Origin of product ions in the MS/MS spectra of peptides in a quadrupole ion trap

Stored waveform inverse Fourier transform and double resonance techniques have been used in conjunction with a quadrupole ion trap to study the dissociation patterns of peptide ions. These experiments provide insight into the origin of individual product ions in an MS/MS spectrum. Results show for a series of leucine enkephalin analogues with five amino acid residues that the b ₄ ion is the main product ion through which many other product ions arise. It was also observed that the percentage of the a ₄ product ions that are formed directly from the protonated molecule (M+H)⁺ depends on the nature of the fourth amino acid residue. In addition, it was determined that in the peptides studied here lower series b ions (e.g., b ₃ arise from direct dissociation of higher series b ions (e.g., b ₄ only about 50% of the time.     

Assigning the ESI mass spectra of organometallic and coordination compounds

Electrospray ionization mass spectrometry (ESI‐MS) is a useful technique for solving organometallic and coordination chemistry characterization problems that are difficult to address using traditional methods. However, assigning the ESI mass spectra of such compounds can be challenging, and the considerations involved in doing so are quite different from assigning the mass spectra of purely organic samples. This is a tutorial article for organometallic/coordination chemists using ESI‐MS to analyze pure compounds or reaction mixtures. The fundamentals of assigning ESI mass spectra are discussed within the context of organometallic and coordination systems. The types of ions commonly observed by ESI‐MS are categorized and described. Finally, a step‐by‐step guide for the assignment of organometallic and coordination chemistry ESI mass spectra is provided along with two case studies.     

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

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

The loss of water from molecular ions of aliphatic ketones in electron-impact mass spectra

In a series of straight chain aliphatic ketones which has been studied, it has been shown that the structural requirement for loss of water from the molecular ions produced by electron-impact is an alkyl group of seven or more carbon atoms attached to the carbonyl function.     

The internal energy of product ions formed in mass spectral reactions

Major factors which determine the distribution of internal energy of a primary product ion A⁺, P(E)_A+, at formation are delineated in terms of the quasi-equilibrium theory and a variety of experimental evidence is offered to support these conclusions. These major factors include: the P(E) of the molecular ion, the rate constants as a function of energy, κ(E), for M⁺·→A⁺ + N⁰ and for competing reactions of M⁺·, and the partitioning of excess internal energy between A⁺ and N⁰. The ‘fluctuation effect’ on this partitioning makes P(E)_A+ relatively insensitive to many structural and energy changes.     

Pseudotropylium and cyclopentadienyl ions in the mass spectra of tri-N-methylborazines

Ion kinetic energy spectra of a series of tri-N-methylborazines suggest the possible formation of cyclopentadienyl-like ions, by metastable decomposition in the first field free region of a mass spectrometer, from their tropylium-like ions.     

Collisional activation mass spectra of pentene and hexene molecular ions

The collisional activation spectra of the molecular ions from fourteen pentene and hexene isomers show substantial differences, some of which can be rationalized using known ion fragmentation mechanisms. These differences, and their negligible dependence on ion internal energy, are advantageous for the structural characterization of such isomeric ions, including those produced by fragmentation of larger molecules. The decompositions of metastable ions of the pentenes were nearly identical, but those of the hexenes showed some differences useful for structural charactrization.     

Automated structural assignment of derivatized complex N-linked oligosaccharides from tandem mass spectra

Glycoprotein function is controlled by several biological factors, one of them being the structure of carbohydrate chains (glycans) attached to specific amino acids of the protein backbone. Changes in glycan structures have been shown to modify the secondary and tertiary conformation of glycoproteins, thus their function. Powerful analytical tools are available for the characterization of sugar structures, and recently mass spectrometry (MS) has been increasingly useful for this purpose. Manual interpretation of tandem mass spectrum is possible but tedious. Automated interpretation should speed the analysis and enhance the results obtained. A new computer program for automated interpretation of tandem MS spectra of complex N-linked glycans oligosaccharides from mammals will be described. N-Linked oligosaccharides standards were derivatized with 1-phenyl-3-methyl-5-pyrazolone (PMP) and analyzed by matrix-assisted laser desorption/ionization (MALDI)-tandem MS. Simulated tandem mass spectra of other common glycans were also generated to test the algorithm. The MALDI-MS/MS spectra featured resolved isotopic distributions for the [M + H](+) and fragment ions of oligosaccharides. These isotopic distributions complicated the automated analysis of the spectra and were removed to leave only monoisotopic peaks. An algorithm was written for this purpose, yielding simplified tandem mass spectra. Another algorithm is then used to determine the structure of the oligosaccharide. A score is then given to each structure, depending on agreement with experimental results. The program successfully assigned the true structure in 24 out of the 28 cases (86%) and the true structure was among the three top scoring structures in all cases.     

Structure and fragmentation of b2 ions in peptide mass spectra

In a number of cases the b2 ion observed in peptide mass spectra fragments directly to the a1 ion. The present study examines the scope of this reaction and provides evidence as to the structure(s) of the b2 ions undergoing fragmentation to the a1 ion. The b2 ion H-Ala-Gly+ fragments, in part, to the a1 ion, whereas the isomeric b2 ion H-Gly-Ala+ does not fragment to the a1 ion. Ab initio calculations of ion energies show that this different behavior can be rationalized in terms of protonated oxazolone structures for the b2 ions provided one assumes a reverse activation energy of approximately 1 eV for the reaction b2-->a2; such a reverse activation energy is consistent with experimental kinetic energy release measurements. Experimentally, the H-Aib-Ala+ b2 ion, which must have a protonated oxazolone structure, fragments extensively to the a1 ion. We conclude that the proposal by Eckart et al. (J. Am. Soc. Mass Spectrom. 1998, 9, 1002) that the b2 ions which undergo fragmentation to a1 ions have an immonium ion structure is not necessary to rationalize the results, but that the fragmentation does occur from a protonated oxazolone structure. It is shown that the b2-->a1 reaction occurs extensively when the C-terminus residue in the b2 ion is Gly and with less facility when the C-terminus residue is Ala. When the C-terminus residue is Val or larger, the b2-->a1 reaction cannot compete with the b2-->a2 fragmentation reaction. Some preliminary results on the fragmentation of a2 ions are reported.     

FiD: a software for ab initio structural identification of product ions from tandem mass spectrometric data

We present FiD (Fragment iDentificator), a software tool for the structural identification of product ions produced with tandem mass spectrometric measurement of low molecular weight organic compounds. Tandem mass spectrometry (MS/MS) has proven to be an indispensable tool in modern, cell-wide metabolomics and fluxomics studies. In such studies, the structural information of the MS(n) product ions is usually needed in the downstream analysis of the measurement data. The manual identification of the structures of MS(n) product ions is, however, a nontrivial task requiring expertise, and calls for computer assistance. Commercial software tools, such as Mass Frontier and ACD/MS Fragmenter, rely on fragmentation rule databases for the identification of MS(n) product ions. FiD, on the other hand, conducts a combinatorial search over all possible fragmentation paths and outputs a ranked list of alternative structures. This gives the user an advantage in situations where the MS/MS data of compounds with less well-known fragmentation mechanisms are processed. FiD software implements two fragmentation models, the single-step model that ignores intermediate fragmentation states and the multi-step model, which allows for complex fragmentation pathways. The software works for MS/MS data produced both in positive- and negative-ion modes. The software has an easy-to-use graphical interface with built-in visualization capabilities for structures of product ions and fragmentation pathways. In our experiments involving amino acids and sugar-phosphates, often found, e.g., in the central carbon metabolism of yeasts, FiD software correctly predicted the structures of product ions on average in 85% of the cases. The FiD software is free for academic use and is available for download from www.cs.helsinki.fi/group/sysfys/software/fragid. Copyright (c) 2008 John Wiley & Sons, Ltd.     

The stability of the molecular and some fragmentary ions in the mass spectra of cardenolides

Summary The stability of the molecular ions of the cardenolides depends to the greatest extent on the nature of the substituent at C₁₀. A tendency is observed to a decrease in the intensities of the peaks of the main ions of the series formed by the cleavage of the bonds of the steroid skeleton with a decrease in the stability of the M⁺ ion. The anomalous increase in the intensity of some fragmentary ions in the spectra of the 19^–COOR compounds is due to the lactonization of the latter under the conditions of mass spectrometry.Institute of the Chemistry of Plant Substances, Academy of Sciences of the Uzbek SSR. Translated from Khimiya Prirodnykh Soedinenii, No. 2, pp. 158–166, March–April, 1975.     

Cluster ions of diquat and paraquat in electrospray ionization mass spectra and their collision-induced dissociation spectra

Cluster ions such as [Cat+X+nM](+) (n = 0-4); [Cat-H+nM](+) (n = 1-3); and [2(Cat-H)+X+nM](+) (n = 0-2), where Cat, X, and M are the dication, anion, and neutral salt (CatX(2)), respectively, are observed in electrospray ionization (ESI) mass spectrometry of relatively concentrated solutions of diquat and paraquat. Collision-induced dissociation (CID) reactions of the clusters were observed by tandem mass spectrometry (MS/MS), including deprotonation to form [Cat-H](+), one-electron reduction of the dication to form Cat(+.), demethylation of the paraquat cation to form [Cat-CH(3)](+), and loss of neutral salt to produce smaller clusters. The difference in acidity and reduction power between diquat and paraquat, evaluated by thermodynamical estimates, can rationalize the different fractional yields of even-electron ([Cat-H](+) and its clusters) and odd-electron (mostly Cat(+)) ions in ESI mass spectra of these pesticides. The [Cat+n. Solv](2+) doubly charged cluster ions, where n 相似文献   

Structural characterizations of lipids A by MS/MS of doubly charged ions on a hybrid linear ion trap/orbitrap mass spectrometer

Here, a new 'one pot' and fast approach is described, based on electrospray ionization (ESI) of negative ions by using a hybrid linear ion trap/orbitrap mass spectrometer (LTQ/orbitrap) for MS and MS/MS analysis. By this method the distribution of the primary and secondary acyl residues of the intact lipid A is inferred by analysis of the ESI spectra measured in positive and negative mode. The analysis of these data allows an unequivocal assignment of the fatty acid distribution. This methodology was successfully tested on two different lipid A with known structures, deriving from the Agrobacterium tumefaciens and Escherichia coli lipopolysaccharides (LPS).     

MS2Grouper: Group assessment and synthetic replacement of duplicate proteomic tandem mass spectra

Shotgun proteomics experiments require the collection of thousands of tandem mass spectra; these sets of data will continue to grow as new instruments become available that can scan at even higher rates. Such data contain substantial amounts of redundancy with spectra from a particular peptide being acquired many times during a single LC-MS/MS experiment. In this article, we present MS2Grouper, an algorithm that detects spectral duplication, assesses groups of related spectra, and replaces these groups with synthetic representative spectra. Errors in detecting spectral similarity are corrected using a paraclique criterion-spectra are only assessed as groups if they are part of a clique of at least three completely interrelated spectra or are subsequently added to such cliques by being similar to all but one of the clique members. A greedy algorithm constructs a representative spectrum for each group by iteratively removing the tallest peaks from the spectral collection and matching to peaks in the other spectra. This strategy is shown to be effective in reducing spectral counts by up to 20% in LC-MS/MS datasets from protein standard mixtures and proteomes, reducing database search times without a concomitant reduction in identified peptides.     

A preconcentrator coupled to a GC/FTMS: Advantages of self-chemical ionization,mass measurement accuracy,and high mass resolving power for GC applications

Coupling of a cryogenic preconcentrator (PC) to a gas chromatograph/Fourier transform ion cyclotron resonance mass spectrometer (GC/FT-ICR MS) is reported. To demonstrate the analytical capabilities of the PC/GC/FT-ICR MS, headspace samples containing volatile organic compounds (VOCs) emitted from detached pine tree twigs were analyzed. Sub-ppm mass measurement accuracy (MMA) for highly resolved (m/Deltam(50%) > 150 k) terpene ions was achieved. Direct PC/GC/FT-ICR MS analyses revealed that detached twigs from pine trees emit acetone, camphor, and four detectable hydrocarbon isomers with C(10)H(16) empirical formula. The unknown analytes were identified based on accurate mass measurement and their mass spectral appearances. Authentic samples were used to confirm initially unknown identifications. Self-chemical-ionization (SCI) reactions furnished an additional dimension for rapid isomer differentiation of GC eluents in real time.     

The mass spectra of carboxylic acids—VI: Metastable dissociations of isomeric ions in the mass spectra of oxalic and formic acids,and malonic and acetic acids

Metastable ion peak shapes and abundances have been studied for competing dissociations of the [H₂CO₂]^+. ions produced in the mass spectra of formic and oxalic acids, and of [H₄C₂O₂]^+. ions produced from acetic and malonic acids. It is concluded that for each pair ions different with respect to structure and energy content are present; the difference is more apparent in the [H₄C₂O₂]^+. ions than in the smaller [H₂CO₂]^+. species.