Unexpected Gas-Phase Nitrogen-Oxygen Smiles Rearrangement: Collision-Induced Dissociation of Deprotonated 2-(N-Methylanilino)ethanol and Morpholinylbenzoic Acid Derivatives.

A nitrogen-oxygen Smiles rearrangement was reported to occur after collisional activation of the PhN(R)CH2CH2O- (R = alkyl) anion, which undergoes a five-membered ring rearrangement to form a phenoxide ion C6H5O-. When R = H, such a Smiles rearrangement is unlikely since the negative charge is more favorably located on the nitrogen atom than the oxygen atom; hence, alternative neutral losses dominate the fragmentation. For example, collisional activation of deprotonated 2-anilinoethanol (PhN-CH2CH2OH) leads to the formation of an anilide anion (C6H5NH-, m/z 92) rather than a phenoxide ion (C6H5O-, m/z 93.0343). However, when the amino hydrogen of 2-anilinoethanol is substituted by a methyl group, i.e., 2-(N-methylanilino)ethanol, a Smiles rearrangement does occur, leading to the phenoxide ion, as the negative charge can only reside on the oxygen atom. To confirm the Smiles rearrangement mechanism, 2-(N-methylanilino)ethanol-18O was synthesized and subjected to collisional activation, leading to an intense peak at m/z 95.0385, which corresponds to the 18O phenoxide ion ([C6H518O]-). The abundance of the phenoxide ion is sensitive to substituents on the N atom, as demonstrated by the observation that an ethyl substituent results in the rearrangement ion with a much lower abundance. The nitrogen-oxygen Smiles rearrangement also occurs for various morpholinylbenzoic acid derivatives with a multistep mechanism, where the phenoxide ion is found to be predominantly formed after loss of CO2, proton transfers, breaking of the morpholine ring, and Smiles rearrangement. The Smiles mechanism is also supported by density functional theory calculations and other observations.

MS_Piano: A Software Tool for Annotating Peaks in CID Tandem Mass Spectra of Peptides and N-Glycopeptides.

Annotating product ion peaks in tandem mass spectra is essential for evaluating spectral quality and validating peptide identification. This task is more complex for glycopeptides and is crucial for the confident determination of glycosylation sites in glycoproteins. MS_Piano (Mass Spectrum Peptide Annotation) software was developed for reliable annotation of peaks in collision induced dissociation (CID) tandem mass spectra of peptides or N-glycopeptides for given peptide sequences, charge states, and optional modifications. The program annotates each peak in high or low resolution spectra with possible product ion(s) and the mass difference between the measured and theoretical m/z values. Spectral quality is measured by two major parameters: the ratio between the sum of unannotated vs all peak intensities in the top 20 peaks, and the intensity of the highest unannotated peak. The product ions of peptides, glycans, and glycopeptides in spectra are labeled in different class-type colors to facilitate interpretation. MS_Piano assists validating peptide and N-glycopeptide identification from database and library searches and provides quality control and optimizes search reliability in custom developed peptide mass spectral libraries. The software is freely available in .exe and .dll formats for the Windows operating system.

CID Fragmentation of Deprotonated N-Acyl Aromatic Sulfonamides. Smiles-Type and Nitrogen-Oxygen Rearrangements.

The NIST tandem mass spectral library (2020 version) includes over 800 aromatic sulfonamides. In negative mode, upon collisional activation most benzenesulfonamides lose a neutral SO2 molecule leading to an anilide anion (C6H5NH-, m/z 92). However, for deprotonated N-benzoyl aromatic sulfonamides, the phenoxide ion (C6H5O-, m/z 93.0343) is the principal product ion. A variety of N-acylbenzenesulfonamide derivatives were also found to overwhelmingly produce the phenoxide ion as the most intense product ion. A mechanism is proposed in which, at low energy, a carbonyl oxygen atom (C═O) is transferred to a benzene ring, known as a Smiles-type rearrangement (the amide oxygen atom attacks the arylsulfonyl group at the ipso position), in parallel and determining the reaction at high energy a nitrogen-oxygen rearrangement mechanism leads to the formation of the phenoxide ion. Tandem mass spectra of deprotonated N-benzoyl-18O-benzenesulfonamide and N-thiobenzoyl-p-toluenesulfonamide confirmed the rearrangement since base peaks at m/z 95.0384 and 123.0270 which correspond to an 18O phenoxide ion ([C6H518O]-) and a 4-methylbenzenethiolate anion ([CH3C6H4S]-) were observed, respectively. The parallel mechanism is supported by the strong correlation between the observed product ion intensities and the corresponding activation energies obtained by Density Functional Theory calculations. This is an example of a relatively simple ion with a complex path to fragmentation, being a cautionary tale for indiscriminate use of in silico spectra in place of actual measurement.

Collision-Induced Dissociation of Deprotonated Peptides. Relative Abundance of Side-Chain Neutral Losses, Residue-Specific Product Ions, and Comparison with Protonated Peptides.

High-accuracy MS/MS spectra of deprotonated ions of 390 dipeptides and 137 peptides with three to six residues are studied. Many amino acid residues undergo neutral losses from their side chains. The most abundant is the loss of acetaldehyde from threonine. The abundance of losses from the side chains of other amino acids is estimated relative to that of threonine. While some amino acids lose the whole side chain, others lose only part of it, and some exhibit two or more different losses. Side-chain neutral losses are less abundant in the spectra of protonated peptides, being significant mainly for methionine and arginine. In addition to the neutral losses, many amino acid residues in deprotonated peptides produce specific negative ions after peptide bond cleavage. An expanded list of fragment ions from protonated peptides is also presented and compared with those of deprotonated peptides. Fragment ions are mostly different for these two cases. These lists of fragments are used to annotate peptide mass spectral libraries and to aid in the confirmation of specific amino acids in peptides. Graphical Abstract ᅟ.

Extending a Tandem Mass Spectral Library to Include MS2 Spectra of Fragment Ions Produced In-Source and MSn Spectra.

Tandem mass spectral library searching is finding increased use as an effective means of determining chemical identity in mass spectrometry-based omics studies. We previously reported on constructing a tandem mass spectral library that includes spectra for multiple precursor ions for each analyte. Here we report our method for expanding this library to include MS2 spectra of fragment ions generated during the ionization process (in-source fragment ions) as well as MS3 and MS4 spectra. These can assist the chemical identification process. A simple density-based clustering algorithm was used to cluster all significant precursor ions from MS1 scans for an analyte acquired during an infusion experiment. The MS2 spectra associated with these precursor ions were grouped into the same precursor clusters. Subsequently, a new top-down hierarchical divisive clustering algorithm was developed for clustering the spectra from fragmentation of ions in each precursor cluster, including the MS2 spectra of the original precursors and of the in-source fragments as well as the MSn spectra. This algorithm starts with all the spectra of one precursor in one cluster and then separates them into sub-clusters of similar spectra based on the fragment patterns. Herein, we describe the algorithms and spectral evaluation methods for extending the library. The new library features were demonstrated by searching the high resolution spectra of E. coli extracts against the extended library, allowing identification of compounds and their in-source fragment ions in a manner that was not possible before. Graphical Abstract ᅟ.

Interconversion of Peptide Mass Spectral Libraries Derivatized with iTRAQ or TMT Labels.

Derivitization of peptides with isobaric tags such as iTRAQ and TMT is widely employed in proteomics due to their compatibility with multiplex quantitative measurements. We recently made publicly available a large peptide library derived from iTRAQ 4-plex labeled spectra. This resource has not been used for identifying peptides labeled with related tags with different masses, because values for virtually all masses of precursor and most product ions would differ for ions containing the different tags as well as containing different tag-specific peaks. We describe a method for interconverting spectra from iTRAQ 4-plex to TMT (6- and 10-plex) and to iTRAQ 8-plex. We interconvert spectra by appropriately mass shifting sequence ions and discarding derivative-specific peaks. After this "cleaning" of search spectra, we demonstrate that the converted libraries perform well in terms of peptide spectral matches. This is demonstrated by comparing results using sequence database searches as well as by comparing search effectiveness using original and converted libraries. At 1% FDR TMT labeled query spectra match 97% as many spectra against a converted iTRAQ library as compared to an original TMT library. Overall this interconversion strategy provides a practical way to extend results from one derivatization method to others that share related chemistry and do not significantly alter fragmentation profiles.

Reaction of arylium ions with the collision gas N2 in electrospray ionization mass spectrometry.

RATIONALE: The tandem mass spectra of many compounds contained peaks which could not have arisen from the precursor ion. Such peaks were found to be due to reaction of arylium ions with N2 in the collision cell. Therefore, this reaction was studied in detail with representative compounds. METHODS: Various classes of compounds were dissolved in acetonitrile/water/formic acid and studied by electrospray ionization mass spectrometry to record their MS(2) and pseudo-MS(3) spectra in a QqQ mass spectrometer and their accurate m/z values in an Orbitrap Elite instrument. Arylium ions were found to react with N2 in the collision cell. The reaction was confirmed by pseudo-MS(3) studies, by comparison with authentic diazonium ions, and by the pressure dependence of the product ion survival yield. RESULTS: Reactions of arylium ions with N2 were observed with p-toluenesulfonic acid, o-toluenesulfonamide, phenylphosphonic acid, phenol, aniline, aminonaphthalenes, benzoic acid, benzophenone, and other compounds. By using a QqQ mass spectrometer, we observed that the protonated compounds produce arylium ions, which then react with N2 to form diazonium ions. The diazonium ion was produced with N2 but not with Ar in the collision cell, and its abundance increased with increasing N2 pressure. CONCLUSIONS: Arylium ions generated from a wide variety of compounds in electrospray ionization tandem mass spectrometry may react with N2 to form diazonium ions. The abundance of the diazonium ions is affected by collision energy and N2 pressure. This reaction should be considered when annotating peaks in MS/MS libraries. Published in 2015. This article is a U.S. Government work and is in the public domain in the USA.

Unexpected peaks in tandem mass spectra due to reaction of product ions with residual water in mass spectrometer collision cells.

RATIONALE: Certain product ions in electrospray ionization tandem mass spectrometry are found to react with residual water in the collision cell. This reaction often leads to the formation of ions that cannot be formed directly from the precursor ions, and this complicates the mass spectra and may distort MRM (multiple reaction monitoring) results. METHODS: Various drugs, pesticides, metabolites, and other compounds were dissolved in acetonitrile/water/formic acid and studied by electrospray ionization mass spectrometry to record their MS(2) and MS(n) spectra in several mass spectrometers (QqQ, QTOF, IT, and Orbitrap HCD). Certain product ions were found to react with residual water in collision cells. The reaction was confirmed by MS(n) studies and the rate of reaction was determined in the IT instrument using zero collision energy and variable activation times. RESULTS: Examples of product ions reacting with water include phenyl and certain substituted phenyl cations, benzoyl-type cations formed from protonated folic acid and similar compounds by loss of the glutamate moiety, product ions formed from protonated cyclic siloxanes by loss of methane, product ions formed from organic phosphates, and certain negative ions. The reactions of product ions with residual water varied greatly in their rate constant and in the extent of reaction (due to isomerization). CONCLUSIONS: Various types of product ions react with residual water in mass spectrometer collision cells. As a result, tandem mass spectra may contain unexplained peaks and MRM results may be distorted by the occurrence of such reactions. These often unavoidable reactions must be taken into account when annotating peaks in tandem mass spectra and when interpreting MRM results. Published in 2014. This article is a U.S. Government work and is in the public domain in the USA.

Loss of H2 and CO from protonated aldehydes in electrospray ionization mass spectrometry.

RATIONALE: Electrospray ionization mass spectrometry (ESI-MS) of many protonated aldehydes shows loss of CO as a major fragmentation pathway. However, we find that certain aldehydes undergo loss of H2 followed by reaction with water in the collision cell. This complicates interpretation of tandem mass (MS/MS) spectra and affects multiple reaction monitoring (MRM) results. METHODS: 3-Formylchromone and other aldehydes were dissolved in acetonitrile/water/formic acid and studied by ESI-MS to record their MS(2) and MS(n) spectra in several mass spectrometers (QqQ, QTOF, ion trap (IT), and Orbitrap HCD). Certain product ions were found to react with water and the rate of reaction was determined in the IT instrument using zero collision energy and variable activation times. Theoretical calculations were performed to help with the interpretation of the fragmentation mechanism. RESULTS: Protonated 3-formylchromones and 3-formylcoumarins undergo loss of H2 as a major fragmentation route to yield a ketene cation, which reacts with water to form a protonated carboxylic acid. In general, protonated aldehydes which contain a vicinal group that forms a hydrogen bridge with the formyl group undergo significant loss of H2. Subsequent losses of CO and C3O are also observed. Theoretical calculations suggest mechanistic details for these losses. CONCLUSIONS: Loss of H2 is a major fragmentation channel for protonated 3-formychromones and certain other aldehydes and it is followed by reaction with water to produce a protonated carboxylic acid, which undergoes subsequent fragmentation. This presents a problem for reference libraries and raises concerns about MRM results.

Quality control for building libraries from electrospray ionization tandem mass spectra.

Electrospray ionization (ESI) tandem mass spectrometry coupled with liquid chromatography is a routine technique for identifying and quantifying compounds in complex mixtures. The identification step can be aided by matching acquired tandem mass spectra (MS(2)) against reference library spectra as is routine for electron ionization (EI) spectra from gas chromatography/mass spectrometry (GC/MS). However, unlike the latter spectra, ESI MS(2) spectra are likely to originate from various precursor ions for a given target molecule and may be acquired at varying energies and resolutions and have characteristic noise signatures, requiring processing methods very different from EI to obtain complete and high quality reference spectra for individual analytes. This paper presents procedures developed for creating a tandem mass spectral library that addresses these factors. Library building begins by acquiring MS(2) spectra for all major MS(1) peaks in an infusion run, followed by assigning MS(2) spectra to clusters and creating a consensus spectrum for each. Intensity-based constraints for cluster membership were developed, as well as peak testing to recognize and eliminate suspect peaks and reduce noise. Consensus spectra were then examined by a human evaluator using a number of criteria, including a fraction of annotated peaks and consistency of spectra for a given ion at different energies. These methods have been developed and used to build a library from >9000 compounds, yielding 230,000 spectra.

Metabolite profiling of a NIST Standard Reference Material for human plasma (SRM 1950): GC-MS, LC-MS, NMR, and clinical laboratory analyses, libraries, and web-based resources.

Recent progress in metabolomics and the development of increasingly sensitive analytical techniques have renewed interest in global profiling, i.e., semiquantitative monitoring of all chemical constituents of biological fluids. In this work, we have performed global profiling of NIST SRM 1950, "Metabolites in Human Plasma", using GC-MS, LC-MS, and NMR. Metabolome coverage, difficulties, and reproducibility of the experiments on each platform are discussed. A total of 353 metabolites have been identified in this material. GC-MS provides 65 unique identifications, and most of the identifications from NMR overlap with the LC-MS identifications, except for some small sugars that are not directly found by LC-MS. Also, repeatability and intermediate precision analyses show that the SRM 1950 profiling is reproducible enough to consider this material as a good choice to distinguish between analytical and biological variability. Clinical laboratory data shows that most results are within the reference ranges for each assay. In-house computational tools have been developed or modified for MS data processing and interactive web display. All data and programs are freely available online at http://peptide.nist.gov/ and http://srmd.nist.gov/ .

Formation of y + 10 and y + 11 ions in the collision-induced dissociation of peptide ions.

Tandem mass spectra of peptide ions, acquired in shotgun proteomic studies of selected proteins, tissues, and organisms, commonly include prominent peaks that cannot be assigned to the known fragmentation product ions (y, b, a, neutral losses). In many cases these persist even when creating consensus spectra for inclusion in spectral libraries, where it is important to determine whether these peaks represent new fragmentation paths or arise from impurities. Using spectra from libraries and synthesized peptides, we investigate a class of fragment ions corresponding to y(n-1) + 10 and y(n-1) + 11, where n is the number of amino acid residues in the peptide. These 10 and 11 Da differences in mass of the y ion were ascribed before to the masses of [+ CO - H(2)O] and [+ CO - NH(3)], respectively. The mechanism is suggested to involve dissociation of the N-terminal residue at the CH-CO bond following loss of H(2)O or NH(3). MS(3) spectra of these ions show that the location of the additional 10 or 11 Da is at the N-terminal residue. The y(n-1) + 10 ion is most often found in peptides with N-terminal proline, asparagine, and histidine, and also with serine and threonine in the adjacent position. The y(n-1) + 11 ion is observed predominantly with histidine and asparagine at the N-terminus, but also occurs with asparagine in positions two through four. The intensities of the y(n-1) + 10 ions decrease with increasing peptide length. These data for y(n-1) + 10 and y(n-1) + 11 ion formation may be used to improve peptide identification from tandem mass spectra.

Charge states of y ions in the collision-induced dissociation of doubly charged tryptic peptide ions.

Bonds that break in collision-induced dissociation (CID) are often weakened by a nearby proton, which can, in principle, be carried away by either of the product fragments. Since peptide backbone dissociation is commonly charge-directed, relative intensities of charge states of product y- and b-ions depend on the final location of that proton. This study examines y-ion charge distributions for dissociation of doubly charged peptide ions, using a large reference library of peptide ion fragmentation generated from ion-trap CID of peptide ions from tryptic digests. Trends in relative intensities of y(2+) and y(1+) ions are examined as a function of bond cleavage position, peptide length (n), residues on either side of the bond and effects of residues remote from the bond. It is found that y(n-2)/b(2) dissociation is the most sensitive to adjacent amino acids, that y(2+)/y(1+) steadily increase with increasing peptide length, that the N-terminal amino acid can have a major influence in all dissociations, and in some cases other residues remote from the bond cleavage exert significant effects. Good correlation is found between the values of y(2+)/y(1+) for the peptide and the proton affinities of the amino acids present at the dissociating peptide bond. A few deviations from this correlation are rationalized by specific effects of the amino acid residues. These correlations can be used to estimate trends in y(2+)/y(1+) ratios for peptide ions from amino acid proton affinities.

Loss of 45 Da from a2 ions and preferential loss of 48 Da from a2 ions containing methionine in peptide ion tandem mass spectra.

While analyzing tandem mass spectra of tryptic tripeptides, intense unassigned peaks were observed, corresponding to neutral loss of 45 Da from a(2) ions. This process was confirmed by MS(3) experiments. Based on exact mass analysis, the loss was ascribed to (NH(3) + CO) or formamide. The proposed mechanism involves a cyclic form of the a(2) ions. The structure of the a(2) - 45 ions was confirmed by their fragmentation in MS(3) experiments. Loss of (NH(3) + CO) from the a(2) ions occurs in competition with other paths, such as the loss of H(2)O or the formation of immonium ions. However, if the a(2) ion contains methionine, a neutral loss of 48 Da (ascribed to CH(3)SH) predominates, and is followed by the loss of (NH(3) + CO). These processes were confirmed by MS(3) experiments. The intensity of the a(2) - 48 peak formed from XaaMet has a maximum value of 42% (of the total intensity of all ions) for Xaa=Gly, varies between 15% and 40% for most other Xaa residues, is lower for residues that can undergo loss of water or ammonia, and is very low for Lys or Arg. When the order of the residues is reversed to MetXaa, the loss of 48 Da is much smaller. This effect can be used to determine the sequence of b(2) ions containing Met in proteomic studies. Considerable loss of CH(3)SH is observed from doubly protonated tryptic tripeptides with N-terminal Met, but the loss is much less when they are singly protonated or when Met is in the center position.

Electrospray tandem quadrupole fragmentation of quinolone drugs and related ions. On the reversibility of water loss from protonated molecules.

Selected reaction monitoring (SRM) of quinolone drugs showed different sensitivities in aqueous solution vs. biological extract. The authors suggested formation of two singly protonated molecules with different behavior, one undergoing loss of H(2)O and the other loss of CO(2), so that SRM transitions might depend on the ratios of these forms generated by the electrospray. These surprising results prompted us to re-examine several quinolone drugs and some simpler compounds to further elucidate the mechanisms. We find that the relative contributions of loss of H(2)O vs. loss of CO(2) in tandem mass spectrometric (MS/MS) experiments depend not only on molecular structure and collision energy, but also, in certain cases, on the cone voltage. We further find that many product ions formed by loss of H(2)O can reattach a water molecule in the collision cell, whereas ions formed by loss of CO(2) do not. Since reattachment of H(2)O can occur after water loss in the cone region and prior to selection of the precursor ion, this effect leads to the dependence of MS/MS spectra on the cone voltage used in creating the precursor ion, which explains the formerly observed effect on SRM ratios. Our results support the earlier conclusion that varying amounts of two ions of the same m/z value are responsible for problems in the analysis of these drugs, but the origin is in dehydration/rehydration reactions. Thus, SRM transitions for certain complex compounds may be comparable only when monitored under equivalent ion-forming conditions, including the voltage used in the production of the protonated molecules in the electrospray ionization (ESI) source.

Effect of N-terminal glutamic acid and glutamine on fragmentation of peptide ions.

A prominent dissociation path for electrospray generated tryptic peptide ions is the dissociation of the peptide bond linking the second and third residues from the amino-terminus. The formation of the resulting b(2) and y(n-2) fragments has been rationalized by specific facile mechanisms. An examination of spectral libraries shows that this path predominates in diprotonated peptides composed of 12 or fewer residues, with the notable exception of peptides containing glutamine or glutamic acid at the N-terminus. To elucidate the mechanism by which these amino acids affect peptide fragmentation, we synthesized peptides of varying size and composition and examined their MS/MS spectra as a function of collision voltage in a triple quadrupole mass spectrometer. Loss of water from N-terminal glutamic acid and glutamine is observed at a lower voltage than any other fragmentation, leading to cyclization of the terminal residue. This cyclization results in the conversion of the terminal amine group to an imide, which has a lower proton affinity. As a result, the second proton is not localized at the N-terminus but is readily transferred to other sites, leading to fragmentation near the center of the peptide. Further confirmation was obtained by examining peptides with N-terminal pyroglutamic acid and N-acetyl peptides. Peptides with N-terminal proline maintain the trend of forming b(2) and y(n-2) because their ring contains an imine rather than imide and has sufficient proton affinity to retain the proton at the N-terminus.

Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses.

A major unmet need in LC-MS/MS-based proteomics analyses is a set of tools for quantitative assessment of system performance and evaluation of technical variability. Here we describe 46 system performance metrics for monitoring chromatographic performance, electrospray source stability, MS1 and MS2 signals, dynamic sampling of ions for MS/MS, and peptide identification. Applied to data sets from replicate LC-MS/MS analyses, these metrics displayed consistent, reasonable responses to controlled perturbations. The metrics typically displayed variations less than 10% and thus can reveal even subtle differences in performance of system components. Analyses of data from interlaboratory studies conducted under a common standard operating procedure identified outlier data and provided clues to specific causes. Moreover, interlaboratory variation reflected by the metrics indicates which system components vary the most between laboratories. Application of these metrics enables rational, quantitative quality assessment for proteomics and other LC-MS/MS analytical applications.

Collisional energy dependence of peptide ion fragmentation.

The energy dependence of fragmentation in a collision cell was measured for 2400 protonated peptide ions derived from the digestion of 24 proteins. The collision voltage at which the sum of the fragment ion abundances was equal to the remaining parent ion (V(1/2)) was the principal measure of fragmentation effectiveness. Each class of peptides was characterized by a linear relation between V(1/2) and m/z whose slope depended on the peptide class and, with little adjustment, intersected the origin. Peptide ions where the number of protons is no greater than the number of arginine residues show the greatest slope, V(1/2)/(m/z) = 0.0472 (all slopes in units of V Da(-1) e). For peptides where the number of protons is greater than the number of arginines, but not greater than the total number of basic residues, the slope decreases to 0.0414 for singly charged ions, 0.0382 for doubly charged, 0.0346 for triply charged, and 0.0308 for more highly charged ions. With one mobile proton, the slope is about 0.029 for singly and doubly charged ions and slightly lower for more highly charged ions. With two or more mobile protons the slope is 0.0207. By removing m/z dependence, the deviation of V(1/2) from a line provides a relative measure of the ease of fragmentation of an ion in each class. This information can guide the selection of optimal conditions for tandem mass spectrometry studies in collision cells for selected peptide ions as well as aid in comparing the reactivity of ions differing in m/z and charge state.

Dehydration versus deamination of N-terminal glutamine in collision-induced dissociation of protonated peptides.

Some of the most prominent "neutral losses" in peptide ion fragmentation are the loss of ammonia and water from N-terminal glutamine. These processes are studied by electrospray ionization mass spectrometry in singly- and doubly-protonated peptide ions undergoing collision-induced dissociation in a triple quadrupole and in an ion trap instrument. For this study, four sets of peptides were synthesized: (1) QLLLPLLLK and similar peptides with K replaced by R, H, or L, and Q replaced by a number of amino acids, (2) QLnK (n = 0, 1, 3, 5, 7, 9, 11), (3) QLnR (n = 0, 1, 3, 5, 7, 9), and (4) QLn (n = 1, 2, 3, 4, 8). The results for QLLLPLLLK and QLLLPLLLR show that the singly protonated ions undergo loss of ammonia and to a smaller extent loss of water, whereas the doubly protonated ions undergo predominant loss of water. The fast fragmentation next to P (forming the y5 ion) occurs to a larger extent than the neutral losses from the singly protonated ions but much less than the water loss from the doubly protonated ions. The results from these and other peptides show that, in general, when N-terminal glutamine peptides have no "mobile protons", that is, the number of charges on the peptide is no greater than the number of basic amino acids (K, R, H), deamination is the predominant neutral loss fragmentation, but when mobile protons are present the predominant process is the loss of water. Both of these processes are faster than backbone fragmentation at the proline. These results are rationalized on the basis of resonance stabilization of the two types of five-membered ring products that would be formed in the neutral loss processes; the singly protonated ion yields the more stable neutral pyrrolidinone ring whereas the doubly protonated ion yields the protonated aminopyrroline ring (see Schemes). The generality of these trends is confirmed by analyzing an MS/MS spectra library of peptides derived from tryptic digests of yeast. In the absence of mobile protons, glutamine deamination is the most rapid neutral loss process. For peptides with mobile protons, dehydration from glutamine is far more rapid than from any other amino acid. Most strikingly, end terminal glutamine is by far the most labile source of neutral loss in excess-proton peptides, but not highly exceptional when mobile protons are not available. In addition, rates of deamination are faster in lysine versus arginine C-terminus peptides and 20 times faster in positively charged than negatively charged peptides, demonstrating that these formal neutral loss reactions are not "neutral reactions" but depend on charge state and stability.

Ionizing radiation-induced destruction of benzene and dienes in aqueous media.

Pulse radiolysis with spectrophotometric and conductometric detection was utilized to study the formation and reactions of radicals from benzene and dienes in aqueous solutions. The benzene OH adduct, *C6H6OH, reacts with O2 (k = 3 x 10(8) L mol(-1) s(-1)) in a reversible reaction. The peroxyl radical, HOC6H6O2*, undergoes O2*- elimination, bimolecular decay, and reaction with benzene to initiate a chain reaction, depending on the dose rate, benzene concentration, and pH. The occurrence of the chain reaction is demonstrated in low-dose-rate gamma radiolysis experiments where the consumption of O2 was monitored. 1,4-Cyclohexadiene, 1,4-hexadiene, and 1,4-pentadiene form OH-adducts and undergo H-abstraction by O*- radicals. The OH-adducts react with O2 to form peroxyl radicals. These peroxyl radicals, however, do not undergo unimolecular O2*- elimination but rather decay by second-order processes, which lead to subsequent steps of O2*- elimination.