‘Fixed charge’ chemical derivatization and data dependant multistage tandem mass spectrometry for mapping protein surface residue accessibility

Protein surface accessible residues play an important role in protein folding, protein-protein interactions and protein-ligand binding. However, a common problem associated with the use of selective chemical labeling methods for mapping protein solvent accessible residues is that when a complicated peptide mixture resulting from a large protein or protein complex is analyzed, the modified peptides may be difficult to identify and characterize amongst the largely unmodified peptide population (i.e., the ‘needle in a haystack’ problem). To address this challenge, we describe here the development of a strategy involving the synthesis and application of a novel ‘fixed charge’ sulfonium ion containing lysine-specific protein modification reagent, S,S′-dimethylthiobutanoylhydroxysuccinimide ester (DMBNHS), coupled with capillary HPLC-ESI-MS, automated CID-MS/MS, and data-dependant neutral loss mode MS³ in an ion trap mass spectrometer, to map the surface accessible lysine residues in a small model protein, cellular retinoic acid binding protein II (CRABP II). After reaction with different reagent:protein ratios and digestion with Glu-C, modified peptides are selectively identified and the number of modifications within each peptide are determined by CID-MS/MS, via the exclusive neutral loss(es) of dimethylsulfide, independently of the amino acid composition and precursor ion charge state (i.e., proton mobility) of the peptide. The observation of these characteristic neutral losses are then used to automatically ‘trigger’ the acquisition of an MS³ spectrum to allow the peptide sequence and the site(s) of modification to be characterized. Using this approach, the experimentally determined relative solvent accessibilities of the lysine residues were found to show good agreement with the known solution structure of CRABP II.     

Analysis of O-glucuronide conjugates in urine by electrospray ion trap mass spectrometry

The application of electrospray ionization (ESI) ion trap mass spectrometry in the characterization of O-glucuronide conjugates of some drugs in urine is described. The conjugated metabolites formed in rabbit and human were separated by reversed-phase high-performance liquid chromatography (HPLC) and characterized by multi-stage mass spectrometry (MSⁿ) experiments in negative ion mode. The ESI mass spectra showed a deprotonated molecule [M–H]^–, which was chosen as precursor ion. Collision-induced dissociation (CID) of [M–H]^– in MSⁿ experiments resulted in the appearance of glucuronate ‘fingerprint’ ions at m/z 175 and 113 as well as prominent aglycone ions which were the same as those produced from authentic specimens. This information can be used to identify this type of compound directly without the need for derivatization or hydrolysis of enzymes, providing a rapid and specific method for guiding the isolation and characterization of similar compounds in complex matrices with LC/MS. Received: 25 January 1999 / Revised: 19 April 1999 / Accepted: 13 May 1999     

Enhanced characterization of singly protonated phosphopeptide ions by femtosecond laser-induced ionization/dissociation tandem mass spectrometry (fs-LID-MS/MS)

To develop an improved understanding of the regulatory role that post-translational modifications (PTMs) involving phosphorylation play in the maintenance of normal cellular function, tandem mass spectrometry (MS/MS) strategies coupled with ion activation techniques such as collision-induced dissociation (CID) and electron-transfer dissociation (ETD) are typically employed to identify the presence and site-specific locations of the phosphate moieties within a given phosphoprotein of interest. However, the ability of these techniques to obtain sufficient structural information for unambiguous phosphopeptide identification and characterization is highly dependent on the ion activation method employed and the properties of the precursor ion that is subjected to dissociation. Herein, we describe the application of a recently developed alternative ion activation technique for phosphopeptide analysis, termed femtosecond laser-induced ionization/dissociation (fs-LID). In contrast to CID and ETD, fs-LID is shown to be particularly suited to the analysis of singly protonated phosphopeptide ions, yielding a wide range of product ions including a, b, c, x, y, and z sequence ions, as well as ions that are potentially diagnostic of the positions of phosphorylation (e.g., ‘a _n+1–98’). Importantly, the lack of phosphate moiety losses or phosphate group ‘scrambling’ provides unambiguous information for sequence identification and phosphorylation site characterization. Therefore, fs-LID-MS/MS can serve as a complementary technique to established methodologies for phosphoproteomic analysis.     

Quantification of Competing H3PO4 Versus HPO3 + H2O Neutral Losses from Regioselective 18O-Labeled Phosphopeptides

Abundant neutral losses of 98 Da are often observed upon ion trap CID-MS/MS of protonated phosphopeptide ions. Two competing fragmentation pathways are involved in this process, namely, the direct loss of H₃PO₄ from the phosphorylated residue and the combined losses of HPO₃ and H₂O from the phosphorylation site and from an additional site within the peptide, respectively. These competing pathways produce product ions with different structures but the same m/z values, potentially limiting the utility of CID-MS³ for phosphorylation site localization. To quantify the relative contributions of these pathways and to determine the conditions under which each pathway predominates, we have examined the ion trap CID-MS/MS fragmentation of a series of regioselective ¹⁸O-phosphate ester labeled phosphopeptides prepared using novel solution-phase amino acid synthesis and solid-phase peptide synthesis methodologies. By comparing the intensity of the –100 Da (–H₃PO₃ ¹⁸O) versus –98 Da (–[HPO₃ + H₂O]) neutral loss product ions formed upon MS/MS, quantification of the two pathways was achieved. Factors that affect the extent of formation of the competing neutral losses were investigated, with the combined loss pathway predominantly occurring under conditions of limited proton mobility, and with increased combined losses observed for phosphothreonine compared with phosphoserine-containing peptides. The combined loss pathway was found to be less dominant under ion activation conditions associated with HCD-MS/MS. Finally, the contribution of carboxylic acid functional groups and backbone amide bonds to the water loss in the combined loss fragmentation pathway was determined via methyl esterification and by examination of a phosphopeptide lacking side-chain hydroxyl groups.

Gas-phase fragmentation characteristics of benzyl-aminated lysyl-containing tryptic peptides

The fragmentation characteristics of peptides derivatized at the side-chain ε-amino group of lysyl residues via reductive amination with benzaldehyde have been examined using collision-induced dissociation (CID) tandem mass spectrometry. The resulting MS/MS spectra exhibit peaks representing product ions formed from two independent fragmentation pathways. One pathway results in backbone fragmentation and commonly observed sequence ion peaks. The other pathway corresponds to the unsymmetrical, heterolytic cleavage of the C_ζ-N_ε bond that links the benzyl derivative to the side-chain lysyl residue. This results in the elimination of the derivative as a benzylic or tropylium carbocation and a (n − l)⁺-charged peptide product (where n is the precursor ion charge state). The frequency of occurrence of the elimination pathway increases with increasing charge of the precursor ion. For the benzylmodified tryptic peptides analyzed in this study, peaks representing products from both of these pathways are observed in the MS/MS spectra of doubly-charged precursor ions, but the carbocation elimination pathway occurs almost exclusively for triply-charged precursor ions. The experimental evidence presented herein, combined with molecular orbital calculations, suggests that the elimination pathway is a charge-directed reaction contingent upon protonation of the secondary ε-amino group of the benzyl-derivatized lysyl side chain. If the secondary ε-amine is protonated, the elimination of the carbocation is observed. If the precursor is not protonated at the secondary ε-amine, backbone fragmentation persists. The application of appropriately substituted benzyl analogs may allow for selective control over the relative abundance of product ions generated from the two pathways.     

Highly specific capture and direct MALDI-MS analysis of phosphorylated peptides using novel multifunctional chitosan-GMA-IDA-Fe (III) nanosphere

In this study, we describe a method for highly specific enrichment of phosphopeptides with multifunctional chitosan–glycidyl methacrylate (GMA)–iminodiacetic acid (IDA)–Fe (III) nanospheres for direct analysis by matrix-assisted laser desorption–ionization mass spectrometry (MALDI-MS). This is the first time that chitosan has been used to create nanospheres support material for selective enrichment of phosphopeptides by modification with GMA, derivatization with IDA, and loading with Fe (III) ions. Chitosan-GMA-IDA-Fe (III) nanospheres with a diameter of 20 to 100 nm have multifunctional chemical moieties which confer unique properties, good dispersibility in highly acidic binding buffers, as well as good biocompatibility and chemical stability which improves their specific interaction with phosphopeptides using various types of acid binding buffers. The process of enrichment is very simple, quick, efficient, and specific. Its high specificity and efficiency for purification of phosphopeptides is reflected in the very low and substoichiometric amounts of phosphopeptides which can be detected, in quantities as low as 1:3,000 M ratios. Compared with other state-of the-art technologies such as the use of conventional Fe³⁺-IMAC and TiO₂, these chitosan nanosphere techniques show superior specificity and sensitivity. Moreover, the resultant chitosan-GMA-IDA-Fe³⁺ nanosphere-absorbed phosphopeptides can be either directly analyzed by MALDI-TOF MS analysis or eluted and further analyzed by nano-LC-MS/MS.     

Zirconium oxide aerogel for effective enrichment of phosphopeptides with high binding capacity

In this study, zirconium oxide (ZrO₂) aerogel was synthesized via a green sol–gel approach, with zirconium oxychloride, instead of the commonly used alkoxide with high toxicity, as the precursor. With such material, phosphopeptides from the digests of 4 pmol of β-casein with the coexistence of 100 times (mol ratio) BSA could be selectively captured, and identified by MALDI-TOF MS. Due to the large surface area (416.0 m² g⁻¹) and the mesoporous structure (the average pore size of 10.2 nm) of ZrO₂ aerogel, a 20-fold higher loading capacity for phosphopeptide, YKVPQLEIVPN[pS]AEER (MW 1952.12), was obtained compared to that of commercial ZrO₂ microspheres (341.5 vs. 17.87 mg g⁻¹). The metal oxide aerogel was further applied in the enrichment of phosphopeptides from 100 ng nonfat milk, and 17 phosphopeptides were positively identified, with a 1.5-fold improvement in phosphopeptide detection compared with previously reported results. These results demonstrate that ZrO₂ aerogel can be a powerful enrichment material for phosphoproteome study.     

On the Preparation of Ni–La Supported on Silica by Sol-gel Process via Propionates

Ni–La/SiO₂ catalysts were prepared by using a new metal organic precursor M(OC₃H₇)_n, dissolved in organic solvent, hydrolysed and finally condensed to form inorganic polymers containing M–O–M or M–(μOH)–M linkages. An optimal distribution of both the active phase ‘Ni’ and the promoter ‘La₂O₃’ was ensured by addition of their corresponding salts, previously dissolved in propionic acid, to a silica solution prior to gelation. After drying under vacuum the precursor was submitted to thermal treatment in air at 600°C with a heating rate of 1°C min^–1. The precursors and the corresponding catalysts were characterised by various techniques (TG-DTA, XRD, FTIR, TEM, BET and porosimetry) and tested for methane dry reforming. This revised version was published online in August 2006 with corrections to the Cover Date.     

Analysis of selective androgen receptor modulators by gas chromatography-microchip atmospheric pressure photoionization-mass spectrometry

A gas chromatography-microchip atmospheric pressure photoionization-mass spectrometric (GC-μAPPI-MS) method was developed and used for the analysis of three 2-quinolinone-derived selective androgen receptor modulators (SARMs). SARMs were analyzed from spiked urine samples, which were hydrolyzed and derivatized with N-methyl-N-(trimethylsilyl)trifluoroacetamide before analysis. Trimethylsilyl derivatives of SARMs formed both radical cations (M^+•) and protonated molecules ([M + H]⁺) in photoionization. Better signal-to-noise ratios (S/N) were obtained in MS/MS analysis using the M^+• ions as precursor ions than using the [M + H]⁺ ions, and therefore the M^+• ions were selected for the precursor ions in selected reaction monitoring (SRM) analysis. Limits of detection (LODs) with the method ranged from 0.01 to 1 ng/mL, which correspond to instrumental LODs of 0.2–20 pg. Limits of quantitation ranged from 0.03 to 3 ng/mL. The mass spectrometric response to the analytes was linear (R ≥ 0.995) from the LOQ concentration level up to 100 ng/mL concentration, and intra-day repeatabilities were 5%–9%. In addition to the GC-μAPPI-MS study, the proof-of-principle of gas chromatography-microchip atmospheric pressure chemical ionization-Orbitrap MS (GC-μAPCI-Orbitrap MS) was demonstrated.     

Synthesis and characterization of Co<Subscript>0.8</Subscript>Zn<Subscript>0.2</Subscript>Fe<Subscript>2</Subscript>O<Subscript>4</Subscript> nanoparticles

Cobalt zinc ferrite, Co_0.8Zn_0.2Fe₂O₄, nanoparticles have been synthesized via autocatalytic decomposition of the precursor, cobalt zinc ferrous fumarato hydrazinate. The X-ray powder diffraction of the ‘as prepared’ oxide confirms the formation of single phase nanocrystalline cobalt zinc ferrite nanoparticles. The thermal decomposition of the precursor has been studied by isothermal, thermogravimetric and differential thermal analysis. The precursor has also been characterized by FTIR, and chemical analysis and its chemical composition has been determined as Co_0.8Zn_0.2Fe₂(C₄H₂O₄)₃·6N₂H_4. The Curie temperature of the ‘as-prepared oxide’ was determined by AC susceptibility measurements.     

Liquid chromatography/tandem mass spectrometric analysis of 7,10‐dihydroxyoctadecenoic acid,its isotopomers,and other 7,10‐dihydroxy fatty acids formed by Pseudomonas aeruginosa 42A2

Pseudomonas aeruginosa is an opportunistic pathogen, which oxidizes oleic acid to 7(S),10(S)‐dihydroxy‐8(E)‐octadecenoic acid (7,10‐(OH)₂‐18:1) of biological and industrial interest. Electrospray tandem mass spectrometric (MS/MS) analysis of hydroxylated fatty acids usually generates characteristic fragments containing the carboxylate anion and formed by α‐cleavage at the oxidized carbon. These fragments indicate the positions of the hydroxyl group. In contrast, liquid chromatography (LC)/MS/MS analysis of 7,10‐(OH)₂‐18:1 yielded a series of other ions with structural information. To study the fragmentation mechanism, we prepared ²H‐ and ¹⁸O‐labeled isotopomers. We also performed MS³ analysis of the major ions, and for comparison we generated the corresponding 7,10‐dihydroxy metabolites of 16:1n‐7, 18:2n‐6, and 20:1n‐11 with a protein extract of P. aeruginosa. The MS/MS spectra of 7,10‐(OH)₂‐18:1 and its isotopomers, 7,10‐(OH)₂‐16:1, and 7,10‐(OH)₂‐20:1, contained a series of prominent fragments that all hold the omega end. The 8,9‐double bond was not essential for this fragmentation, as 7,10‐(OH)₂‐18:0, and its isotopomers, formed essentially the same fragments in the lower mass range. In contrast, 7,10‐dihydroxy‐8(E),12(Z)‐octadecadienoic acid (7,10‐(OH)₂‐18:2) fragmented by α‐cleavage at the oxidized carbons with formation of carboxylate anions. Our results demonstrate that C₁₆–C₂₀ fatty acids with a 7,10‐dihydroxy‐8(E) functionality undergo charge‐driven fragmentation after charge migration to the ω‐end, whereas the main ions of 7,10‐(HO)₂‐18:2 retain charge at the carboxyl group. Copyright © 2010 John Wiley & Sons, Ltd.     

Phosphorylated serine and threonine residues promote site‐specific fragmentation of singly charged,arginine‐containing peptide ions

In order to investigate gas‐phase fragmentation reactions of phosphorylated peptide ions, matrix‐assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) tandem mass (MS/MS) spectra were recorded from synthetic phosphopeptides and from phosphopeptides isolated from natural sources. MALDI‐TOF/TOF (TOF: time‐of‐flight) spectra of synthetic arginine‐containing phosphopeptides revealed a significant increase of y ions resulting from bond cleavages on the C‐terminal side of phosphothreonine or phosphoserine. The same effect was found in ESI‐MS/MS spectra recorded from the singly charged but not from the doubly charged ions of these phosphopeptides. ESI‐MS/MS spectra of doubly charged phosphopeptides containing two arginine residues support the following general fragmentation rule: Increased amide bond cleavage on the C‐terminal side of phosphorylated serines or threonines mainly occurs in peptide ions which do not contain mobile protons. In MALDI‐TOF/TOF spectra of phosphopeptides displaying N‐terminal fragment ions, abundant b–H₃PO₄ ions resulting from the enhanced dissociation of the pSer/pThr–X bond were detected (X denotes amino acids). Cleavages at phosphoamino acids were found to be particularly predominant in spectra of phosphopeptides containing pSer/pThr–Pro bonds. A quantitative evaluation of a larger set of MALDI‐TOF/TOF spectra recorded from phosphopeptides indicated that phosphoserine residues in arginine‐containing peptides increase the signal intensities of the respective y ions by almost a factor of 3. A less pronounced cleavage‐enhancing effect was observed in some lysine‐containing phosphopeptides without arginine. The proposed peptide fragmentation pathways involve a nucleophilic attack by phosphate oxygen on the carbon center of the peptide backbone amide, which eventually leads to cleavage of the amide bond. Copyright © 2009 John Wiley & Sons, Ltd.     

Activated Ion ETD Performed in a Modified Collision Cell on a Hybrid QLT-Oribtrap Mass Spectrometer

We describe the implementation and characterization of activated ion electron transfer dissociation (AI-ETD) on a hybrid QLT-Orbitrap mass spectrometer. AI-ETD was performed using a collision cell that was modified to enable ETD reactions, in addition to normal collisional activation. The instrument manifold was modified to enable irradiation of ions along the axis of this modified cell with IR photons from a CO₂ laser. Laser power settings were optimized for both charge (z) and mass to charge (m/z) and the instrument control firmware was updated to allow for automated adjustments to the level of irradiation. This implementation of AI-ETD yielded 1.6-fold more unique identifications than ETD in an nLC-MS/MS analysis of tryptic yeast peptides. Furthermore, we investigated the application of AI-ETD on large scale analysis of phosphopeptides, where laser power aids ETD, but can produce b- and y-type ions because of the phosphoryl moiety’s high IR adsorption. nLC-MS/MS analysis of phosphopeptides derived from human embryonic stem cells using AI-ETD yielded 2.4-fold more unique identifications than ETD alone, demonstrating a promising advance in ETD sequencing of PTM containing peptides.

The nature of collision-induced dissociation processes of doubly protonated peptides: comparative study for the future use of matrix-assisted laser desorption/ionization on a hybrid quadrupole time-of-flight mass spectrometer in proteomics.

Comparative MS/MS studies of singly and doubly charged electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) precursor peptide ions are described. The spectra from these experiments have been evaluated with particular emphasis on the data quality for subsequent data processing and protein/amino acid sequence identification. It is shown that, once peptide ions are formed by ESI or MALDI, their charge state, as well as the collision energy, is the main parameter determining the quality of collision-induced dissociation (CID) MS/MS fragmentation spectra of a given peptide. CID-MS/MS spectra of singly charged peptides obtained on a hybrid quadrupole orthogonal time-of-flight mass spectrometer resemble very closely spectra obtained by matrix-assisted laser desorption/ionization post-source decay time-of-flight mass spectrometry (MALDI-PSD-TOFMS). On the other hand, comparison of CID-MS/MS spectra of either singly or doubly charged ion species shows no dependence on whether ions have been formed by ESI or MALDI. This observation confirms that, at the time of precursor ion selection, further mass analysis is effectively decoupled from the desorption/ionization event. Since MALDI ions are predominantly formed as singly charged species and ESI ions as doubly charged, the associated difference in the spectral quality of MS/MS spectra as described here imposes direct consequences on data processing, database searching using ion fragmentation data, and de novo sequencing when ionization techniques are changed.     

Synthesis, Crystal Structure, Photophysical Properties, and DFT Calculations of a Bis(tetrathia-calix[4]arene) Tetracadmium Complex

Abstract  

Thiacalix[4]arenes are a unique family of polydentate ligands that offer a combination of four soft sulfur atoms together with four hard phenol oxygen atoms for binding to metal ions. In this study, the tetranuclear cadmium (II) complex Cd₄^II(tca)₂·1.5CH₂Cl₂ (tca⁴⁻ = tetra-anionic p-tert-butylthiacalix[4]arene) (1) was synthesized by reaction of a deprotonated p-tert-butylthiacalix[4]arene and various Cd^II salts. The structure of 1 was established by single crystal X-ray diffraction analysis. The neutral complex 1 contains a square arrangement of four cadmium (II) ions sandwiched between two tca⁴⁻ ligands that have a ‘cone’ conformation similar to that of the free ligand. The absorption and emission properties of the free ligand H₄tca and complex 1 have been recorded and explained by DFT calculations of the molecular orbitals and electronic transitions between them.     

Charge Reversal Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

We report the first charge reversal experiments performed by tandem-in-time rather than tandem-in-space MS/MS. Precursor odd-electron anions from fullerene C₆₀, and even-electron ions from 2,7-di-tert-butylfluorene-9-carboxylic acid and 3,3′-bicarbazole were converted into positive product ions (^–CR⁺) inside the magnet of a Fourier transform ion cyclotron resonance mass spectrometer. Charge reversal was activated by irradiating precursor ions with high energy electrons or UV photons: the first reported use of those activation methods for charge reversal. We suggest that high energy electrons achieve charge reversal in one step as double electron transfer, whereas UV-activated ^–CR⁺ takes place stepwise through two single electron transfers and formally corresponds to a neutralization-reionization (^–NR⁺) experiment.      

Poly(2-methoxyphenylene vinylene): Synthesis,electrical conductivity,and control of electronic properties

Poly(2-methoxyphenylene vinylene) has been synthesized by a four step reaction sequence beginning with the bromination of 2,5-dimethylanisole and proceeding to the formation of an intermediate sulfonium salt precursor polymer. The infrared and UV-visible spectra of the PPV derivative asymmetrically substituted on the phenyl ring are presented. Films of poly(2-methoxyphenylene vinylene) can be doped with iodine to give a conductivity of 1 S cm^?1. Films doped with AsF₅ exhibited activated charge transport behavior with room temperature conductivities of about 100 S cm^?1.     

Tandem mass spectrometry of low solubility polyamides

The structural characterization of polyamides (PA) was achieved by tandem mass spectrometry (MS/MS) with a laser induced dissociation (LID) strategy. Because of interferences for precursor ions selection, two chemical modifications of the polymer end groups were proposed as derivatization strategies. The first approach, based on the addition of a trifluoroacetic acid (TFA) molecule, yields principally to complementary b_n and y_n product ions. This fragmentation types, analogous to those obtained with peptides or other PA, give only poor characterization of polymer end-groups [1]. A second approach, based on the addition of a basic diethylamine (DEA), permits to fix the charge and favorably direct the fragmentation. In this case, b_n ions were not observed. The full characterization of ω end group structure was obtained, in addition to the expected y_n and consecutive fragment ions.     

Synthesis and characterization of Ni<Subscript>0.6</Subscript>Zn<Subscript>0.4</Subscript>Fe<Subscript>2</Subscript>O<Subscript>4</Subscript> nano-particles obtained by auto catalytic thermal decomposition of carboxylato-hydrazinate complex

Ni_0.6Zn_0.4Fe₂O₄ nano-particles have been synthesized by self-propagating auto-combustion of nickel zinc ferrous fumarato-hydrazinate complex. The precursor complex has been characterized by chemical analysis, IR, AAS, thermal analysis and isothermal mass loss studies. The precursor on ignition undergoes self-propagating auto combustion to give Ni_0.6Zn_0.4Fe₂O₄. The X-ray diffraction studies confirmed the single phase formation of nano-size ‘as synthesized’ Ni_0.6Zn_0.4Fe₂O₄. TEM observation showed the average particle size to be 20 nm. Infrared and magnetization studies were also carried out on the ‘as synthesized’ Ni_0.6Zn_0.4Fe₂O₄. The lower value of saturation magnetization and higher Curie temperature of ‘as synthesized’ ferrite also hint at the nano size nature.     

Identification of isobaric product ions in electrospray ionization mass spectra of fentanyl using multistage mass spectrometry and deuterium labeling

Isobaric product ions cannot be differentiated by exact mass determinations, although in some cases deuterium labeling can provide useful structural information for identifying isobaric ions. Proposed fragmentation pathways of fentanyl were investigated by electrospray ionization ion trap mass spectrometry coupled with deuterium labeling experiments and spectra of regiospecific deuterium labeled analogs. The major product ion of fentanyl under tandem mass spectrometry (MS/MS) conditions (m/z 188) was accounted for by a neutral loss of N‐phenylpropanamide. 1‐(2‐Phenylethyl)‐1,2,3,6‐tetrahydropyridine (1) was proposed as the structure of the product ion. However, further fragmentation (MS³) of the fentanyl m/z 188 ion gave product ions that were different from the product ion in the MS/MS fragmentation of synthesized 1, suggesting that the m/z 188 product ion from fentanyl includes an isobaric structure different from the structure of 1. MS/MS fragmentation of fentanyl in deuterium oxide moved one of the isobars to 1 Da higher mass, and left the other isobar unchanged in mass. Multistage mass spectral data from deuterium‐labeled proposed isobaric structures provided support for two fragmentation pathways. The results illustrate the utility of multistage mass spectrometry and deuterium labeling in structural assignment of isobaric product ions. Copyright © 2010 John Wiley & Sons, Ltd.