Ion Collision-induced Dissociation Research Articles

Electrospray Collision-induced Dissociation Mass Spectra of Positively Charged Oligonucleotides

Positive ion collision-induced dissociation (CID) mass spectra of oligonucleotides provide qualitatively similar fragmentation patterns to CID mass spectra generated from negative ion precursors. The major sequence ion series w and a-base are still abundant enough to be useful for the determination of the sequence of an oligonucleotide. The application of sequencing to both positively and negatively charged precursor ions up to the 20-mer level are shown. The positive ion electrospray charge-state distributions are found to be sensitive to the base composition of the oligonucleotide. In the case of homopolymers containing the bases adenine, guanine and cytodine the average charge state is found to be similar. However, the average charge state of a homopolymer containing the base thymine is significantly lower. In addition, the CID mass spectra of this oligonucleotide results in the formation of x-2H and z-2H type ions exclusively. These differences are thought to be caused due to the phosphate backbone being the site of protonation rather than the base. © 1997 John Wiley & Sons, Ltd.

Generation and Identification of Neutral CpFeC5H4X (X = O, CH2, CO) Complexes in the Gas Phase by Tandem Mass Spectrometry

Tandem mass spectrometry experiments were performed to generate and identify neutral FcX (Fc = CpFeC5H4; X = O, CH2, CO) complexes having a formal 19-electron configuration. Neutralization−reionization mass spectra of FcX+ ions showed recovery signals corresponding to the formation of their neutral counterparts. FcO• and FcCH2• were also identified by means of the collision-induced (dissociative) ionization method as neutral products of the unimolecular fragmentation of molecular ions of the monosubstituted ferrocenes. Appearance energies of FcX ions and neutrals were measured. Activation energies for the [FcX−R]•+ bond cleavage were significantly higher than those in similar aromatic systems, PhXR•+. It was proposed that only a part of this energy was related to the FcX−R bond dissociation, the remainder being required for the intramolecular electron transfer from the ligand to the metal atom. The Fc+−CO bond dissociation energy in [FcCO]+ ions was substantially lower than that in the benzoyl ion. The weakness of the (neutral) Fc−CO bond was considered to be the major reason for the poor survival of FcCO• radicals in the neutralization−reionization of FcCO+ ions.

Previously uncharacterized ions observed in the high energy collision-induced dissociation mass spectra of peptides containing S-alkyl cysteine

The high-energy collision-induced dissociation (CID) spectra of a number of peptides containing S-β-(4-pyridylethyl)-, S-carbamidomethyl- and S-carboxymethylcysteine have been generated and several hitherto undescribed fragmentation pathways identified. For peptides containing pyridylethylcysteine at the nth position, these include x n − 105, a n+1 + 1 − 106, a n+1 + 1 − 138, z n+1 + 1 − 106, z n+1 + 1 − 138, and combined side chain loss ions. The analogous fragment ions were also observed in the spectra of peptides containing other S-alkylcysteines. Also, two fragmentations unique to pyridylethylcysteine-containing peptides, resulting in the formation of b n+ ≥ 1 - R C + H and CO + peC ions, were studied. Precursor scanning, exact mass measurement and CID of the appropriate source-generated fragment ions have been employed to identify the origin of these ions and to facilitate the proposal of mechanisms for their formation.

Tandem mass spectrometry of peptides. III—differentiation between leucine and isoleucine based on neutral losses

AbstractThe neutral species generated during the collisionally activated dissociation (CAD) of the protonated dipeptides Ala–Leu, Ala–Ile, Leu–Ala and Ile–Ala are post‐ionized by collision and detected in neutral fragment‐reionization (+NfR+) mass spectra. These spectra are dominated by fragment ions diagnostic for the C‐terminal amino acid, as confirmed by comparison with reference collision‐induced dissociative ionization (CIDI) mass spectra of authentic Ala, Leu and Ile. CIDI of Leu and Ile yields distinct and structurally indicative products. These are also observed upon +NfR+ of [Ala–Leu]H+ and [Ala–Ile]H+, respectively, thus allowing one to deduce the correct sequence. In contrast, [Leu–Ala]H+ and [Ile–Ala]H+, which possess identical C‐termini, form no differentiating neutral losses upon CAD.

Liquid chromatography/electrospray tandem mass spectrometry of amino acid conjugates of jasmonic acid under positive and negative ionisation

The positive and negative ion electrospray mass spectra of a series of (N)-jasmonoyl amino acid conjugates were measured by combined high performance liquid chromatography (HPLC)/mass spectrometry (MS). The mass spectra obtained of both positive and negative ions exhibit mostly a single abundant peak of [M + H]+ and [M – H]−, respectively, which indicates the molecular mass of the conjugate. From these ions detailed structural information can be obtained by liquid chromatography/tandem mass spectrometry. The positive daughter ion mass spectra obtained by collision-induced dissociation (CID) of [M + H]+ give information about both the jasmonoyl moiety and the amino acid component. The negative ion daughter spectra of [M – H]− are dominated by an ion originating from the deprotonated amino acid. Therefore, the conjugating amino acid can structurally be assigned by both the positive and negative ion CID mass spectra.

A tandem mass spectrometric investigation of (C 2H 5) 2X + ions (X = Cl, Br, I): the involvement of classical and nonclassical ethyl structures therein

The formation of diethyl halonium ions (C 2H 5) 2X + (X = Cl, Br, I) by a variety of ion-molecule reactions is described. The dissociation characteristics (metastable and collision-induced dissociation mass spectra) of these ions and their isomers were studied in detail. Some of the neutral fragmentation products were examined by their collision-induced dissociative ionization mass spectra. The participation of classical ( 1, CH 3CH 2X +CH 2CH 3) and nonclassical ▪ forms of the ions was considered. Dissociation reactions for which loss of positional identity of H-D atoms took place, for example, C 2H 4 loss (a common fragmentation of metastable ions) and C 2H + 5 formation, were interpreted as involving nonclassical ions, 2. It was concluded that the ion-molecule reactions produced both ion structures, but in different halogen-dependent proportions. For (C 2H 5) 2Cl + ions, 2 is the major species, for (C 2H 5) 2Br + both 1- and 2-type ions are generated, whereas for (C 2H 5) 2I + the classical form 1 must be the predominant structure.

Tandem mass spectrometry of peptides: Mechanistic aspects and structural information based on neutral losses. II—Tri‐ and larger peptides

AbstractThe neutral products arising during the collisionally activated dissociation of protonated oligopeptides (MH+) are post‐ionized by collision and detected in neutral fragment‐reionization (+NfR+) mass spectra. For the isomeric tripeptides Ala‐Gly‐Gly, Gly‐Ala‐Gly and Gly‐Gly‐Ala, the amino acid and dipeptide losses from the C‐terminus and the diketopiperazine losses from the N‐terminus allow for differentiation. These neutral fragments are identified in the corresponding +NfR+ spectra by comparison to reference collision‐induced dissociative ionization (CIDI) mass spectra of individual amino acids, dipeptides and diketopiperazines. Peptides with distinct C‐termini but otherwise identical sequences are found to yield +NfR+ products that are characteristic of the respective C‐terminal amino acid. This is demonstrated for several peptide pairs, including leucine‐ and methionine‐enkephalin. In general, +NfR+ spectra are dominated by the heavier neutral losses; further, +NfR+ and CIDI cause extensive dissociation, indicating that the collisional ionization process imparts high average internal energies.

Tandem mass spectrometric investigation of the phytosiderophores mugineic acid, deoxymugineic acid and nicotianamine

Phytosiderophores are low molecular mass iron chelating compounds that are secreted from the roots of graminaceous plants to allow iron solubilization and transport. To date no mass spectrometric investigation has been carried out on these novel structures or their metal complexes. This report describes a detailed analysis of the collision-induced dissociation (CID) spectra of mugineic acid, deoxymugineic acid, and nicotianamine in both positive and negative ion modes obtained using fast atom bombardment mass spectrometry in conjunction with tandem mass spectrometry. The CID spectra in the positive ion mode are dominated by loss of neutral fragments in the higher mass region, whereas in the lower mass region, charge retention on the azetidine ring is especially prominent. The negative ion CID spectra are more complicated than the positive ion spectra, but as the three structures are closely related this simplifies the interpretation. Mass spectrometric analysis of the FeIII complex of mugineic acid showed that the complex underwent a one-electron reduction under the fast atom bombardment measurement conditions.

Tandem mass spectrometry of peptides: Sequence information based on neutral losses. I—isomeric dipeptides

AbstractThe neutral losses arising on the collisionally activated dissociation (CAD) of protonated dipeptides (MH+) are reionized by collision and detected in neutral fragment‐reionization (NfR) mass spectra. For the dipeptides investigated, which encompass Ala–Gly/Gly–Ala, Asp–Gly/Gly–Asp, Phe–Gly/Gly–Phe and Trp–Ala/Ala–Trp, the NfR spectra of each pair of isomers are distinct and permit the identification of the correct C‐terminal amino acid. The precise structure of this amino acid is elucidated by comparison of the NfR spectra with reference collision‐induced dissociative ionization (CIDI) mass spectra of authentic Gly, Ala, Asp, Phe and Trp, acquired from beams of these amino acids formed by dissociation of their proton‐bound dimers.

Low-energy tandem mass spectrometry of the molecular ion derived from fatty acid methyl esters: A novel method for analysis of branched-chain fatty acids

Low-energy collision-induced dissociation (CID) of the molecular ions of fatty acid methyl esters obtained by electron ionization (70 eV) decompose in the tandem quadrupole mass spectrometer to yield a regular homologous series of carbomethoxy ions. Even at energies up to 200 eV ( E lab), primarily carbomethoxy ions are present, with the most abundant found at m/z 101 at higher energies. The lack of any other CID ions, including m/z 74 (McLafferty rearrangement) or m/z 87, suggest a rearranged molecular ion structure on leaving the first quadrupole mass analyzer. Analyses of various stable isotope variants support the hypothesis of alkyl radical migration to the carboxy carbonyl oxygen atom, with subsequent radical site directed cleavage eiher with or without a cyclization event. Decomposition of the molecular ions (70 eV) of several methyl branched fatty acid methyl esters, including phytanic acid, iso-methyl and anteiso-methyl branched acids, and tuberculostearic acid, reveals enhanced radical site cleavage at the alkyl branching positions. This method can be used to readily determine methyl (or alkyl) branching positions in a saturated fatty acid methyl esters.

Gas‐phase chemistry of the methyl carbamate radical cation, H2NCOOCH. II—A test case for ion structure assignment

AbstractThe unimolecular chemistry of the methyl carbamate radical cation, H2NCOOCH, 1, has been further investigated by a combination of mass spectrometry‐based experiments (metastable ion (MI), collisional activation (CA), collision‐induced dissociative ionization (CIDI), neutralization‐reionization (NR) Spectrometry and 2H labelling) and ab initio molecular orbital calculations, executed at the MP3/6–31G*//4–31G level of theory and corrected for zero‐point vibrational energies. Apart from the previously located maxima, i.e. H2NCOOCH3+·, 1, the distonic ion H2NC(OH)OCH3+·, 2, hydrogen‐bridged ions [H2NCO…︁ H…︁OCH2]+·, 5, and [H2NCHO…︁…︁H…︁OCH]+·, 7, there exist at least two other equilibrium structures, viz. the iminol ion HNC(OH)OCH, la, and the hydrogen‐bridged species [H2CO…︁H…︁N(H)COH], 6a, which is closely related to ion 5. Although the iminol ion la lies only 30 kJ mol−1 above 1, our calculations indicate that the barriers for its formation either directly from ionized methyl carbamate 1 via a 1,3‐hydrogen shift or indirectly via 1,4‐hydrogen shifts from the distonic ion 2 are too high to allow the iminol ion to be involved in the unimolecular chemistry of ionized methyl carbamate. This explains the earlier observation that there are no H‐D exchange reactions prior to decomposition of ionized labelled methyl carbamate, in contrast to the related ion methyl acetate. However, attempts to generate the iminol ion by loss of CH3CN from CH3CHNNHCOOCH3 produced the more stable distonic ion 2 instead, but it proved very difficult to assign its structure unequivocally because 2 can rapidly interconvert with 1 and so virtually identical dissociation characteristics ensue. Only by integration of results obtained from many experiments and from ab initio calculations could structure 2 be assigned. The distonic ion 2 can undergo two transformations: after stretching of the COCH2 bond the incipient formaldehyde can migrate within the electrostatic field of ionized hydroxyaminocarbene to the OH end to generate 5, but it can also migrate to the NH end to generate 6a. This explains the previous puzzling observation that H2NCOOCD forms both CD2OD· and CD2OH· in CA and NR experiments. The calculations and experiments indicate that, although the ion is exceedingly difficult to characterize, the distonic ion 2 is the key intermediate for all the observed dissociations of methyl carbamate.

Tandem mass spectrometry of negative ions from choline phospholipid molecular species related to platelet activating factor

Fast atom bombardment mass spectrometry of choline phospholipids produces negative ions characteristic of the intact molecule and tandem mass spectrometry of collision-induced decomposition of M-15 anions characterizes both the identity and substituent position of radyl groups. Certain choline phospholipid molecular species which may be of special interest in the generation of platelet activating factor contain a highly unsaturated fatty acyl substituent at sn-2 and an ether radyl group at sn-1; other choline phospholipid molecular species which contain esterified arachidonic acid are of interest as potential sources of arachidonate for eicosanoid biosynthesis. Collisional activated decomposition of 1-hexadecanoyl-2-arachidonoyl-sn-glycero-phosphocholine produce abundant carboxylate anions at m/z 303 (arachidonate) and m/z 255 (hexadecanoate) in a ratio of 3:1, diagnostic for the sn-2 arachidonoyl position. The ether analog, 1-O-hexadecyl-2-arachidonoyl glycerophosphocholine, produces only one collision-induced dissociation ion at m/z 303 and no product ions corresponding to the ether substituent at sn-1. Molecular weight information from the M-15 ion combined with the CID generated carboxylate anions completely characterize these important phospholipids. Precursor ion studies of M-15 anions from glycero-phosphocholine lipids indicate that this ion is derived directly from a unique adduct ion formed by attachment of the molecular species to a matrix alkoxide ion, neutralizing the positive charge of the quaternary choline nitrogen. Decomposition of this adduct ion yields a methylated matrix molecule and the nominal M-15 ion.

Fast atom bombardment and collision-induced dissociation of prostaglandins and thromboxanes: Some examples of charge remote fragmentation

The mass spectra of products found by collisional activation of selected prostaglandins and thromboxanes were studied by tandem mass spectrometry as barium carboxylate salts and as carboxylate anions. Collision-induced dissociation (CID) of these closed shell ions generated by fast atom bombardment mass spectrometry reveals a wealth of structural information for these hydroxy acids. Decomposition reactions were found to be dependent upon the eicosanoid ring structure and the type of ion being studied, either positive or negative ion. The bariated carboxylate salts undergo reactions by processes that are similar to those previously characterized as charge remote mechanisms in which neutral species are lost as in thermal and photolytic decompositions. The most abundant ion is formed by loss of water from each of the hydroxyl groups present on the prostaglandin or thromboxane structure. For these multifunctionalized eicosanoids, typical patterns of decomposition emerge as characteristic of the oxygen substituents present along the carbon chain of the eicosanoid structure. The structural information obtained from the barium salts along with those from the carboxylate anions is substantially different, yet the structural information from each process is complementary. The CIDs of positive ions (metalated salts) provide structural information concerning the substituents between the carboxyl group and C 12 of the eicosanoid structure, whereas the decompositions of the carboxylate anions (negative ion mode) provide data concerning structure alterations of the eicosanoid structure between C 15 and C 20.

Determination of the fragmentation mechanisms of organophosphorus ions by H2O and D2O atmospheric‐pressure ionization tandem mass spectrometry II—dialkyl alkylphosphonate ions

AbstractDiethyl methylphosphonate (DEMP), diisopropyl methylpbosphonate (DIMP), diethyl isopropylphosphonate (DEIP) and diethyl ethylphosphonate (DEEP) were characterized by H2O and D2O atmospheric pressure ionization tandem mass Spectrometry (API‐MS/MS). Collision‐induced dissociation (CID)/fragmentation pathways included alkyl ions by direct cleavage, alkyl radical and water loss processes and McLafferty and McLafferty‐type rearrangements by six‐ and five‐membered ring transition states, respectively. D2O API proved particularly useful in that certain decomposition pathways (i.e. water and methanol neutral losses) had a statistical distribution as to the loss of an acid deuteron and proton(s). This phenomenon was manifested by two pairs of ions in the D2O API daughter‐ion mass spectrum for each phosphonate compound (e.g. both m/z 79/80 and 65/66 for DEMP and DIMP). The observed ion intensity ratios for these pairs of ions served as guides in the determination of their predicted ion relative abundance ratios and CID decomposition pathways.Water neutral losses as opposed to ether and alcohol neutral losses were favored for most of the protonated organophosphonate molecular ion decomposition schemes.

Formation and detection of neutral half-sandwich complexes MC 5H 5 (M = Fe, Co, Ni) using neutralization-reionization mass spectrometry (NRMS)

Beams of fast moving MC 5H + 5 ion (M = Fe, Co, Ni), generated by electron impact ionization of M(η 5-C 5H 5) 2, can be collisionally reduced in the gas phase to neutral MC 5H 5. Reionization is brought about in a second collision step. The resulting neutralization-reionization (NR) mass spectra, in conjunction with collisional activation (CA) and collision-induced dissociative ionization (CIDI) experiments are used to characterize some of the gas phase properties of MC 5H + 5 and MC 5H 5.

Neutralization-reionization of CH 4+•: At which stage does fragmentation occur?

Experimental (collision-induced dissociative ionization (CIDI) and neutralization-reionization mass spectrometry (NRMS)) and theoretical (ab initio molecular orbital) procedures were used to examine the origin of the fragmentation observed in NRMS experiments on the methane radical cation. Both theory and experiment indicate that in NRMS experiments involving neutralization by species of high ionization energy (e.g. Hg or Xe), the fragmentation occurs largely at the reionization rather than the neutralization stage. The reverse is true for the strongly exothermic neutralization with Na. Corresponding experiments [C 2H 6] +• ions showed similar behaviour.

H 3O + does not survive neutralization-reionization

An unsuccessful attempt has been made to verify the existence of the H 3O . radical over a brief time interval of 4 × 10 −7 s, which is the transit time between collision cell centres. The method employed was that of successive neutralization and reionization in spatially separated collision cells. Low-energy collision-induced dissociative ionization was employed to identify the reionized species of m/z 19 as DHO +..

Fragmentation isotope effects in the neutralization—reionization of the ethyne- d1 cation

A pronounced isotope effect has been observed in the neutralization—reionization mass spectrum (NRMS) of C 2HD + . The signal intensity ratios for each of C 2D + :C 2H + and CD + :CH + were found to be equal to 1.91 and 2.12, respectively. It is proposed that the major isotope effects observed occur in the collision-induced dissociative ionization (CIDI) of fast neutral C 2HD.

An investigation of the structures of isomeric ions derived from acetone, diacetone alcohol, and mesityl oxide

An investigation of the structures of isomeric ions formed in ion/molecule reactions occurring in 2-propanone (acetone), 4-hydroxy-4-mefhyl-2-pentanone (diacetone alcohol), and 4-methyl-3-penten-2-one (mesityl oxide) has been performed using a hybrid mass spectrometer of reversed geometry. Ions of m/z 117, which have been observed as products of ion/molecule reactions in acetone and in diacetone alcohol, may have a single structure if an aldol type condensation reaction occurs under acidic conditions in the gas phase; however, high energy collision induced dissociation (CID) results proved the two ions to be isomeric only.Dehydration of the m/z 117 ions produced a species of m/z 99 which, in the case of diacetone alcohol, may have the structure of protonated mesityl oxide. That the m/z 99 ion formed was unique to each system was demonstrated by high energy CID and kinetic energy release (KER) spectrometry. In the acetone system, CID results suggested that m/z 99 was an ion–dipole complex of [Formula: see text]; this hypothesis was tested by clustering [Formula: see text]with (CD3)2CO and comparison of its CID results with those obtained above. In the case of m/z 99 derived from diacetone alcohol or mesityl oxide, the neutral lost via metastable decomposition in the second field-free region was found to be C4H8, presumably 2-methyl propene. While the ion of m/z 99 may also eliminate methane to yield a species of m/z 83, the dominant metastable elimination from this ion is carbon monoxide rather than ethene as shown by collision induced dissociative ionization (CIDI). The ions of m/z 83 observed in the two systems exhibit very similar CID spectra; however, a small variation in the yield of products of m/z 41 and 43 suggests two structures for the ion derived from diacetone alcohol, one of which is identical to that seen in mesityl oxide.

Some general aspects of the chemistry of Organo-alkali metal ions. An overview of recent work

Organo-alkali metal ions of the type [M + xNa - ( x - 1)H] + ( x=1–3) are commonly observed in the desorption ionization mass spectra of polar organic molecules. An overview of our work on the formation and selected applications of organo-alkali metal ions is presented. We interpret our data as evidence that ions of the type [M + xA - ( x - 1)H] + are formed from [M + A(AX) n ] + cluster ions. Another important aspect of this work deals with the dissociation reactions of organo-alkali metal ions. We have found that structurally significant fragment ions are observed in the collision-induced dissociation (CID) spectra of [M + A] + ions that are not observed in the [M + H] + ion CID spectrum. We attribute these differences to functional group basicity and organo-alkali metal ion binding energies. That is, alkali metal ions are bound to specific sites of the organic molecule and the fragment ions formed upon CID are indications of the structure of the ionic organo-alkali metal ion complex.