Estimation of peptide N–Cα bond cleavage efficiency during MALDI‐ISD using a cyclic peptide

Matrix‐assisted laser desorption/ionization in‐source decay (MALDI‐ISD) induces N–C_α bond cleavage via hydrogen transfer from the matrix to the peptide backbone, which produces a c′/z? fragment pair. Subsequently, the z? generates z′ and [z + matrix] fragments via further radical reactions because of the low stability of the z?. In the present study, we investigated MALDI‐ISD of a cyclic peptide. The N–C_α bond cleavage in the cyclic peptide by MALDI‐ISD produced the hydrogen‐abundant peptide radical [M + 2H]⁺? with a radical site on the α‐carbon atom, which then reacted with the matrix to give [M + 3H]⁺ and [M + H + matrix]⁺. For 1,5‐diaminonaphthalene (1,5‐DAN) adducts with z fragments, post‐source decay of [M + H + 1,5‐DAN]⁺ generated from the cyclic peptide showed predominant loss of an amino acid with 1,5‐DAN. Additionally, MALDI‐ISD with Fourier transform‐ion cyclotron resonance mass spectrometry allowed for the detection of both [M + 3H]⁺ and [M + H]⁺ with two ¹³C atoms. These results strongly suggested that [M + 3H]⁺ and [M + H + 1,5‐DAN]⁺ were formed by N–C_α bond cleavage with further radical reactions. As a consequence, the cleavage efficiency of the N–C_α bond during MALDI‐ISD could be estimated by the ratio of the intensity of [M + H]⁺ and [M + 3H]⁺ in the Fourier transform‐ion cyclotron resonance spectrum. Because the reduction efficiency of a matrix for the cyclic peptide cyclo(Arg‐Gly‐Asp‐D‐Phe‐Val) was correlated to its tendency to cleave the N–C_α bond in linear peptides, the present method could allow the evaluation of the efficiency of N–C_α bond cleavage for MALDI matrix development. Copyright © 2016 John Wiley & Sons, Ltd.     

A new method for analysis of disulfide-containing proteins by matrix-assisted laser desorption ionization (MALDI) mass spectrometry

A simple and high-throughput method for the identification of disulfide-containing peptides utilizing peptide-matrix adducts is described. Some commonly used matrices in MALDI mass spectrometry were found to specifically react with sulfhydryl groups within peptide, thus allowing the observation of the peptide-matrix adduct ion [M+n+n′ matrix+H]⁺ or [M+n+n′ matrix+Na]⁺ (n = the number of cysteine residues, n′=1, 2,…, n) in MALDI mass spectra after chemical reduction of disulfide-linked peptides. Among several matrices tested, α-cyano-4-hydroxycinnamic acid (CHCA, molecular mass 189 Da) and α-cyano-3-hydroxycinnamic acid (3-HCCA) were found to be more effective for MALDI analysis of disulfide-containing peptides/proteins. Two reduced cysteines involved in a disulfide bridge resulted in a mass shift of 189 Da per cysteine, so the number of disulfide bonds could then be determined, while for the other matrices (sinapinic acid, ferulic acid, and caffeic acid), a similar addition reaction could not occur unless the reaction was carried out under alkaline conditions. The underlying mechanism of the reaction of the matrix addition at sulfhydryl groups is proposed, and several factors that might affect the formation of the peptide-matrix adducts were investigated. In general, this method is fast, effective, and robust to identify disulfide bonds in proteins/peptides.     

Sodiation as a tool for enhancing the diagnostic value of MALDI‐TOF/TOF‐MS spectra of complex astaxanthin ester mixtures from Haematococcus pluvialis

The microalga Haematococcus pluvialis produces the pigment astaxanthin mainly in esterified form with a multitude of fatty acids, which results in a complex mixture of carotenol mono‐ and diesters. For rapid fingerprinting of these esters, matrix‐assisted laser desorption ionization time of flight mass spectrometry (MALDI‐TOF/TOF‐MS) might be an alternative to traditional chromatographic separation combined with MS. Investigation of ionization and fragmentation of astaxanthin mono‐ and diester palmitate standards in MALDI‐TOF/TOF‐MS showed that sodium adduct parent masses [M + Na]⁺ gave much simpler MS² spectra than radical / protonated [M]^+● / [M + H]⁺ parents. [M + Na]⁺ fragments yielded diagnostic polyene‐specific eliminations and fatty acid neutral losses, whereas [M]^+● / [M + H]⁺ fragmentation resulted in a multitude of non‐diagnostic daughters. For diesters, a benzonium fragment, formed by polyene elimination, was required for identification of the second fatty acid attached to the astaxanthin backbone. Parents were forced into [M + Na]⁺ ionization by addition of sodium acetate, and best signal‐to‐noise ratios were obtained in the 0.1 to 1.0 mM range. This method was applied to fingerprinting astaxanthin esters in a crude H. pluvialis extract. Prior to MALDI‐TOF/TOF‐MS, the extract was fractionated by normal phase Flash chromatography to obtain fractions enriched in mono‐ and diesters and to remove pheophytin a, which compromised monoester signals. All 12 types of all‐trans esterified esters found in LC were identified with MALDI‐TOF/TOF‐MS, with the exception of two minor monoesters. Copyright © 2013 John Wiley & Sons, Ltd.     

Use of a hand-portable gas chromatograph-toroidal ion trap mass spectrometer for self-chemical ionization identification of degradation products related to O-ethyl S-(2-diisopropylaminoethyl) methyl phosphonothiolate (VX)

The chemical warfare agent O-ethyl S-(2-diisopropylaminoethyl) methyl phosphonothiolate (VX) and many related degradation products produce poorly diagnostic electron ionization (EI) mass spectra by transmission quadrupole mass spectrometry. Thus, chemical ionization (CI) is often used for these analytes. In this work, pseudomolecular ([M+H]⁺) ion formation from self-chemical ionization (self-CI) was examined for four VX degradation products containing the diisopropylamine functional group. A person-portable toroidal ion trap mass spectrometer with a gas chromatographic inlet was used with EI, and both fixed-duration and feedback-controlled ionization time. With feedback-controlled ionization, ion cooling (reaction) times and ion formation target values were varied. Evidence for protonation of analytes was observed under all conditions, except for the largest analyte, bis(diisopropylaminoethyl)disulfide which yielded [M+H]⁺ ions only with increased fixed ionization or ion cooling times. Analysis of triethylamine-d₁₅ provided evidence that [M+H]⁺ production was likely due to self-CI. Analysis of a degraded VX sample where lengthened ion storage and feedback-controlled ionization time were used resulted in detection of [M+H]⁺ ions for VX and several relevant degradation products. Dimer ions were also observed for two phosphonate compounds detected in this sample.     

Positive electron impact and chemical ionization mass spectra of some nitramine nitrates

The positive electron impact (EI) and isobutane chemical ionization (CI) mass spectra of six nitramine nitrates were studied with the aid of some accurate mass measurements. In the EI spectra, β fission relative to both the nitramine and nitrate ester is important. In the CI spectra a major ion occurs at [MH – 45]⁺ and was found to be mainly due to [M + 2H ? NO₂]⁺. All of the compounds except N-(2 hydroxyethyl)-N-(2′,4′,6′-trinitrophenyl)nitramine nitrate gave an [MH]⁺ ion. The [MH – 45]⁺ ion in the isobutane CI mass spectra of tetryl is also due to [M + 2H ? NO₂]⁺.     

Adduct ion formation by metal complexes under methane negative chemical ionization conditions

Negative chemical ionization mass spectrometry is used as a probe to examine reactions between hydrocarbon radicals and metal complexes in the gas phase. The methane negative chemical ionization mass spectra of 27 complexes of cobalt(II ), nickel(II ) and copper(II ) in the presence of O₄, O₂N₂ and N₄ donor atom sets are characterized by two dominant series of adduct ions of the form [M + C_nH_2n]^? and [M + C_nH_2n+1]^? at m/z values above the molecular ion, [M]^?. Insertion of the CH radical into the ligand followed by radical/radical recombination and electron capture is proposed as the major mechanism leading to the formation of [M + C_nH_2n]^? adduct ions. A second pathway involves ligand substitution by C_nH_2n+1 radicals concomitant with H elimination and electron capture. Oxidative addition at the metal followed by ionization is suggested as the principal pathway for the formation of [M + C_nH_2n+1]^? adduct ions.     

Study on the redox reactions for organic dyes and S‐nitrosylated peptide in electrospray droplet impact

Reduction of analytes in ionization processes often obscures the determination of molecular structure. The reduction of analytes is found to take place in various desorption/ionization methods such as fast atom bombardment (FAB), secondary ion mass spectrometry (SIMS), matrix‐assisted laser desorption/ionization (MALDI) and desorption ionization on porous silicon (DIOS). To examine the extent of the reduction reactions taking place in electrospray droplet impact (EDI) processes, reduction‐sensitive dyes and S‐nitrosylated peptide were analyzed by EDI. No reduction was observed for methylene blue. While methyl red has a lower reduction potential than methylene blue, the reduction product ions were detected. For S‐nitrosylated peptide, protonated molecule ion [M + H]⁺ and NO‐eliminated molecular ion [M − NO + H]^+• were observed but reduction reactions are largely suppressed in EDI compared with that in MALDI. As such, the analytes examined suffer from little reduction reactions in EDI. Copyright © 2008 John Wiley & Sons, Ltd.     

Electrospray ionization and atmospheric pressure matrix‐assisted laser desorption/ionization mass spectrometry of antioxidants applied in lubricants

The aim of this study was to investigate the utility of ion trap mass spectrometry (ITMS) in combination with the two desorption/ionization methods, electrospray (ESI) and atmospheric pressure matrix‐assisted laser desorption/ionization (AP‐MALDI), for the detection of antioxidants which are applied in lubricants. These experiments should form the base for future investigations of antioxidants in tribologically formed thin layers on the surface of frictional systems. Seventeen different antioxidants were selected out of the group of hindered phenolic and aromatic aminic compounds. Practically all antioxidants could be characterized by positive ion ESI‐ and AP‐MALDI‐ITMS, forming various types/species of molecular ions (e.g. [M]^{+ .} , [M+H]⁺, [M+Na]⁺ or [M–2H+H]⁺). A few compounds could be analyzed by negative ion ESI‐MS, too, but none by negative ion AP‐MALDI‐MS. The influence of target materials in AP‐MALDI‐MS (gold‐ and titanium nitride (TiN)‐covered stainless steel, micro‐diamond‐covered hard metal, hand‐polished and sand‐blasted stainless steel targets) with respect to the molecular ion intensity and type of molecular ion of two selected antioxidants was evaluated. The surface properties are of particular interest because in friction tests different materials with different surface characteristics are used. However, the MS results indicate that optimal target surfaces have to be found for individual antioxidants in AP‐MALDI‐MS but in general smooth surfaces were superior to rough surfaces. Finally the gold‐covered stainless steel MALDI target provided the best mass spectra and was selected for all the antioxidants investigated. Copyright © 2009 John Wiley & Sons, Ltd.     

Selective reagents in chemical ionization mass spectrometry: Tetramethylsilane with ethers

Chemical ionization mass spectra of several ethers obtained with He/(CH₃)₄Si mixtures as the reagent gases contain abundant [M + 73]⁺ adduct ions which identify the relative molecular mass. For the di-n-alkyl ethers, these [M + 73]⁺ ions are formed by sample ion/sample molecule reactions of the fragment ions, [M + 73 ? C_nH_2n]⁺ and [M + 73 ? 2CnH_2n]⁺. Small amounts of [M + H]⁺ ions are also formed, predominantly by proton transfer reactions of the [M + 73 ? 2CnH_2n]⁺ or [(CH₃)₃SiOH₂]⁺ ions with the ethers. The di-s-alkyl ethers give no [M + 73] ⁺ ions, but do give [M + H]⁺ ions, which allow the determination of the relative molecular mass. These [M + H]⁺ ions result primarily from proton transfer reactions from the dominant fragment ion, [(CH₃)₃SiOH₂]⁺ with the ether. Methyl phenyl ether gives only [M + 73]⁺ adduct ions, by a bimolecular addition of the trimethylsilyl ion to the ether, not by the two-step process found for the di-n-alkyl ethers. Ethyl phenyl ether gives [M + 73]⁺ by both the two-step process and the bimolecular addition. Although the mass spectra of the alkyl etherr are temperature-dependent, the sensitivities of the di-alkyl ethers and ethyl phenyl ether are independent of temperature. However, the sensitivity for methyl phenyl ether decreases significantly with increasing temperature.     

Fast atom bombardment (FAB) mass spectrometry of piperidine N-oxide derivatives and free radical quenching under FAB conditions

Mechanisms are proposed for the formation of M⁺, [M + 2H]⁺ and [M + 3H]⁺ ions in the fast atom bombardment (FAB) mass spectra of 4-(2,2,6,6-tetramethyl-1-oxyl)-piperidol and its carboxylates. Free radical quenching induced by the fast atom beam has been observed. The effects of temperature on the radical quenching and of acid on the FAB mass spectra are discussed. The experiment showed that the volatile liquid samples with vapour pressures higher than that for glycerol produced M⁺ even-electron molecular ions, and the FAB mass spectra were similar to the corresponding electron ionization mass spectra. For the solid samples, it was found that the free radicals were quenched during the FAB process so that the mononitroxide and dinitroxide compounds produced [M + 2H]⁺ and [M + 3H]⁺ ions, respectively. Further experiments showed that the intensities and stabilities of [M + 2H]⁺ and [M + 3H]⁺ ions could be improved by addition of acids.     

The unexpected formation of [M − H]+ species during MALDI and dopant‐free APPI MS analysis of novel antineoplastic curcumin analogues

Unusual ionization behavior was observed with novel antineoplastic curcumin analogues during the positive ion mode of matrix‐assisted laser desorption ionization (MALDI) and dopant‐free atmospheric pressure photoionization (APPI). The tested compounds produced an unusual significant peak designated as [M ? H]⁺ ion along with the expected [M + H]⁺ species. In contrast, electrospray ionization, atmospheric pressure chemical ionization and the dopant‐mediated APPI (dopant‐APPI) showed only the expected [M + H]⁺ peak. The [M ? H]⁺ ion was detected with all evaluated curcumin analogues including phosphoramidates, secondary amines, amides and mixed amines/amides. Our experiments revealed that photon energy triggers the ionization of the curcumin analogues even in the absence of any ionization enhancer such as matrix, solvent or dopant. The possible mechanisms for the formation of both [M ? H]⁺ and [M + H]⁺ ions are discussed in this paper. In particular, three proposed mechanisms for the formation of [M ? H]⁺ were evaluated. The first mechanism involves the loss of H₂ from the protonated [M + H]⁺ species. The other two mechanisms include hydrogen transfer from the analyte radical cation or hydride abstraction from the neutral analyte molecule. Copyright © 2014 John Wiley & Sons, Ltd.     

Dehydrogenation and dehalogenation of amines in MALDI‐TOF MS investigated by isotopic labeling

Secondary and tertiary amines have been reported to form [M–H]⁺ that correspond to dehydrogenation in matrix‐assisted laser desorption ionization time of flight mass spectrometry (MALDI‐TOF MS). In this investigation, we studied the dehydrogenation of amines in MALDI‐TOF MS by isotopic labeling. Aliphatic amines were labeled with deuterium on the methylene of an N‐benzyl group, which resulted in the formation of [M–D]⁺ and [M–H]⁺ ions by dedeuteration and dehydrogenation, respectively. This method revealed the proton that was removed. The spectra of most tertiary amines with an N‐benzyl group showed high‐intensity [M–D]⁺ and [M–H]⁺ ion peaks, whereas those of secondary amines showed low‐intensity ion peaks. Ratios between the peak intensities of [M–D]⁺ and [M–H]⁺ greater than 1 suggested chemoselective dehydrogenation at the N‐benzyl groups. The presence of an electron donor group on the N‐benzyl groups enhanced the selectivity. The dehalogenation of amines with an N‐(4‐halobenzyl) group was also observed alongside dehydrogenation. The amino ions from dehalogenation can undergo second dehydrogenation. These results provide the first direct evidence about the position at which dehydrogenation of an amine occurs and the first example of dehalogenation of haloaromatic compounds in MALDI‐TOF MS. These results should be helpful in the structural identification and elucidation of synthetic and natural molecules. Copyright © 2013 John Wiley & Sons, Ltd.     

Electron impact and chemical ionization mass spectra of alkyldiphenylphosphine oxides

In the 70 e V electron impact mass spectra of a series of alkyldiphenylphosphine oxides (R?₂PO, R = Me, Et, n-Pr, i-Pr, n-Bu, i-Bu, t-Bu, neopentyl, n-decyl), molecular ions of low abundance are observed and [M + H]⁺ ions are formed to a small extent at high sample pressures. The major ions include [?₂PO]⁺, [?₂POH]⁺; [?₂CH₂PO]⁺ and [?₂CH₂POH]⁺ which are formed by rearrangement and cleavage processes. The chemical ionization mass spectra obtained with methane and isobutane reagents consist of [M + H]⁺ ions. The proton affinity of R?₂PO was found to be 219 ± 2.5 kcal mol^?1.     

Comparison of ionization behaviors of ring and linear carbohydrates in MALDI-TOFMS

Ionization efficiencies of cyclodextrins and their linear compounds in matrix-assisted laser desorption and ionisation (MALDI) analysis were compared, and differences in the ionization efficiencies of α- and β-cyclodextrins were also studied. The mass spectra showed a series of the [M+cation]⁺ ions but not the [M+H]⁺ ions. Alkali metal salts of Li⁺, Na⁺, K⁺, and Cs⁺ were used as the cationizing agents to enhance the ionization efficiency. Relative ion intensities of the ring compounds (α- and β-cyclodextrins) were much larger than those of the linear ones (maltohexaose and maltoheptaose), and the difference showed an increasing trend with the size of the alkali metal cation. β-Cyclodextrin had higher ionization efficiency than α-cyclodextrin and the difference increased by increasing the size of the alkali metal cation. It was also found that the ionization efficiency was affected by the counter anion of the salt. The higher ionization efficiencies of cyclodextrins were explained with the number of coordination sites and the binding energies.     

Repeller-Induced dissociation of alkyl alcohols in thermospray mass spectrometry

Six alkyl alcohols were studied using thermospray mass Spectrometry. Whereas the dominant ion in the spectrum up to a repeller potential of 120 V was [M + NH₄]⁺, above that potential [M + H]⁺ and fragment ions appeared. The fragments observed were largely due to hydrogen release from alkyl ions ([C_nH_2n+1]⁺ – H2 → [C_nH_2n-1]⁺) and loss of water or some other stable molecule from the same species. The results are compared with those from ionization of the same alcohols under electron impact and photoionization conditions and with results obtained for methanol under thermospray conditions.     

Theoretical and experimental study of the structure and stability of multiply Na-substituted glucose and 2,4,6-trihydroxyacetophenone derivatives

The equilibrium geometric parameters and the energetic and spectroscopic characteristics of low lying conformers for series of polyhydroxyl molecules and ions in which sodium atoms are successively substituted for the hydroxyl hydrogen atoms have been calculated by the density functional theory B3LYP method with the 6−31G* and 6−311+G** basis sets. The glucose derivatives [Glu − nH + nNa] and [Glu − nH + (n + 1)Na]⁺ (n = 1−5) and the 2,4,6-trihydroxyacetophenone derivatives [THAP − nH + nNa] and [THAP − nH + (n + 1)Na]⁺ (n = 1−4) have been considered. The affinities of the neutral [Glu − nH + nNa] and [THAP − nH + nNa] molecules for adding Na⁺ cations, as well as the energies of successive substitution of Na atoms for H atoms in the Glu and THAP molecules and the Glu⁺ and THAP⁺ ions in their reaction with sodium acetate molecules, have been estimated. Computations show that the first substitution of Na for H in ions is slightly exothermic and, presumably, can spontaneously occur under common conditions. Further substitutions are endothermic, but the required energy inputs are small. Therefore, successive substitutions for two, three, or more hydroxyl H atoms in the molecules and ions under consideration are possible at relatively low energy inputs. The computation results and conclusions are compared with the MALDI TOF mass spectral data for Na-substituted glucose and 2,4,6-trihydroxyacetophenone derivatives in the [glucose + CH₃COONa + THAP] system where, in addition to common Glu · Na⁺ and THAP · Na⁺ ion-molecular complexes, multiply substituted positive ions of the [Glu − nH + (n + 1)Na]⁺ (n = 1−4) and [THAP − nH + (n + 1)Na]⁺ (n = 1−3) type have been identified.     

In-source decay and fragmentation characteristics of peptides using 5-aminosalicylic acid as a matrix in matrix-assisted laser desorption/ionization mass spectrometry

The use of 5-aminosalicylic acid (5-ASA) as a new matrix for in-source decay (ISD) of peptides including mono- and di-phosphorylated peptides in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is described. The use of 5-ASA in MALDI-ISD has been evaluated from several standpoints: hydrogen-donating ability, the outstanding sharpness of molecular and fragment ion peaks, and the presence of interference peaks such as metastable peaks and multiply charged ions. The hydrogen-donating ability of several matrices such as α-cyano-4-hydroxycinnamic acid (CHCA), 2,5-dihydroxybenzoic acid (2,5-DHB), 1,5-diaminonaphthalene (1,5-DAN), sinapinic acid (SA), and 5-ASA was evaluated by using the peak abundance of a reduction product [M + 2H + H]⁺ to that of non-reduced protonated molecule [M + H]⁺ of the cyclic peptide vasopressin which contains a disulfide bond (S-S). The order of hydrogendonating ability was 1,5-DAN > 5-ASA > 2,5-DHB > SA = CHCA. The chemicals 1,5-DAN and 5-ASA in particular can be classified as reductive matrices. 5-ASA gave peaks with higher sharpness for protonated molecules and fragment ions than other matrices and did not give any interference peaks such as multiply-protonated ions and metastable ions in the ISD mass spectra of the peptides used. Particularly, 1,5-DAN and 5-ASA gave very little metastable peaks. This indicates that 1,5-DAN and 5-ASA are more “cool” than other matrices. The 1,5-DAN and 5-ASA can therefore be termed “reductive cool” matrix. Further, it was confirmed that ISD phenomena such as N-Cα bond cleavage and reduction of S-S bond is a single event in the ion source. The characteristic fragmentations, which form a− and (a + 2)-series ions, [M + H − 15]⁺, [M + H − 28]⁺, and [M + H − 44]⁺ ions in the MALDI-ISD are described.     

Electron ionization and chemical ionization mass spectra of pyridinium and isoquinolinium ylides

Electron ionization (EI) spectra and both positive and negative chemical ionization (CI) spectra have been obtained for four isoquinolinium ylides and two pyridinium ylides. Electron transfer reactions dominate the CI mass specra. The base peak in negative chemical ionization is the [M]^?· ion, formed by electron capture. In the positive methane CI spectra the molecular ion, [M]^+·, is relatively more intense than [MH]⁺ showing electron transfer to be the main positive ionization process. In the positive ammonia CI spectra, proton transfer to give [MH]⁺ is the main ionization process, but electron transfer is also observed. The EI spectra show fragmentations in which the aromatic nitrogen moiety retains the charge and fragmentation is by loss of radicals or small neutral molecules from the side-chains. Radical driven reactions are proposed to explain these spectra.     

Chemical ionization and collisional activation spectra of α,β-unsaturated nitriles

A study of the chemical ionization (CI) and collisional activation (CA) spectra of a number of α, β-unsaturated nitriles has revealed that the even-electron ions such as [MH]⁺ and [MNH₄]⁺ produced under chemical ionization undergo decomposition by radical losses also. This results in the formation of M ⁺˙ ions from both [MH]⁺ and [MNH₄]⁺ ions. In the halogenated molecules losses of X˙ and HX compete with losses of H˙ and HCN. Elimination of X˙ from [MH]⁺ is highly favoured in the bromoderivative. The dinitriles undergo a substitution reaction in which one of the CN groups is replaced with a hydrogen radical and the resulting mononitrile is ionized leading to [M ? CN + 2H]⁺ under CI(CH₄) or [M ? CN + H + NH₄] and [M ? CN + H + N₂H₇]⁺ under CI(NH₃) conditions.     

Detection of oxygen addition peaks for terpendole E and related indole–diterpene alkaloids in a positive‐mode ESI‐MS

This report describes that a regular positive electrospray ionization mass spectrometry (MS) analysis of terpendoles often causes unexpected oxygen additions to form [M + H + O]⁺ and [M + H + 2O]⁺, which might be a troublesome in the characterization of new natural analogues. The intensities of [M + H + O]⁺ and [M + H + 2O]⁺ among terpendoles were unpredictable and fluctuated largely. Simple electrochemical oxidation in electrospray ionization was insufficient to explain the phenomenon. So we studied factors to form [M + H + O]⁺ and [M + H + 2O]⁺ using terpendole E and natural terpendoles together with some model indole alkaloids. Similar oxygen addition was observed for 1,2,3,4‐tetrahydrocyclopent[b]indole, which is corresponding to the substructure of terpendole E. In tandem MS experiments, a major fragment ion at m/z 130 from protonated terpendole E was assigned to the substructure containing indole. When the [M + H + O]⁺ was selected as a precursor ion, the ion shifted to m/z 146. The same 16 Da shift of fragments was also observed for 1,2,3,4‐tetrahydrocyclopent[b]indole, indicating that the oxygen addition of terpendole E took place at the indole portion. However, the oxygen addition was absent for some terpendoles, even whose structure resembles terpendole E. The breakdown curves characterized the tandem MS features of terpendoles. Preferential dissociation into m/z 130 suggested the protonation tendency at the indole site. Terpendoles that are preferentially protonated at indole tend to form oxygen addition peaks, suggesting that the protonation feature contributes to the oxygen additions in some degrees. © 2014 The Authors. Journal of Mass Spectrometry published by John Wiley & Sons, Ltd.