Does the reagent gas influence collisional activation when performing in situ chemical ionization with an ion trap mass spectrometer?

Users of ion trap mass spectrometers frequently develop methods that associate chemical ionization with tandem mass spectrometry detection. With apparatus using internal ionization, the chemical reagent is present in the trap during the collision induced dissociation (CID) step and one may wonder if the reagent influences the fragmentation ratios in MS/MS. We report a comparison of the fragmentation ratios of protonated molecules when using the most common reagents (methane, ammonia, methanol, acetonitrile, isobutane) for performing in situ chemical ionization. Four molecules were chosen in the medical field to serve as models: alprazolam, diazepam, flunitrazepam and acetaminophen. In the non-resonant CID mode, the influence of the reagent mass is clearly seen in spite of its low partial pressure in the ion trap; the reagent acts as a "heavy target": the degree of fragmentation increases with the molecular weight of the reagent. In the resonant CID mode, there is no evident correlation between the fragmentation ratio of MH(+) ions and the nature of the CI reagent; a slight shift of the secular frequency of the precursor ion, which tends to reduce the CID efficiency, could compensate for the "heavy target" effect underscored in the non-resonant mode.     

Instrument dependence of electrospray ionization and tandem mass spectrometric fragmentation of the gingerols

The gingerols, including [6]-, [8]-, and [10]-gingerols, a series of chemical homologs differentiated by the length of their unbranched alkyl chains, have been identified as major active components in fresh ginger rhizome. The purpose of this study was to investigate the utility of ion trap liquid chromatography/tandem mass spectrometry (LC/MS/MS) as an online tool to identify and quantify these compounds in raw or processed ginger rhizome samples. Negative mode electrospray ionization (ESI) was used in MS, MS/MS and MS(n) experiments in quadrupole ion trap instruments from two different manufacturers and in high-resolution and accurate mass MS and MS/MS experiments in a Fourier transform ion cyclotron resonance mass spectrometer to elucidate the ionization and fragmentation mechanisms of these compounds in these instruments. Positive mode ESI, which generated many more fragment ions in full scan MS even under gentle ionization conditions, was also used in LC/MS and MS/MS experiments and in direct infusion MS and MS/MS experiments. Consistent and predictable ionization and fragmentation behaviors were observed for all gingerols when analyzed in the same instrument. Instruments from different manufacturers, however, had different ionization mechanisms. The major difference between instruments was their ability to form covalent dimer adducts of the gingerols. Subsequent fragmentation patterns of the precursor ions were essentially identical. These results clearly demonstrate that LC/MS instruments produce data that cannot necessarily be replicated in other laboratories, especially if those laboratories do not have the same instrument model from the same manufacturer. This presents major problems for metabolite target analysis, metabolic profiling and metabolomics investigations, which would benefit from LC/MS mass spectrum libraries as they do from GC/MS mass spectrum libraries, because such libraries may not be valid across platforms.     

Atmospheric pressure laser desorption/chemical ionization mass spectrometry: a new ionization method based on existing themes

We have designed and constructed an atmospheric pressure laser desorption/chemical ionization (AP-LD/CI) source that utilizes a laser pulse to desorb intact neutral molecules, followed by chemical ionization via reagent ions produced by a corona discharge. This source employs a heated capillary atmospheric pressure inlet coupled to a quadrupole ion trap mass spectrometer and allows sampling under normal ambient air conditions. Preliminary results demonstrate that this technique provides approximately 150-fold increase in analyte ions compared to the ion population generated by atmospheric pressure infrared matrix-assisted laser desorption/ionization (AP-IR-MALDI).     

Substituent effects on the gas-phase fragmentation reactions of sulfonium ion containing peptides

The multistage mass spectrometric (MS/MS and MS3) gas-phase fragmentation reactions of methionine side-chain sulfonium ion containing peptides formed by reaction with a series of para-substituted phenacyl bromide (XBr where X=CH2COC6H4R, and R=--COOH, --COOCH3, --H, --CH3 and --CH2CH3) alkylating reagents have been examined in a linear quadrupole ion trap mass spectrometer. MS/MS of the singly (M+) and multiply ([M++nH](n+1)+) charged precursor ions results in exclusive dissociation at the fixed charge containing side chain, independently of the amino acid composition and precursor ion charge state (i.e., proton mobility). However, loss of the methylphenacyl sulfide side-chain fragment as a neutral versus charged (protonated) species was observed to be highly dependent on the proton mobility of the precursor ion, and the identity of the phenacyl group para-substituent. Molecular orbital calculations were performed at the B3LYP/6-31+G** level of theory to calculate the theoretical proton affinities of the neutral side-chain fragments. The log of the ratio of neutral versus protonated side-chain fragment losses from the derivatized side chain were found to exhibit a linear dependence on the proton affinity of the side-chain fragmentation product, as well as the proton affinities of the peptide product ions. Finally, MS3 dissociation of the nominally identical neutral and protonated loss product ions formed by MS/MS of the [M++H]2+ and [M++2H]3+ precursor ions, respectively, from the peptide GAILM(X)GAILK revealed significant differences in the abundances of the resultant product ions. These results suggest that the protonated peptide product ions formed by gas-phase fragmentation of sulfonium ion containing precursors in an ion trap mass spectrometer do not necessarily undergo intramolecular proton 'scrambling' prior to their further dissociation, in contrast to that previously demonstrated for peptide ions introduced by external ionization sources.     

A fragmentation study of isoflavones in negative electrospray ionization by MSn ion trap mass spectrometry and triple quadrupole mass spectrometry

This study has elucidated the fragmentation pathway for deprotonated isoflavones in electrospray ionization using MS(n) ion trap mass spectrometry and triple quadrupole mass spectrometry. Genistein-d(4) and daidzein-d(3) were used as references for the clarification of fragment structures. To confirm the relationship between precursor and product ions, some fragments were traced from MS(2) to MS(5). The previous literature for the structurally related flavones and flavanones located the loss of ketene (C(2)H(2)O) to ring C, whereas the present fragmentation study for isoflavones has shown that the loss of ketene occurs at ring A. In the further fragmentation of the [M-H-CH(3)](-*) radical anion of methoxylated isoflavones, loss of a hydrogen atom was commonly found. [M-H-CH(3)-CO-B-ring](-) is a characteristic fragment ion of glycitein and can be used to differentiate glycitein from its isomers. Neutral losses of CO and CO(2) were prominent in the fragmentation of deprotonated anions in ion trap mass spectrometry, whereas recyclization cleavage accounted for a very small proportion. In comparison with triple quadrupole mass spectrometry, ion trap MS(n) mass spectrometry has the advantage of better elucidation of the relationship between precursor and product ions.     

Electrospray Ionization Tandem Mass Spectrometry of Ammonium Cationized Polyethers

Quaternary ammonium salts (Quats) and amines are known to facilitate the MS analysis of high molar mass polyethers by forming low charge state adduct ions. The formation, stability, and behavior upon collision-induced dissociation (CID) of adduct ions of polyethers with a variety of Quats and amines were studied by electrospray ionization quadrupole time-of-flight, quadrupole ion trap, and linear ion trap tandem mass spectrometry (MS/MS). The linear ion trap instrument was part of an Orbitrap hybrid mass spectrometer that allowed accurate mass MS/MS measurements. The Quats and amines studied were of different degree of substitution, structure, and size. The stability of the adduct ions was related to the structure of the cation, especially the amine’s degree of substitution. CID of singly/doubly charged primary and tertiary ammonium cationized polymers resulted in the neutral loss of the amine followed by fragmentation of the protonated product ions. The latter reveals information about the monomer unit, polymer sequence, and endgroup structure. In addition, the detection of product ions retaining the ammonium ion was observed. The predominant process in the CID of singly charged quaternary ammonium cationized polymers was cation detachment, whereas their doubly charged adduct ions provided the same information as the primary and tertiary ammonium cationized adduct ions. This study shows the potential of specific amines as tools for the structural elucidation of high molar mass polyethers.     

Negative chemical ionization in quadrupole ion trap mass spectrometry: Effects of applied voltages and reaction times

The effects of applied voltages and reaction times on negative ion chemical ionization in the quadrupole ion trap are investigated. Mass-selected ejection of undesired reagent ions and selective mass storage of only negative ions are required for practical negative ion chemical ionization. This is achieved by application of rf and dc voltages to the ring electrode to control the mass-to-charge ratios one polarity) of ions stored, as well as by application of a supplemental rf voltage applied across the endcap electrodes to selectively eject ions of a particular mass-to-charge ratio. Even with careful control of these parameters, negative chemical ionization is not as sensitive as electron ionization and positive chemical ionization because of the lack of thermal electrons in the ion trap. Mass selection of the hydroxide anion as a reagent ion and exclusion of all positive ions provide [M ? H]^? ions with little or no fragmentation for a wide variety of compounds.     

Analysis of curcuminoids by positive and negative electrospray ionization and tandem mass spectrometry

The curcuminoids are a group of diarylheptanoid molecules that possess important pharmacological activities, particularly acting as anti-inflammatory agents. The main purpose of this study was to investigate the fragmentation behavior of the three major curcuminoids in ion trap liquid chromatography/tandem mass spectrometry (LC/MS/MS). Both positive and negative mode electrospray ionization in tandem and multidimensional MS(n) experiments in quadrupole ion trap instruments and high-resolution and accurate mass MS and sustained off-resonance irradiation (SORI) MS/MS experiments in a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer were used to elucidate the main fragmentation channels of these compounds. These experiments yielded essentially the same fragmentation results in both ion trap and ICR instruments for all three curcuminoids and for their phenolic monoacetates. Major and diagnostic fragment ions were identified and their origins are proposed.     

A comparative study of the fragmentation of neutral lactooligosaccharides in negative-ion mode by UV-MALDI-TOF and UV-MALDI ion-trap/TOF mass spectrometry

Structure analyses of underivatized neutral lacto oligosaccharides are systematically performed by ultraviolet matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (UV-MALDI TOF MS) and UV-MALDI ion-trap time-of-flight mass spectrometry (ion-trap/TOF MS) acquired in negative-ion mode. Interestingly, their fragmentation significantly differ each other. In postsource decay (PSD) in UV-MALDI TOF MS, cross-ring cleavage at the reducing terminal predominates. On the other hand, glycosyl bond cleavage (C-type fragmentation) takes place preferentially in collision induced dissociation (CID) in UV-MALDI ion-trap/TOF MS. The cross-ring cleavage in PSD similar to that in in-source decay occurs via a prompt reaction path characteristic of the UV-MALDI process itself. The product ion spectra of UV-MALDI ion-trap/TOF MS are similar to the electrospray ionization (ESI) ion-trap or quadrupole/TOF CID product ion spectra. During ion-trap/TOF MS experiments, the deprotonated molecular ions survive for several tens of milliseconds after CID event because the high internal energy chlorinated precursor ions are cooled by collisional cooling in the ion trap. The results obtained suggest that the PSD from the chlorinated precursor ion in UV-MALDI TOF MS might proceed as a two-step reaction; in the first, a high internal energy deprotonated molecular ion is generated as a reaction intermediate during the flight in the drift tube, and in the second, the rapid decomposition from the deprotonated molecular ion takes place.     

How does a CC double bond cleave in the gas phase? Fragmentation of protonated ketotifen in mass spectrometry

In the literature, it is reported that the protonated ketotifen mainly undergoes C?C double bond cleavage in electrospray ionization tandem mass spectrometry (ESI‐MS/MS); however, there is no explanation on the mechanism of this fragmentation reaction. Therefore, we carried out a combined experimental and theoretical study on this interesting fragmentation reaction. The fragmentation of protonated ketotifen (m/z 310) always generated a dominant fragment ion at m/z 96 in different electrospray ionization mass spectrometers (ion trap, triple quadrupole and linear trap quadrupole (LTQ)‐orbitrap). The mechanism of the generation of this product ion (m/z 96) through the C?C double bond cleavage was proposed to be a sequential hydrogen migration process (including proton transfer, continuous two‐step 1,2‐hydride transfer and ion‐neutral complex‐mediated hydride transfer). This mechanism was supported by density functional theory (DFT) calculations and a deuterium labeling experiment. DFT calculations also showed that the formation of the product ion m/z 96 was most favorable in terms of energy. This study provides a reasonable explanation for the fragmentation of protonated ketotifen in ESI‐MS/MS, and the fragmentation mechanism is suitable to explain other C?C double bond cleavage reactions in mass spectrometry. Copyright © 2016 John Wiley & Sons, Ltd.     

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.     

Improvements in ion-trap chemical-ionization performance.

Ion-trap chemical-ionization performance has been improved by application of a modified scan function for the rejection of the undesired electron-ionization-like (EI-like) ions formed at the beginning of the reaction ionization period. The net effect of this software modification to the automatic reaction control is to produce chemical ionization (CI) spectra that are no longer adulterated with concentration-dependent EI-like ions. Under such improved conditions, CI spectra from an ion trap can now be directly compared with CI spectra produced on conventional quadrupole and magnet-scanning instruments.     

Structural analysis of underivatized neutral human milk oligosaccharides in the negative ion mode by nano-electrospray MS(n) (part 1: methodology)

Underivatized neutral oligosaccharides from human milk were analyzed by nano-electrospray ionization (ESI) using a quadrupole ion trap mass spectrometer (QIT-MS) in the negative-ion mode. Under these conditions neutral oligosaccharides are observed as deprotonated molecules [M-H]- with high intensity. CID-experiments of these species with the charge localized at the reducing end lead to C-type fragment ions forming a "new" reducing end. Fragmentations are accompanied by cross-ring cleavages that yield information about linkages of internal monosaccharides. Several isomeric compounds with distinct structural features, such as different glycosidic linkages, fucosylation and branching sites were investigated. The rules governing the fragmentation behavior of this class of oligosaccharides were elucidated and tested for a representative number of certain isomeric glycoforms using the MS/MS and MS(n) capabilities of the QIT. On the basis of the specific fragmentation behavior of deprotonated molecules, the position of fucoses and the linkage type (Gal beta-->3 GlcNAc or Gal beta1-->4 GlcNAc) could be determined and linear and branched could be differentiated. Rules could be established which can be applied in further investigations of these types of oligosaccharides even from heterogenous mixtures.     

Gas chromatography/mass spectrometry determination of amphetamine-related drugs and ephedrines in plasma, urine and hair samples after derivatization with 2,2,2-trichloroethyl chloroformate

A new analytical approach, based on derivatization with 2,2,2-trichloroethyl chloroformate and gas chromatography/mass spectrometry (GC/MS), was investigated for qualitative and quantitative analyses of a large range of amphetamine-related drugs and ephedrines in plasma, urine and hair samples. Sample preparation involved alkaline extraction of analytes from biological samples using Extrelut columns, after addition of the internal standard 3,4-methylenedioxypropylamphetamine (MDPA), and subsequent derivatization to produce 2,2,2-trichloroethylcarbamates. GC/MS analyses, in splitless mode using a slightly polar 30-m capillary column, were performed with quadrupole or ion trap instruments. MS acquisition modes were electron ionization (EI) in full-scan or selected ion monitoring (SIM) modes (quadrupole), and full-scan MS or MS/MS modes with chemical ionization (CI) conditions (ion trap). EI spectra of 2,2,2-trichloroethylcarbamates showed variably abundant molecular ions as well as abundant diagnostic fragment ions, both characterized by ion clusters reflecting the isotope distribution of three chlorine atoms in the derivatized molecules. CI spectra showed abundant protonated molecules. Quantitative studies using EI SIM conditions gave recoveries in the range 74-89%, linear response over ranges of 10-2000 ng/mL (plasma and urine) and 0.20-20 ng/mg (hair), with corresponding limits of detection in the ranges 2-5 ng/mL and 0.1-0.2 ng/mg. Potential applications (following full method validation) include clinical and forensic toxicology, as well as doping control.     

Detection of pharmaceutical compounds in tissue by matrix-assisted laser desorption/ionization and laser desorption/chemical ionization tandem mass spectrometry with a quadrupole ion trap

A novel quadrupole ion trap mass spectrometer laser microprobe instrument with an external ionization source was constructed and used to investigate the matrix-assisted laser desorption/ionization (MALDI) detection of pharmaceutical compounds in intact tissue. In addition to MALDI, laser desorption coupled with chemical ionization (LD/CI) was investigated. MALDI, using 2,5-dihydroxybenezoic acid (DHB) as a matrix, was employed to detect the anticancer drug paclitaxel from a thin section of rat liver tissue which had been incubated in a solution of paclitaxel. The results of that experiment showed that the ability to perform tandem mass spectrometry (MS/MS) with the quadrupole ion trap was crucial in the identification of drug compounds at trace levels in the complex tissue matrix. MALDI MS/MS was then used to detect the presence of paclitaxel in a human ovarian tumor at a concentration of approximately 50 mg/kg. Finally, the drug spiperone was detected in incubated rat liver tissue at an approximate level of 25 mg/kg using LD/CI (no MALDI matrix). Again, the MS/MS capability of the quadrupole ion trap was crucial in the identification of the drug at trace levels in the complex tissue matrix.     

The behaviour of stereoisomeric ions in the gas phase: 3—The case of homosubstituted bicyclooctenes

In the electron impact mass spectroscopy of four 2,3,5,6-bicyclo(2.2.2)–7-octenetetramethoxycarbonyl stereoisomers differences in relative abaundances of product ions and also different fragmentation pathways are observed. The stereospecificity is retained also under positive ion chemical ionization (CI(methane), CI(isobutane)) and negative ion chemical ionization (NICI) (OH^?) conditions. Interesting correlations between fragmentation and molecular symmetry are suggested.     

Structural analysis of 2,6-[bis(alkyloxy)methyl]-phenyltin derivatives using electrospray ionization mass spectrometry

Electrospray ionization (ESI) mass spectrometry was applied to the structural analysis of 23 2,6-[bis(alkyloxy)methyl]phenyltin(IV) derivatives. The mass spectra were measured in both polarity modes and multistage tandem mass spectrometric (MS(n)) measurements were performed on the ion trap analyser for positively charged tin-containing ions. The sum of complementary ions observed in the positive-ion mode (i.e. [M-R(3)](+) ion) and in the negative-ion mode (i.e. [R(3)](-) ion) permits molecular mass determination in spite of the fact that the molecular adducts were often missing even in the first-order mass spectra. The subsequent fragmentation of [M-R(3)](+) ions studied by MS(n) and the correlation of observed fragment ions with the expected structures of synthesized organotin(IV) compounds allowed us to understand the fragmentation behaviour and the mechanism of the ion formation for studied compounds. The typical neutral losses are alkenes, alcohols and aldehydes. The fragmentation pattern of one selected compound was supported by MS(n) measurements of an isotopically labelled analogue to confirm unusual ion-molecule reactions of some fragment ions with water in the ion trap.     

Pulsed gas introduction into quadrupole ion traps

Two different Paul-type quadrupole ion traps were equipped with pulsed-valve gas inlets. The duration of a gas pulse inside the trap is variable, and pulses as short as 50 ms (FWHH) have been measured, allowing the use of several gas pulses during one experiment. The benefits of pulsed valves are outlined and demonstrated for chemical ionization experiments and for the use of selective ion-molecule reactions in structure determination of ions and neutral molecules.     

"Dueling" ESI: instrumentation to study ion/ion reactions of electrospray-generated cations and anions

Novel instrumentation has been developed which allows for the sequential injection and subsequent reaction of oppositely-charged ions generated via electrospray ionization (ESI) in a quadrupole ion trap mass spectrometer. The instrument uses a DC turning quadrupole to sequentially direct the two ion polarities into the ion trap from ESI sources which are situated 90 degrees from the axial (z) dimension of the trap, and 180 degrees from one another. This arrangement significantly expands the range of ionic reactants amenable to study over previously-used instrumentation. For example, ion/ion reactions of multiply-charged positive ions with multiply-charged negative ions can be studied. Also, reactions of multiply-charged ions with singly-charged ions of opposite polarity that could not be generated by previously used ionization methods, or that could not be efficiently injected through the ion trap ring electrode, can be studied with the new instrument. This capability allows, for example, the charge state manipulation of negatively-charged precursor and product ions derived from proteins and oligonucleotides via proton transfer reactions with singly-charged cations generated by ESI.     

Dual parallel electrospray ionization and atmospheric pressure chemical ionization mass spectrometry (MS), MS/MS and MS/MS/MS for the analysis of triacylglycerols and triacylglycerol oxidation products

Two mass spectrometers, in parallel, were employed simultaneously for analysis of triacylglycerols in canola oil, for analysis of triolein oxidation products, and for analysis of triacylglycerol positional isomers separated using reversed-phase high-performance liquid chromatography. A triple quadrupole mass spectrometer was interfaced via an atmospheric pressure chemical ionization (APCI) interface to two reversed-phase liquid chromatographic columns in series. An ion trap mass spectrometer was coupled to the same two columns using an electrospray ionization (ESI) interface, with ammonium formate added as electrolyte. Electrospray ionization mass spectrometry (ESI-MS) under these conditions produced abundant ammonium adduct ions from triacylglycerols, which were then fragmented to produce MS/MS spectra and then fragmented further to produce MS/MS/MS spectra. ESI-MS/MS of the ammoniated adduct ions gave product ion mass spectra which were similar to mass spectra obtained by APCI-MS. ESI-MS/MS produced diacylglycerol fragment ions, and additional fragmentation (MS/MS/MS) produced [RCO](+) (acylium) ions, [RCOO+58](+) ions, and other related ions which allowed assignment of individual acyl chain identities. APCI-MS of triacylglycerol oxidation products produced spectra like those reported previously using APCI-MS. APCI-MS/MS produced ions related to individual fatty acid chains. ESI-MS of triacylglycerol oxidation products produced abundant ammonium adduct ions, even for those molecules which previously produced little or no intact molecular ions under APCI-MS conditions. Fragmentation (MS/MS) of the [M+NH(4)](+) ions produced results similar to those obtained by APCI-MS. Further fragmentation (MS/MS/MS) of the diacylglycerol fragments of oxidation products provided information on the oxidized individual fatty acyl chains. ESI-MS and APCI-MS were found to be complementary techniques, which together contributed to a better understanding of the identities of the products formed by oxidation of triacylglycerols.