During collision-induced dissociation (CID)-, phosphoserine- and phosphothreonine-containing peptides frequently undergo neutral
loss of phosphoric acid. Subsequent amide bond cleavage N-terminal to the site of phosphorylation results in a y ion with
a mass 18 Da lower than the corresponding unmodified y fragment. We report here that when the phosphoserine or phosphothreonine
is directly preceded by a proline, an unusual fragment with a mass 10 Da higher than the corresponding unmodified y ion is
frequently observed. Accurate mass measurements are consistent with elimination of the phosphoric acid followed by fragmentation
between the α carbon and the carbonyl group of the proline residue. We propose a cyclic oxazoline structure for this fragment.
Our observation may be explained by the charge-directed SN2 neighboring group participation reaction proposed for the phosphoric acid elimination by Palumbo et al. [Palumbo, A. M.,
Tepe, J. J., Reid, G. E. Mechanistic Insights into the Multistage Gas-Phase Fragmentation Behavior of Phosphoserine- and Phosphothreonine-Containing
Peptides. J. Protein Res. 7(2), 771–779 (2008)]. Considering such specific fragment ions for confirmation purposes after regular database searches
may boost the confidence of peptide identifications as well as phosphorylation site assignments. 相似文献
Mass spectrometry faces considerable difficulties in de novo sequencing of long non-tryptic peptides with S–S bonds. Long
disulfide-containing peptides brevinins 1E and 2Ec from frog Rana ridibunda were reduced and alkylated with nine novel and three known derivatizing agents. Eight of the novel reagents are maleimide
derivatives. Modified samples were subjected to MS/MS studies on FT-ICR and Orbitrap mass spectrometers using CAD/HCD or ECD/ETD
techniques. Procedures, fragmentation patterns, and sequence coverage for two peptides modified with 12 tags are described.
ECD/ETD and CAD fragmentation revealed complementary sequence information. Higher-energy collisionally activated dissociation
(HCD) sufficiently enhanced y-ions formation for brevinin 1E, but not for brevinin 2Ec. Some novel tags [N-benzylmaleimide, N-(2,6-dimethylphenyl)maleimide] along with known N-phenylmaleimide and iodoacetic acid showed high total sequence coverage taking into account combined ETD and HCD fragmentation.
Moreover, modification of long (34 residues) brevinin 2Ec with N-benzylmaleimide or N-(2,6-dimethylphenyl)maleimide yielded high sequence coverage and full C-terminal sequence determination with ECD alone. 相似文献
A method for structural elucidation of biomolecules dating to the 1980s utilized high-energy collisions (~10 keV, laboratory frame) that induced charge-remote fragmentations (CRF), a class of fragmentations particularly informative for lipids, steroids, surfactants, and peptides. Unfortunately, the capability for high-energy activation has largely disappeared with the demise of magnetic sector instruments. With the latest designs of tandem time-of-flight mass spectrometers (TOF/TOF), however, this capability is now being restored to coincide with the renewed interest in metabolites and lipids, including steroid-sulfates and other steroid metabolites. For these metabolites, structure determinations are required at concentration levels below that appropriate for NMR. To meet this need, we explored CRF with TOF/TOF mass spectrometry for two groups of steroid sulfates, 3-sulfates and 21-sulfates. We demonstrated that the current generation of MALDI TOF/TOF instruments can generate charge-remote fragmentations for these materials. The resulting collision-induced dissociation (CID) spectra are useful for positional isomer differentiation and very often allow the complete structure determination of the steroid. We also propose a new nomenclature that directly indicates the cleavage sites on the steroid ring with carbon numbers.
The fragmentation chemistry of peptides containing intrachain disulfide bonds was investigated under electron transfer dissociation
(ETD) conditions. Fragments within the cyclic region of the peptide backbone due to intrachain disulfide bond formation were
observed, including: c (odd electron), z (even electron), c-33 Da, z + 33 Da, c + 32 Da, and z–32 Da types of ions. The presence
of these ions indicated cleavages both at the disulfide bond and the N–Cα backbone from a single electron transfer event.
Mechanistic studies supported a mechanism whereby the N–Cα bond was cleaved first, and radical-driven reactions caused cleavage
at either an S–S bond or an S–C bond within cysteinyl residues. Direct ETD at the disulfide linkage was also observed, correlating
with signature loss of 33 Da (SH) from the charge-reduced peptide ions. Initial ETD cleavage at the disulfide bond was found
to be promoted amongst peptides ions of lower charge states, while backbone fragmentation was more abundant for higher charge
states. The capability of inducing both backbone and disulfide bond cleavages from ETD could be particularly useful for sequencing
peptides containing intact intrachain disulfide bonds. ETD of the 13 peptides studied herein all showed substantial sequence
coverage, accounting for 75%–100% of possible backbone fragmentation. 相似文献
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.
Abstract A variety of substituted arylglyoxylic acids (2a?g) were synthesized via oxidation of the corresponding aryl-methylketones (1a–e) using selenium dioxide or Friedel–Crafts acylation of phenol (3) with ethyl chlorooxoacetate and further transformations. It was found that the arylglyoxylic acids (2) undergo facile unimolecular dissociation with loss of carbon monoxide to give the corresponding arylcarboxylic acids (7) under collisionally induced mass spectrometric conditions. 相似文献
Electron-transfer dissociation (ETD) is a useful peptide fragmentation technique that can be applied to investigate post-translational
modifications (PTMs), the sequencing of highly hydrophilic peptides, and the identification of large peptides and even intact
proteins. In contrast to traditional fragmentation methods, such as collision-induced dissociation (CID), ETD produces c-
and z·-type product ions by randomly cleaving the N–Cα bonds. The disappointing fragmentation efficiency of ETD for doubly charged
peptides and phosphopeptide ions has been improved by ETcaD (supplemental activation). However, the ETD data derived from
most database search algorithms yield low confidence scores due to the presence of unreacted precursors and charge-reduced
ions within MS/MS spectra. In this work, we demonstrate that eight out of ten standard doubly charged peptides and phosphopeptides
can be effortlessly identified by electron-transfer coupled with collision-induced dissociation (ET/CID) using the SEQUEST
algorithm without further spectral processing. ET/CID was performed with the further dissociation of the charge-reduced ions
isolated from ETD ion/ion reactions. ET/CID had high fragmentation efficiency, which elevated the confidence scores of doubly
charged peptide and phosphospeptide sequencing. ET/CID was found to be an effective fragmentation strategy in “bottom-up”
proteomic analysis. 相似文献
The dissociative behavior of peptide amides and free acids was explored using low-energy collision-induced dissociation and high level computational theory. Both positive and negative ion modes were utilized, but the most profound differences were observed for the deprotonated species. Deprotonated peptide amides produce a characteristic c(m-2) (-) product ion (where m is the number of residues in the peptide) that is either absent or in low abundance in the analogous peptide acid spectrum. Peptide acids show an enhanced formation of c(m-3) (-); however, this is not generally as pronounced as c(m-2) (-) production from amides. The most notable occurrence of an amide-specific product ion is for laminin amide (YIGSR-NH(2)) and this case was investigated using several modified peptides. Mechanisms involving 6- and 9-membered ring formation were proposed, and their energetic properties were investigated using G3(MP2) molecular orbital theory calculations. For example, with C-terminal deprotonation of pentaglycine amide, formation of c(m-2) (-) and a 6-membered ring diketopiperazine neutral requires >31.6?kcal/mol, which is 26.1?kcal/mol less than the analogous process involving the peptide acid. The end group specific fragmentation of peptide amides in the negative ion mode may be useful for identifying such groups in proteomic applications. 相似文献
ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option. 相似文献
Sequence scrambling from y-type fragment ions has not been previously reported. In a study designed to probe structural variations among b-type fragment ions, it was noted that y fragment ions might also yield sequence-scrambled ions. In this study, we examined the possibility and extent of sequence-scrambled fragment ion generation from collision-induced dissociation (CID) of y-type ions from four peptides (all containing basic residues near the C-terminus) including: AAAAHAA-NH2 (where “A” denotes carbon thirteen (13C1) isotope on the alanine carbonyl group), des-acetylated-α-melanocyte (SYSMEHFRWGKPV-NH2), angiotensin II antipeptide (EGVYVHPV), and glu-fibrinopeptide b (EGVNDNEEGFFSAR). We investigated fragmentation patterns of 32 y-type fragment ions, including y fragment ions with different charge states (+1 to +3) and sizes (3 to 12 amino acids). Sequence-scrambled fragment ions were observed from ~50 % (16 out of 32) of the studied y-type ions. However, observed sequence-scrambled ions had low relative intensities from ~0.1 % to a maximum of ~12 %. We present and discuss potential mechanisms for generation of sequence-scrambled fragment ions. To the best of our knowledge, results on y fragment dissociation presented here provide the first experimental evidence for generation of sequence-scrambled fragments from CID of y ions through intermediate cyclic “b-type” ions.
Prostaglandins (PGs) are biologically active metabolites of arachidonic acid containing 20 carbon atoms, a cyclic moiety, and two side chains (A and B) in common. The bioassay of PGs requires high sensitivity because of their low concentration in tissues and blood and has usually been carried out by electrospray ionization tandem mass spectrometry (ESI-MS/MS) in the negative ion mode. Chemical derivatization of PG carboxylic acid groups to introduce positive charge-carrying groups is an established strategy to improve the sensitivity and selectivity of such assays. In this study, we exploited this approach for structural identification of a series of PGs using cholamine derivatization through an amidation reaction. However, we observed that collision-induced dissociation of these derivatives gave rise to unexpected product ions that we postulated were formed by unique long-range intramolecular reactions resulting in dehydration of the B chain accompanied by fragmentation of the A chain through an unusual Hofmann rearrangement. Evidence for the proposed mechanism is presented based on ESI-MS/MS and high resolution mass spectrometry studies of cholamine derivatives of PGE1, PGE2, PGD2, PGI2, and C-17 methyl deuterium-labeled limaprost.
Collision-induced fragmentation of protonated N-alkyl-p-toluenesulfonamides primarily undergo either an elimination of the amine to form CH3-(C6H4)-SO2+ cation (m/z 155) or an alkene to form a cation for the protonated p-toluenesulfonamide (m/z 172). To comprehend the fragmentation pathways, several deuterated analogs of N-decyl-p-toluenesulfonamides were prepared and evaluated. Hypothetically, two mechanisms, both of which involve ion-neutral complexes, can be envisaged. In one mechanism, the S–N bond fragments to produce an intermediate [sulfonyl cation/amine] complex, which dissociates to afford the m/z 155 cation (Pathway A). In the other mechanism, the C–N bond dissociates to produce a different intermediate complex. The fragmentation of this [p-toluenesulfonamide/carbocation] complex eliminates p-toluenesulfonamide and releases the carbocation (Pathway B). Computations carried out by the Hartree-Fock method suggested that the Pathway B is more favorable. However, a peak for the carbocation is observed only when the carbocation formed is relatively stable. For example, the spectrum of N-phenylethyl-p-toluenesulfonamide is dominated by the peak at m/z 105 for the incipient phenylethyl cation, which rapidly isomerizes to the remarkably stable methylbenzyl cation. The peaks for the carbocations are weak or absent in the spectra of most of N-alkyl-p-toluenesulfonamides because alkyl carbocations, such as the decyl cation, rearrange to more stable secondary cations by 1,2-hydride and alkyl shifts. The energy freed is not dissipated, but gets internalized, causing the carbocation to dissociate either by transferring a proton to the sulfonamide or by releasing smaller alkenes to form smaller carbocations. The loss of the positional integrity in this way was proven by deuterium labeling experiments.
Here we investigate the effect of S-dipalmitoylation on the electron capture dissociation (ECD) behavior of peptides. The ECD and collision induced dissociation (CID) of peptides modified by covalent attachment of [(RS)-2,3-di(palmitoyloxy)-propyl] (PAM2) group to cysteine residues [C(PAM2)LEYDTGFK and RPPGC(PAM2)SPFK] were examined. The results suggest that ECD of S-dipalmitoylated peptides can provide both primary sequence information and structural information regarding the modification. The structural information provided by CID is complementary to that provided by ECD.
Tandem mass spectrometry (MS/MS) confirmed decarboxylation as the major collision-induced dissociation (CID) pathway of deprotonated hydrocinnamic acid (C6H5CH2CH2CO2H), N-phenylglycine (C6H5NHCH2CO2H) and 3-pyridin-2-ylpropanoic acid (C5H4NCH2CH2CO2H). The structure and stability of isomeric precursor and product anions were examined using density functional theory and ab initio methods. Geometry optimizations and frequency calculations were performed using the B3LYP/6-31++G(2d,p) level of theory and basis set with additional single point energies calculated at the MP2/6-311++G(2d,p) level. The formation of a delocalized product anion by carboxyl group-mediated migration of a benzylic proton to the ortho position of the ring and subsequent Cα–CO2– bond cleavage was energetically more favorable than direct decarboxylation and rearrangements of anions within ion-neutral complexes with carbon dioxide. The energy barrier for rearrangement of the delocalized product anion to the more stable benzylic anion was lowest in the fragmentation pathway of 3-pyridin-2-ylpropanoate. More energetically demanding fragmentation processes were indicated by the formation of other product anions at higher collision energy. Computations supported the feasibility of the formation of hydroxycarbonyl, styrene, and phenide ions from the benzylic anion of hydrocinnamate and the corresponding product anions from the nitrogen-containing analogues. The loss of dihydrogen from decarboxylated 3-pyridin-2-ylpropanoate was characterized computationally as hydride abstraction of an aryl proton. Overall, the results highlight the importance of exploring rearrangements in the fragmentation pathways of ions formed by electrospray ionization (ESI).
We report here surface-induced dissociation spectra of three multiply charged peptides: doubly protonated angiotensin I, doubly protonated renin substrate, and triply protonated melittin. For comparison, the collision-activated dissociation spectra of renin substrate and melittin are also presented. The spectra show that surface-induced dissociation provides structural information on multiply charged peptides at the picomole per microliter sample concentrations compatible with electrospray ionization. For multiply protonated angiotensin I, renin substrate, and melittin, surface collisions (100–165 eV) favor a limited number of fragmentation pathways, which are the same as those favored in collision-activated dissociation experiments. 相似文献
The visible photodissociation mechanisms of QSY7-tagged peptides of increasing size have been investigated by coupling a mass spectrometer and an optical parametric oscillator laser beam. The experiments herein consist of energy resolved collision- and laser-induced dissociation measurements on the chromophore-tagged peptides. The results show that fragmentation occurs by similar channels in both activation methods, but that the branching ratios are vastly different. Observation of a size-dependent minimum laser pulse energy required to induce fragmentation, and collisional cooling rates in time resolved experiments show that laser-induced dissociation occurs through the absorption of multiple photons by the chromophore and the subsequent heating through vibrational energy redistribution. The differences in branching ratio between collision- and laser-induced dissociation can then be understood by the highly anisotropic energy distribution following absorption of a photon.
A method of fragmenting ions over a wide range of m/z values while balancing energy deposition into the precursor ion and available product ion mass range is demonstrated. In the method, which we refer to as “multigenerational collision-induced dissociation”, the radiofrequency (rf) amplitude is first increased to bring the lowest m/z of the precursor ion of interest to just below the boundary of the Mathieu stability diagram (q = 0.908). A supplementary AC signal at a fixed Mathieu q in the range 0.2–0.35 (chosen to balance precursor ion potential well depth with available product ion mass range) is then used for ion excitation as the rf amplitude is scanned downward, thus fragmenting the precursor ion population from high to low m/z. The method is shown to generate high intensities of product ions compared with other broadband CID methods while retaining low mass ions during the fragmentation step, resulting in extensive fragment ion coverage for various components of complex mixtures. Because ions are fragmented from high to low m/z, space charge effects are minimized and multiple discrete generations of product ions are produced, thereby giving rise to “multigenerational” product ion mass spectra.
A disulfide click strategy is disclosed for stapling to enhance the metabolic stability and cellular permeability of therapeutic peptides. A 17-membered library of stapling reagents with adjustable lengths and angles was established for rapid double/triple click reactions, bridging S-terminal peptides from 3 to 18 amino acid residues to provide 18- to 48-membered macrocyclic peptides under biocompatible conditions. The constrained peptides exhibited enhanced anti-HCT-116 activity with a locked α-helical conformation (IC50=6.81 μM vs. biological incompetence for acyclic linear peptides), which could be unstapled for rehabilitation of the native peptides under the assistance of tris(2-carboxyethyl)phosphine (TCEP). This protocol assembles linear peptides into cyclic peptides controllably to retain the diverse three-dimensional conformations, enabling their cellular uptake followed by release of the disulfides for peptide delivery. 相似文献
Here, we present liquid extraction surface analysis (LESA) coupled with electron-induced dissociation (EID) mass spectrometry in a Fourier-transform ion cyclotron resonance mass spectrometer for the analysis of small organic pharmaceutical compounds directly from dosed tissue. First, the direct infusion electrospray ionisation EID and collision-induced dissociation (CID) behaviour of erlotinib, moxifloxacin, clozapine and olanzapine standards were compared. EID mass spectra were also compared with experimental or reference electron impact ionisation mass spectra. The results show that (with the exception of erlotinib) EID and CID result in complementary fragment ions. Subsequently, we performed LESA EID MS/MS and LESA CID MS/MS on singly charged ions of moxifloxacin and erlotinib extracted from a thin tissue section of rat kidney from a cassette-dosed animal. Both techniques provided structural information, with the majority of peaks observed for the drug standards also observed for the tissue-extracted species. Overall, these results demonstrate the feasibility of LESA EID MS/MS of drug compounds from dosed tissue and extend the number of molecular structures for which EID behaviour has been determined.
