrast to the fragment ions observed upon UVPD (A- and C-type ions), CID produces mainly reducing end fragments retaining the fluorophore (Y-type ions). UVPD affords better isomeric differentiation of both the lacto-N-fucopentaoses series and the lacto-N-difucohexaoses series, but in general, the combination of UVPD and CID offers the most diagnostic elucidation of complex branched oligosaccharides. Four fluorophores yielded similar MS/MS results; however, 6-aminoquinoline (6-AQ), 2-amino-9(10 H)-acridone (AMAC) and 7-aminomethylcoumarin (AMC) afforded more efficient photon absorption and subsequent dissociation than 2-aminobenzamide (2-AB). UVPD also was useful for characterization of glycans released from ribonuclease B and derivatized with 6-AQ. Lastly, electron photodetachment dissociation of oligosaccharides derivatized with 7-amino-1,3-naphthalenedisulfonic acid (AGA) yielded unique cross-ring cleavages similar to those obtained by electron detachment dissociation.

Sequencing and characterization of oligosaccharides using infrared multiphoton dissociation and boronic acid derivatization in a quadrupole ion trap

A simplified method for determining the sequence and branching of oligosaccharides using infrared multiphoton dissociation (IRMPD) in a quadrupole ion trap (QIT) is described. An IR-active boronic acid (IRABA) reagent is used to derivatize the oligosaccharides before IRMPD analysis. The IRABA ligand is designed to both enhance the efficiency of the derivatization reaction and to facilitate the photon absorption process. The resulting IRMPD spectra display oligosaccharide fragments that are formed from primarily one type of diagnostic cleavage, thus making sequencing straightforward. The presence of sequential fragment ions, a phenomenon of IRMPD, permit the comprehensive sequencing of the oligosaccharides studied in a single stage of activation. We demonstrate this approach for two series of oligosaccharides, the lacto-N-fucopentaoses (LNFPs) and the lacto-N-difucohexaoses (LNDFHs).

Probing ligand binding to duplex DNA using KMnO4 reactions and electrospray ionization tandem mass spectrometry

An electrospray ionization tandem mass spectrometry (ESI-MS/MS) strategy employing the thymine-selective KMnO4 oxidation reaction to detect conformational changes and ligand binding sites in noncovalent DNA/drug complexes is reported. ESI-MS/MS is used to detect specific mass shifts of the DNA ions that are associated with the oxidation of thymines. This KMnO4 oxidation/ESI-MS/MS approach is an alternative to conventional gel-based oxidation methods and affords excellent sensitivity while eliminating the reliance on radiolabeled DNA. Comparison of single-strand versus duplex DNA indicates that the duplexes exhibit a significant resistance to the reaction, thus confirming that the oxidation process is favored for unwound or single-strand regions of DNA. DNA complexes containing different drugs including echinomycin, actinomycin-D, ethidium bromide, Hoechst 33342, and cis-C1 were subjected to the oxidation reaction. Echinomycin, a ligand with a bisintercalative binding mode, was found to induce the greatest KMnO4 reactivity, while Hoechst 33342, a minor groove binder, caused no increase in the oxidation of DNA. The oxidation of echinomycin/DNA complexes containing duplexes with different sequences and lengths was also assessed. Duplexes with thymines closer to the terminal ends of the duplex demonstrated a greater increase in the degree of oxidation than those with thymines in the middle of the sequence. Collisional activated dissociation (CAD) and infrared multiphoton dissociation (IRMPD) experiments were used to determine the site of oxidation based on oligonucleotide fragmentation patterns.

Infrared multiphoton dissociation for enhanced de novo sequence interpretation of N-terminal sulfonated peptides in a quadrupole ion trap

Infrared multiphoton dissociation (IRMPD) of N-terminal sulfonated peptides improves de novo sequencing capabilities in a quadrupole ion trap mass spectrometer. Not only does IRMPD promote highly efficient dissociation of the N-terminal sulfonated peptides but also the entire series of y ions down to the y(1) fragment may be detected due to alleviation of the low-mass cutoff problem associated with conventional collisional activated dissociation (CAD) methods in a quadrupole ion trap. Commercial de novo sequencing software was applied for the interpretation of CAD and IRMPD MS/MS spectra collected for seven unmodified peptides and the corresponding N-terminal sulfonated species. In most cases, the additional information obtained by N-terminal sulfonation in combination with IRMPD provided significant improvements in sequence identification. The software sequence tag results were combined with a commercial database searching algorithm to interpret sequence information of a tryptic digest on alpha-casein s1. Energy-variable CAD studies confirmed a 30-40% reduction in the critical energies of the N-terminal sulfonated peptides relative to unmodified peptides. This reduction in dissociation energy facilitates IRMPD in a quadrupole ion trap.

Infrared multiphoton dissociation of duplex DNA/drug complexes in a quadrupole ion trap

Noncovalent duplex DNA/drug complexes formed between one of three 14-base pair non-self-complementary duplexes with variable GC content and one of eight different DNA-interactive drugs are characterized by infrared multiphoton dissociation (IRMPD), and the resulting spectra are compared to conventional collisionally activated dissociation (CAD) mass spectra in a quadrupole ion trap mass spectrometer. IRMPD yielded comparable information to previously reported CAD results in which strand separation pathways dominate for complexes containing the more AT-rich sequences and/or minor groove binding drugs, whereas drug ejection pathways are prominent for complexes containing intercalating drugs and/or duplexes with higher GC base content. The large photoabsorptive cross section of the phosphate backbone at 10.6 mum promotes highly efficient dissociation within short irradiation times (<2 ms at 50 W) or using lower laser powers and longer irradiation times (<15 W at 15 ms), activation times on par with or shorter than standard CAD experiments. This large photoabsorptivity leads to a controllable ion activation method which can be used to produce qualitatively similar spectra to CAD while minimizing uninformative base loss dissociation pathways or instead be tuned to yield a high degree of secondary fragmentation. Additionally, the low-mass cutoff associated with conventional CAD plays no role in IRMPD, resulting in richer MS/MS information in the low m/z region. IRMPD is also used for multiadduct dissociation in order to increase MS/MS sensitivity, and a two-stage IRMPD/IRMPD method is demonstrated as a means to give specific DNA sequence information that would be useful when screening drug binding by mixtures of duplexes.

Amplification of infrared multiphoton dissociation efficiency in a quadruple ion trap using IR-active ligands

A strategy for increasing the efficiency of infrared multiphoton dissociation (IRMPD) in a quadrupole ion trap (QIT) is described. IR-active ligands (IRALs) are incorporated into noncovalent complexes of the type [M2+(analyte) IRAL]+, where M is a transition metal such as copper or cobalt and IRAL is an auxiliary ligand with an IR-active phosphonate functional group. The complexes are formed via self-assembly in solution directly prior to ESI-MS analysis. We demonstrate this new IRMPD approach for the structural characterization of flavonoids. The fragment ions obtained by IRMPD are similar to those obtained by CAD and allow facile isomer differentiation of flavonoids. Fourier transform infrared absorption attenuated total reflectance (FTIR-ATR) and energy-variable CAD experiments indicate that the high IRMPD efficiencies stem from the very large IR absorptivities of the IR-active ligands.

Identification of the adduct between a 4-Aza-3-ene-1,6-diyne and DNA using electrospray ionization mass spectrometry

The interactions between a novel enediyne [1-methyl-2-(phenylethynyl)-3-(3-phenylprop-2-ynyl)-3H-benzimidazolium] (1) and various cytosine-containing oligonucleotides were studied using electrospray ionization mass spectrometry (ESI-MS) in a flow injection analysis mode useful for small volumes. This enediyne ligand, developed as a potential alternative to the highly cytotoxic natural enediynes, some of which have been successfully used as anti-tumor agents, has previously been shown to interact with DNA through frank strand scission as well as via the formation of adducts that lead to 2'-deoxycytidine-specific cleavage. Through ESI-MS, the structures of these adducts were examined and a sequence dependence of the 2'-deoxycytidine-specific cleavage was noted. Collisionally activated dissociation of the observed adducts confirmed the strength of the interactions between the enediyne and DNA and supports a direct linkage between the enediyne and the cytosine nucleobase, likely the result of a nucleophilic attack of the phenylethynyl group by the cytosine amine.

Determination of cooling rates in a quadrupole ion trap

Collisional cooling rates of infrared excited ions are measured in a quadrupole ion trap (QIT) mass spectrometer at different combinations of temperature and pressure. Measurements are carried out by monitoring fragmentation efficiency of leucine enkephalin as a function of irradiation time by an infrared laser after a short excitation and incrementally increasing cooling periods. Cooling rates are observed to be directly related to bath gas pressure and inversely related to bath gas temperature. The cooling rate at typical ion trap operating pressure (1 mTorr) and temperature (room T) is faster than can be measured. At elevated temperature and the lowest pressure used for the studies, the rate of collisional cooling becomes negligible compared to the rate of radiative cooling.

Influence of initial charge state on fragmentation patterns for noncovalent drug/DNA duplex complexes

The charge state-dependent dissociation of various DNA duplexes and drug/duplex complexes has been investigated using collisionally activated dissociation (CAD) in a quadrupole ion trap mass spectrometer (QIT-MS). Several non-self-complementary 14-residue oligonucleotides were employed, in addition to an array of known DNA-interactive ligands, including the intercalators daunomycin and nogalamycin, as well as the minor groove binding agents distamycin, netropsin, 4',6-diamidino-2-phenylindole, and Hoechst 33342. In general, the dissociation pathways exhibited by both the duplexes and the drug/duplex complexes were found to be markedly sensitive to initial charge state. Time- and activation voltage-independent duplex strand separation predominated for higher charge states, which was interpreted to be a result of internal Coulombic repulsion or partial unzipping in the interface, while time- and activation voltage-dependent covalent cleavage predominated for lower charge states. The identity of the drug and the sequence of the duplex were both found to affect the competition between different dissociation processes. The dissociation pathways for the lower charge state complexes are probably more reflective of specific drug-DNA interactions because Coulombic and/or conformational effects are less marked for these precursors.

Charge state-dependent fragmentation of oligonucleotide/metal complexes

Collision-activated dissociation (CAD) has been employed to assess the gas-phase fragmentation behavior of a series of 1:1 oligodeoxynucleotide (ODN):metal complexes over a range of charge states, using several ten-residue ODNs and a wide array of alkali, alkaline earth, and transition metals. For parent species in low to intermediate charge states, complexation with Ca(+2), Sr(+2), or Ba(+2) altered the relative intensity of M-B species, promoting loss of cytosine over loss of guanine. The relative intensities of sequence ions were largely unaffected. This behavior was most prevalent for isomeric sequences with complementary residues at the 5'- and 3'-termini, suggesting that metal complexation may change the gas-phase conformation and/or conformational dynamics for some sequences. In higher charge states, some ODN/Ba(+2) complexes produced abundant fragment ions corresponding to metallated a(n)(-m) species, which are not commonly observed in CAD mass spectra for deprotonated ODNs. The formation of these ions was most favored for complexes between Ba(+2) and ODN sequences with a thymine residue at Position 6. Literature precedent exists for the formation of a(n)(-m) ions from sequences in which covalent modification generates one or more neutral sites along the phosphate backbone. ODN/metal adducts in high charge states possess only a few acidic protons, and the juxtaposition of these neutral phosphate groups near thymine residues and the bound Ba(+2) ion may direct formation of the metallated a(n)(-m) species.

Energy-resolved in-source collisionally induced dissociation for the evaluation of the relative stability of noncovalent complexes in the gas phase

Energy-resolved in-source collisionally induced dissociation (CID) studies on the complexation of alkali metal cations by some crown ethers, nucleic acid bases, and amino acids have been performed. It has been shown that the cone voltage corresponding to the maximum ion abundance (V(c,Imax)) of the breakdown curve is characteristic of a given ion and not influenced by the cone desolvation process or the composition of the solution. Very good agreement of the V(c,Imax) value with the bond strength of the ion has been observed. Determination of the V(c,Imax) values for different ionic species is a useful, simple, and inexpensive way to obtain their relative stabilities in in-source CID conditions.

Infrared multiphoton dissociation (IRMPD) and collisionally activated dissociation of peptides in a quadrupole ion trap with selective IRMPD of phosphopeptides

Dissociation of protonated peptides via infrared multiphoton dissociation (IRMPD) provides more extensive sequence information than is obtained with collisionally activated dissociation (CAD) in a quadrupole ion trap due to the lack of the CAD low m/z cutoff and the ability to form secondary and higher order fragments with the non-resonant photoactivation technique. In addition, IRMPD is shown to be useful for the selective dissociation of phosphopeptides over those which are not phosphorylated because the greater photon absorption efficiency of the phosphorylated peptides leads to their more rapid dissociation. Finally, the selectivity of the IRMPD technique for phosphorylated species in complex mixtures is confirmed with the analysis of a mock peptide mixture and a tryptic digest of alpha-casein.