Computer-based system for correlating molecular structures with mass spectral data

Algorithms are described for correlating a proposed molecular structure with a mass spectrum. All molecular substructures of a proposed structure are determined which have the same masses as the fragment ions. The most likely fragment ion structures are those molecular substructures formed with the fewest number of bond cleavages in the proposed structure. The algorithms, which incorporate methods for handling rearrangement and adduct ions, utilize either nominal or exact data originating from any ionization method. The algorithms are demonstrated using the mass spectra of a substituted azetidinyl ketone and the macrolide antibiotic avermectin A_1a.     

MASSPEC: a graphics-based data system for correlating a mass spectrum with a proposed structure

A graphics-based user-friendly data system called MASSPEC was developed to aid in the analysis of a mass spectrum when a proposed structure is provided. The proposed chemical structure is drawn and combinatorial algorithms correlate the masses of the substructures with the masses of the fragment ions observed in the mass spectrum. These substructures are subsequently drawn on the terminal screen. The commands and algorithms for operating MASSPEC are described. The MASSPEC data system can be used to interpret either nominal or exact mass data generated from relatively large molecules in any ionization mode. Illustrations utilizing MASSPEC include the interpretation of mass spectra generated on tandem mass spectrometers in the thermospray and fast atom bombardment (FAB) modes and the analysis of a FAB mass spectrum of a digested polypeptide to reveal post-translational modifications.     

Laser desorption ionization and MALDI time-of-flight mass spectrometry for low molecular mass polyethylene analysis

Polyethylene's inert nature and difficulty to dissolve in conventional solvents at room temperature present special problems for sample preparation and ionization in mass spectrometric analysis. We present a study of ionization behavior of several polyethylene samples with molecular masses up to 4000 Da in laser desorption ionization (LDI) time-of-flight mass spectrometers equipped with a 337 nm laser beam. We demonstrate unequivocally that silver or copper ion attachment to saturated polyethylene can occur in the gas phase during the UV LDI process. In LDI spectra of polyethylene with molecular masses above approximately 1000 Da, low mass ions corresponding to metal-alkene structures are observed in addition to the principal distribution. By interrogating a well-characterized polyethylene sample and a long chain alkane, C94H190, these low mass ions are determined to be the fragmentation products of the intact metal-polyethylene adduct ions. It is further illustrated that fragmentation can be reduced by adding matrix molecules to the sample preparation.     

Core trees and consensus fragment sequences for molecular representation and similarity analysis

A new type of molecular representation is introduced that is based on activity class characteristic substructures extracted from random fragment populations. Mapping of characteristic substructures is used to determine atom match rates in active molecules. Comparison of match rates of bonded atoms defines a hierarchical molecular fragmentation scheme. Active compounds are encoded as fragmentation pathways isolated from core trees. These paths are amenable to biological sequence alignment methods in combination with substructure-based scoring functions. From multiple core path alignments, consensus fragment sequences are derived that represent compound activity classes. Consensus fragment sequences weighted by increasing structural specificity can also be used to map molecules and search databases for active compounds.     

Unravelling ionization and fragmentation pathways of carotenoids using orbitrap technology: a first step towards identification of unknowns

Vegetables are a major source of carotenoids and carotenoids are identified as potentially important natural antioxidants that may aid in the prevention of several human chronic degenerative diseases. Characterization of carotenoids in organic biological matrices is a crucial step in any research valorization trajectory. This study reports for the first time the use of high mass resolution and exact mass orbitrap technology for the elucidation of carotenoid fragmentation pathways. This contributes to the generation of new tools for identifying unknown carotenoids based on fragmentation patterns. Two different chromatographic methods making use of different mobile phases resulted in the generation of different ion species because of the large influence of the mobile phase solvent composition on ionization. It was shown that depending on the molecular ion species that are generated (protonated ions or radical molecular ions), different fragments are formed when applying higher energy collisional dissociation. Fragmentation and the abundance of fragments provide valuable structural information on the type of functional groups, the polyene backbone and the location of double bonds in ring structures of carotenoids. Furthermore, coherence between specific substructures in the molecules and characteristic fragmentation patterns was observed allowing the assignment of fragmentation patterns for carotenoid substructures that can theoretically be extrapolated to carotenoids with similar (sub)structures. Differentiation between isomeric carotenoids by compound specific fragments could however not be made for all the isomeric groups under study. As a wide variety of isomeric forms of carotenoids exist in nature, the combination of good chromatographic separation with high resolution mass spectrometry and other complementary qualitative structure elucidation techniques such as a photo diode array detector and/or nuclear magnetic resonance spectroscopy are indispensable for unambiguous identification of unknown carotenoids. Copyright © 2013 John Wiley & Sons, Ltd.     

Secondary-ion and electron production from surfaces bombarded by large polyatomic ions.

Heavy molecular ions with energies in the range 10-20 keV and masses from 276 u to 132,000 u, produced by matrix-assisted laser desorption, were used as primary projectiles to produce secondary-ion spectra from a variety of surfaces in a tandem time-of-flight mass spectrometer. In the negative mode the ratio of electron emission to secondary-ion emission was found to decrease rapidly with increasing projectile mass. Ion emission was found to dominate for primary ions larger than approximately 10,000 u. Positive or negative molecular ions and cations were observed from several organic targets of masses up to 1140 u (gramicidin S) for incident projectiles up to mass 132,000 u, i.e., for projectile speeds down to approximately 7000 m/s. Other ions characteristic of the target were also observed for these projectiles. Thus, large polyatomic ions can cause secondary-ion desorption even at very low velocity. The background ions of both polarities are similar to those found in keV particle bombardment by monatomic projectiles. The same ions are observed for all the projectiles; most can be identified with hydrocarbon background. The relative intensities of the background positive ions are largely independent of projectile, and for both polarities the ratio of the ions characterizing the target to those forming the background is approximately constant for all the projectiles. These results strongly suggest that the background ions come from the usual layer of organic impurities attached to the target surface. No direct evidence for surface-induced dissociation was observed in this mass and energy range.     

Very high-mass ions derived from carbonaceous samples in laser microprobe mass spectrometry

An extended series of positive ions occurring at regular intervals of 24 D is observed in the laser-induced ionization mass spectra of several solid carbonaceous materials. These ions occur with masses up to 3000 D, and can exceed the mass of the parent compound. This effect was found with some polynuclear aromatic hydrocarbons, coal and soots.     

A new tandem mass spectrometer for the study of molecular dissociations

A new tandem mass spectrometer has been developed for the study of molecular fragmentation reactions. The first stage of this tandem mass spectrometer is a double-focusing sector field instrument in the BE configuration. The second stage is a double-focusing combination of a Wien filter and a sector magnet that allows simultaneous detection of a wide range of masses owing to the approximately equal velocities of the fragment ions. By using a microchannel plate as a collision target, high fragmentation effi.ciency and high ion transmission were achieved.     

Characteristic fragmentation of thromboxane B2 in thermospray high-performance liquid chromatography-mass spectrometry

Cyclo- and lipo-oxygenase metabolites of arachidonic acid have been reported to have very simple thermospray mass spectra. However, thromboxane B2 (TXB) in ammonium acetate-methanol and at interface temperatures below the point of total vaporization shows a mass spectral pattern characterized by abundant ions at low masses. The more abundant TXB fragment ions have been characterized as adducts from four principal fragments with molecular masses of 156, 170, 196 and 326. Positive- and negative-ion mass spectra, and mass spectra obtained with an alternative thermospray buffer (butylammonium acetate) support the molecular masses of these fragments. A tentative assignment of the fragments can be made by comparison of the thermospray mass spectra of TXB, 2,3-dinor-TXB and some of their methyl ester and methyl oxime derivatives. Interface temperature and solvent composition effects on the fragmentation, as well as in the electron-capture processes observed when working in the filament-on mode, are discussed. Fragmentation mechanisms can be related to those observed for monosaccharides, and imply retro-Diels-Alder as well as retroaldolic condensation-type rearrangements.     

Multiply charged ions in ionspray tandem mass spectrometry

Multiply charged anions of some 30 species containing multiple carboxylic, sulphonic and/or phosphoric groups generated by ionspray were studied by using tandem mass spectrometry (MS/MS). Two trends emerged: (1) lower-charged ions are preferentially evaporated, and (2) for more highly charged ions, evaporability is a function of ion size. Triply and quadruply charged ions were observed for azo dyes with molecular masses in the 700-900 Dalton range. Daughter-ion mass spectra of selected multiply charged ions are presented.     

Comparison of Triple Quadrupole and Double Focusing Mass Spectrometers to Investigate Collision-Induced Dissociation and Metastable Ions of Glycoconjugates

Glycoconjugates, such as chromophore-labeled disaccharides and permethylated glycosphingolipids (GSL) were used for comparison of triple quadrupole and double focusing mass spectrometers in analysis of product ions. A profound effect of collision energy was observed in the product ion spectra of ceramide ions (fragment ions of permethylated GSL): more product ions were observed from a double focusing mass spectrometer. Besides collision energy, the structure of the analyte had a significant effect on the formation of product ions. Despite the fact that masses of protonated molecular ions (MH⁺) of permethylated GSL are significantly larger than their ceramide fragments, the low-energy and high-energy product ion spectra of MH⁺ are, in general, similar. In a double focusing mass spectrometer of reversed geometry, more metastable ions were observed in the first field free region (FFR) than in the second FFR. The metastable ions observed in the second FFR were similar to those observed in low-energy collision-induced dissociation (CID). Although a double focusing mass spectrometer is superior to triple quadrupole instrument for detection of product ions, the poor resolution in either the selection of precursor ion or in the product ion spectra can be a serious problem in analysis of a mixture with similar masses.     

Utility of three types of mass spectrometers for determining elemental compositions of ions formed from chromatographically separated compounds

Concentration factors of 1000 and more reveal dozens of compounds in extracts of water supplies. Library mass spectra for most of these compounds are not available, and alternative means of identification are needed. Determination of the elemental compositions of the ions in mass spectra makes feasible searches of commercial and chemical literature that often lead to compound identification. Instrumental capabilities that constrain the utility of a mass spectrometer for determining ion compositions for compounds that elute from a chromatographic column are scan speed, mass accuracy, linear dynamic range, and resolving power. Mass peak profiling from selected ion recording data (MPPSIRD) performed with a double-focusing mass spectrometer provides the best combination of these capabilities. This technique provides unique ion compositions for ions of higher mass from compounds eluting from a gas chromatograph than can be obtained by orthogonal acceleration time-of-flight (oa-TOF) or Fourier transform ion cyclotron resonance mass spectrometry. Multiple compositions are usually possible for an ion with a mass exceeding 150 Da within the error limits of the mass measurement. The correct composition is selected based on measured exact masses of the mass peak profiles resulting from isotopic ions higher in mass by 1 and 2 Da and accurate measurement of the summed abundances of these isotopic ions relative to the monoisotopic ion. A profile generation model (PGM) automatically determines which compositions are consistent with measured exact masses and relative abundances. The utility of oa-TOF and double-focusing mass spectrometry using ion composition elucidation (MPPSIRD plus the PGM) are considered for determining ion compositions of two compounds found in drinking water extracts and a third compound from a monitoring well at a landfill. Published in 2002 by John Wiley & Sons, Ltd.     

The computation of some molecular weights

A method is described for deducing the molecular weight of a compound, the mass spectrom of which does not extend as far as the molecular weight, It is based upon the combination of fragment ions and restricted to limits determined by an approximate estimate of that weight.     

Usefulness of field desorption mass spectrometry in determining molecular masses of carotenoids,natural carotenoid derivatives and their chemical derivatives

Field desorption (FD) mass spectrometry was applied to the determination of the molecular masses of carotenoids, natural carotenoid derivatives and their chemical derivatives. All the carotenoids examined gave the molecular ion as the base peak with negligible fragment ions. Carotenoid glucoside and its fatty acid monoester were successfully determined without acetylation, whereas carotenoic acids (carboxylate and sulphate) needed to be converted into methyl esters prior to analysis. The applicable ranges of molecular masses and polarity were very wide. In addition, carotenoid glycoside gave only [M]⁺˙ without [M + H]⁺˙ and [M + cation]⁺˙. The numbers of carbonyl groups, primary and/or secondary hydroxyl groups and total hydroxyl groups could be directly determined according to the increase in mass units of the carotenoids after chemical reduction, acetylation and trimethylsilylation, respectively. Owing to the negligible fragment ions, FD analysis was also suitable for carotenoids containing small amounts of impurities or other carotenoids. Hence this technique is useful for determining the molecular masses of carotenoids and the number of modifiable groups in carotenoids.     

Measurement of unimolecular decay in peptides of masses greater than 1200 units by a reflecting time-of-flight mass spectrometer

Daughter ions from decomposition of [M + H]+ parent ions have been observed in a time-of-flight mass spectrometer fitted with an ion mirror. Unit mass resolution is obtained for parent ions of masses up to several thousand u when the mirror voltage is set at a value determined by the usual velocity-focusing criterion for parent ions. Under this condition the daughter-ion resolution in the low-mass range suffers. Considerable improvement is obtained when the daughter-ion spectrum is examined in several segments, with the mirror voltage optimized for each segment. The daughter-ion spectrum from decay of metastable [M + H]+ parent ions in Substance P is measured using this technique. Reasons are suggested for differences between the spectrum obtained and a spectrum for the same compound recently obtained using a tandem double-focusing instrument.     

Second hydrogen atom abstraction by molecular ions

We report the observation of a new physical phenomenon of the addition of 2 hydrogen atoms to molecular ions thus forming [M + 2H]⁺ ions. We demonstrate such second hydrogen atom abstraction onto the molecular ions of pentaerythritol and trinitrotoluene (TNT). We used both gas chromatography mass spectrometry (GC‐MS) with supersonic molecular beam (SMB) with methanol added into its make‐up gas and electron ionization (EI) liquid chromatography mass spectrometry (LC‐MS) with SMB with methanol as the LC solvent. We found that the formation of methanol clusters resulted upon EI in the formation of dominant protonated pentaerythritol ion at m/z = 137 plus about 70% relative abundance of pentaerythritol molecular ion with 2 additional hydrogen atoms at m/z = 138 which is well above the 5.7% natural C¹³ isotope abundance of protonated pentaerythritol. Similarly, we found an abundant protonated TNT ion at m/z = 228 and a similar abundance of TNT molecular ion with 2 additional hydrogen atoms at m/z = 229. Upon the use of deuterated methanol (CD₃OD) as the solvent, we observed an abundant m/z = 231 (M + 2D)⁺ of TNT with 2 deuterium atoms. We found such abundant second hydrogen atom abstraction with butylglycolate and at low abundances in dioctylphthalate, Vitamin K3, phenazine, and RDX. At this time, we are unable to report the magnitude and frequency of occurrence of this phenomenon in standard electrospray LC‐MS. This observation could have important implications on the provision of elemental formula from mass spectra that are involved with protonated molecules. Accordingly, while accurate mass measurements can serve for the generation of elemental formula, their further support and improvement via isotope abundance analysis are questionable. Consequently, if a given compound can be analyzed by both GC‐MS and LC‐MS, its GC‐MS analysis can be superior for the provision of accurate elemental formulae if its EI mass spectrum exhibits abundant molecular ions such as with GC‐MS with SMB (also known as cold EI).     

Improved abundance sensitivity of molecular ions in positive-ion APCI MS analysis of petroleum in toluene

Positive-ion atmospheric pressure chemical ionization (APCI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) analyses of petroleum sample were performed with higher sensitivity by switching the solvent composition from toluene and methanol or acetonitrile to a one-component system consisting only of toluene. In solvent blends, molecular ions were more abundant than were protonated ions with increasing percentages of toluene. In 100% toluene, the double-bond equivalence (DBE) distributions of molecular ions obtained by APCI MS for each compound class were very similar to those obtained in dopant assisted atmospheric pressure photo ionization (APPI) MS analyses. Therefore, it was concluded that charge-transfer reaction, which is important in toluene-doped APPI processes, also plays a major role in positive-ion APCI. In the DBE distributions of S₁, S₂, and SO heteroatom classes, a larger enhancement in the relative abundance of molecular ions at fairly specific DBE values was observed as the solvent was progressively switched to toluene. This enhanced abundance of molecular ions was likely dependent on molecular structure.     

Investigations on cluster and molecular ion formation by plasma mass spectrometry

The formation of molecular and cluster ions of different inorganic materials in plasma mass spectrometry – spark source mass spectrometry (SSMS), radiofrequency glow discharge mass spectrometry (rf GDMS), laser ionization mass spectrometry (LIMS), inductively coupled plasma mass spectrometry (ICP-MS) and laser ablation ICP-MS (LA-ICP-MS) – was investigated and compared. Similar abundance distributions of cluster ions were observed for a graphite sample, for boron nitride/ graphite and for metal oxide/graphite mixtures using different plasma mass spectrometric methods. A correlation of intensities of metal argide ions in ICP-MS with their bond dissociation energies was used to estimate unknown dissociation energies of molecular ionic species. For the elements of the 2nd or 3rd period in the periodic table, the intensities of most argon molecular ions (ArX⁺) measured by ICP-MS rise with increasing atomic number in a similar manner to the theoretically calculated bond dissociation energies of argon molecular ions.     

Collison-induced dissociation and photodissociation of nitroaromatic molecular ions: A unique isomerization for p-nitrotoluene and p-ethylnitrobenzene ions

The photodissociation and low-energy collision-induced dissociation of p-nitrotoluene and p-ethylnitrobenzene molecular ions were studied using Fourier transform ion cyclotron resonance mass spectrometry. The dissociation of these ions is highly dependent on the time-scale of the experiment and the pressure of the nitroaromatic compound. Collisions of the ions with nitroaromatic neutral species increase the abundance of fragment ions due to NO elimination, while collisions with inert gases such as sulfur hexafluoride and argon have no effect. Evidence is presented for the occurrence of an ion–molecule reaction between p-alkylnitrobenzene ions and nitroaromatic neutral species that induces isomerization of the ion. This isomerization is proposed to involve a nitro-to-nitrite rearrangement. Although the mechanism of this process is unknown, isotopic labeling experiments have shown that it does not involve nitrogen atom transfer between the two reactants. The dissociations of o-nitrotoluene, m-nitrotoluene and nitrobenzene ions are also discussed. For these ions, no pressure- or time-scale-dependent behavior was observed, indicating that an isomerization did not occur.     

Collision induced decomposition of peptides. Choice of collision parameters

Collision-induced dissociation product ion spectra of a series of doubly charged tryptic peptide ions produced by electrospray ionization were obtained by triple-quadrupole tandem mass spectrometry. The sequence information content of the product ion spectra was explored as a function of collision energy and collision-cell gas pressure for parent ions with molecular masses ranging from 300 to 2000 u. The energy range (at a given pressure) in which the degree of fragmentation is acceptable was found to be narrow for parent ions of a given mass, and the optimal collision energy was observed to exhibit a strong linear correlation with parent ion mass. This observed correlation opens the way for on-line software-controled selection of optimal mass spectrometric conditions in the enzymatic digestion-liquid chromatography-tandem mass spectrometric strategy of amino acid sequencing of proteins.