IRMPD and ECD fragmentation of intermolecular cross-linked peptides

Despite the increasing number of studies using mass spectrometry for three dimensional analyses of proteins (MS3D), the identification of cross-linked peptides remains a bottleneck of the method. One of the main reasons for this is the lack of knowledge about the fragmentation of these species. Intermolecular cross-linked peptides are considered the most informative species present in MS3D experiment, since different peptides are connected by a cross-linker, the peptides chain can be either from a single protein, providing information about protein folding, or from two different proteins in a complex, providing information about binding partners, complex topology and interaction sites. These species tend to be large and highly charged in ESI, making comprehensive fragmentation by CID MS/MS problematic. On the other hand, these highly charged peptides are very suitable for dissociation using both infrared multiphoton dissociation (IRMPD) and electron capture dissociation (ECD). Herein, we report the fragmentation study of intermolecular cross-linked peptides using IRMPD and ECD. Using synthetic peptides and different commercial cross-linkers, a series of intermolecular cross-linked peptides were generate, and subsequently fragmented by IRMPD and ECD in a FT-ICR-MS instrument. Due to the high mass accuracy and resolution of the FT-ICR, the fragment ions could be attributed with high confidence. The peptides sequence coverage and fragmentation features obtained from IRMPD and ECD were compared for all charge states.     

Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometric analysis of metal-ion selected dynamic protein libraries

The application of electrospray ionization (ESI) Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry to the investigation of the relative stabilities (and thus packing efficiencies) of Fe-bound trihelix peptide bundles is demonstrated. Small dynamic protein libraries are created by metal-ion assisted assembly of peptide subunits. Control of the trimeric aggregation state is coupled to stability selection by exploiting the coordination requirements of Fe(2+) in the presence of bidentate 2,2'-bipyridyl ligands covalently appended to the peptide monomers. At limiting metal-ion concentration, the most thermodynamically stable, optimally packed peptide trimers dominate the mass spectrum. The identities of optimally stable candidate trimers observed in the ESI FT-ICR mass spectra are confirmed by resynthesis of exchange-inert analogues and measurement of their folding free energies. The peptide composition of the trimers may be determined by infrared multiphoton dissociation (IRMPD) MS(3) experiments. Additional sequence information for the peptide subunits is obtained from electron capture dissociation (ECD) of peptides and metal-bound trimers. The experiments also suggest the presence of secondary structure in the gas phase, possibly due to partial retention of the solution-phase coiled coil structure.     

傅立叶变换离子回旋共振质谱及其研究进展

本文综述了傅立叶变换离子回旋共振质谱的基本原理及其颇具特色的数据处理方法.以两种典型的离子化方法为代表,介绍了目前主要使用的离子源,并总结了该方法在分析科学,尤其是在大分子分析、气相离子反应动力学研究和复杂体系分析等领域中的广泛应用.     

Generation and detection of multiply-charged peptides and proteins by matrix-assisted laser desorption electrospray ionization (MALDESI) fourier transform ion cyclotron resonance mass spectrometry

We report the coupling of a hybrid ionization source, matrix-assisted laser desorption electrospray ionization (MALDESI), to a Fourier transform-ion cyclotron resonance mass spectrometer (FT-ICR MS). The details of the source design and initial data are presented. Analysis of peptides and proteins ranging from 1 to 8.6 kDa resulted in high resolving power single-acquisition FT-ICR mass spectra with average charge-states highly correlated to those obtained by nanoESI, thus, providing strong evidence that the ESI process dictates the observed charge-state distribution. Importantly, unlike the recently introduced electrospray assisted laser desorption ionization (ELDI) source reported by Shiea and coworkers [1, 2], the data we have obtained to date rely on the use of an organic acid matrix. The results presented herein provide insight into the charging mechanism of this emerging ionization approach, while also expanding the utility of FT-ICR MS for top-down protein and complex mixture analysis.     

Mass spectrometric studies of the gas phase retro-<Emphasis Type="Italic">Michael</Emphasis> type fragmentation reactions of 2-hydroxybenzyl-<Emphasis Type="Italic">N</Emphasis>-pyrimidinylamine derivatives

The gas-phase fragmentation reactions of 2-hydroxybenzyl-N-pyrimidinylamine derivatives (Compounds 1 to 6), the O-N-type acid-catalyzed Smiles rearrangement products of 2-pyrimidinyloxy-N-arylbenzylamine derivatives, have been examined via positive ion matrix-assisted laser desorption/ionization (MALDI) infrared multiphoton dissociation (IRMPD) mass spectrometry in FT-ICR MS and via negative ion electrospray ionization (ESI) in-source collision-induced dissociation (CID) mass spectrometry, respectively. The major fragmentation pathway of protonated 1 to 6 gives the F ions under IRMPD; theoretical results show that the retro-Michael reaction channel is more favorable in both thermodynamics and kinetics. This explanation is supported by H/D exchange experiments and the MS/MS experiment of acetylated 1. Deprotonated 1 to 6 give rise to the solitary E ions (aromatic nitrogen anions) in the negative ion in-source CID; theoretical calculations show that a retro-Michael mechanism is more reasonable than a gas-phase intramolecular nucleophilic displacement (SN2) mechanism to explain this reaction process.     

Fourier transform ion cyclotron resonance mass spectrometry with NanoLC/microelectrospray ionization and matrix-assisted laser desorption/ionization: analytical performance in peptide mass fingerprint analysis

Protein identifications by peptide mass fingerprint analyses with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) were performed using microelectrospray ionization coupled to nano liquid chromatography (NanoLC), as well as using matrix-assisted laser desorption/ionization (MALDI). Tryptic digests of bovine serum albumin (BSA), diluted down to femtomole quantities, have been desalted by fast NanoLC under isocratic elution conditions as the high resolving power of FT-ICR MS enables peptides to be separated during the mass analysis stage of the experiment. The high mass accuracy achieved with FT-ICR MS (a few ppm with external calibration) facilitated unambiguous protein identification from protein database searches, even when only a few tryptic peptides of a protein were detected. Statistical confidence in the database search results was further improved by internal calibration due to increased mass accuracy. Matrix-assisted laser desorption/ionization and micro electrospray ionization (ESI) FT-ICR showed good mass accuracies in the low femtomole range, yet a better sensitivity was observed with MALDI. However, in higher femtomole ranges slightly lower mass accuracies were observed with MALDI FT-ICR than with microESI FT-ICR due to scan-to-scan variations of the ion population in the ICR cell. Database search results and protein sequence coverage results from NanoLC FT-ICR MS and MALDI FT-ICR MS, as well as the effect of mass accuracy on protein identification for the peptide mass fingerprint analysis are evaluated.     

Two-dimensional turbulent flow chromatography coupled on-line to liquid chromatography–mass spectrometry for solution-based ligand screening against multiple proteins

We present herein a novel bioseparation/chemical analysis strategy for protein–ligand screening and affinity ranking in compound mixtures, designed to increase screening rates and improve sensitivity and ruggedness in performance. The strategy is carried out by combining on-line two-dimensional turbulent flow chromatography (2D-TFC) with liquid chromatography–mass spectrometry (LC–MS), and accomplished through the following steps: (1) a reversed-phase TFC stage to separate the protein/ligand complex from the unbound free molecules, (2) an on-line dissociation process to release the bound ligands from the complexes, and (3) a second mixed-mode cation-exchange/reversed-phase TFC stage to trap the bound ligands and to remove the proteins and salts, followed by LC–MS analysis for identification and determination of the binding affinities. The technique can implement an ultra-fast isolation of protein/ligand complex with the retention time of a complex peak in about 5 s, and on-line prepare the “clean” sample to be directly compatible with the LC–MS analysis. The improvement in performance of this 2D-TFC/LC–MS approach over the conventional approach has been demonstrated by determining affinity-selected ligands of the target proteins acetylcholinesterase and butyrylcholinesterase from a small library with known binding affinities and a steroidal alkaloid library composed of structurally similar compounds. Our results show that 2D-TFC/LC–MS is a generic and efficient tool for high-throughput screening of ligands with low-to-high binding affinities, and structure-activity relationship evaluation.     

The impact of chromatography and mass spectrometry on the analysis of protein phosphorylation sites

Protein phosphorylation analysis is an enormous challenge. This review summarises the currently used techniques, which are based on radiolabelling and mass spectrometry as well as electrophoretic and chromatographic separation. Many methods exist, but there is still no single procedure applicable to all phosphoproteins. MS is able to deliver information about the location of phosphorylation sites, but phosphospecific properties with respect to ionisation present obstacles. Therefore, multidimensional approaches involving several analytical methods are often necessary to conquer phosphorylation site identification.Abbreviations 2D Two-dimensional - CE Capillary electrophoresis - CID Collision-induced dissociation - ECD Electron capture dissociation - ESI Electrospray ionisation - FT-ICR Fourier transform ion cyclotron resonance - HPLC High performance liquid chromatography - ICAT Isotope coded affinity tags - ICP Inductively-coupled plasma - IDA Immino-diacetic acid - IMAC Immobilised metal affinity chromatography - IRMPD Infrared multiphoton dissociation - IT Ion trap - MALDI Matrix-assisted laser desorption/ionisation - MRP14 Myeloid-related protein 14 - MS Mass spectrometry - NTA Nitrilo-triacetic acid - PAGE Polyacrylamide gel electrophoresis - PDI Protein disulfide isomerase - pS Phosphoserine residue - PSD Post-source decay - pT Phosphothreonine residue - PVDF Polyvinylidene fluoride - pY Phosphotyrosine residue - Q-TOF Quadrupole-time-of-flight - RP Reversed phase - SIM Single-ion monitoring - SDS Sodium dodecyl sulfate - SORI Sustained off-resonance irradiation - TLC Thin-layer chromatography - TOF Time-of-flight An erratum to this article can be found at     

Infrared Multiple Photon Dissociation Action Spectroscopy and Theoretical Studies of Diethyl Phosphate Complexes: Effects of Protonation and Sodium Cationization on Structure

The gas-phase structures of deprotonated, protonated, and sodium-cationized complexes of diethyl phosphate (DEP) including [DEP − H]⁻, [DEP + H]⁺, [DEP + Na]⁺, and [DEP − H + 2Na]⁺ are examined via infrared multiple photon dissociation (IRMPD) action spectroscopy using tunable IR radiation generated by a free electron laser, a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) with an electrospray ionization (ESI) source, and theoretical electronic structure calculations. Measured IRMPD spectra are compared to linear IR spectra calculated at the B3LYP/6-31G(d,p) level of theory to identify the structures accessed in the experimental studies. For comparison, theoretical studies of neutral complexes are also performed. These experiments and calculations suggest that specific geometric changes occur upon the binding of protons and/or sodium cations, including changes correlating to nucleic acid backbone geometry, specifically P–O bond lengths and ∠OPO bond angles. Information from these observations may be used to gain insight into the structures of more complex systems, such as nucleotides and solvated nucleic acids.     

Studies of rearrangement reactions of protonated and lithium cationized 2-pyrimidinyloxy-N-arylbenzylamine derivatives by MALDI-FT-ICR mass spectrometry

The rearrangement reactions of protonated and lithium-cationized 2-pyrimidinyloxy-N-arylbenzylamine derivatives were studied by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and infrared multiphoton dissociation mass spectrometry (IRMPD). Our results show that three kinds of rearrangement reactions occur in IRMPD processes. First, nearly all protonated 2-pyrimidinyloxy-N-arylbenzylamine derivatives undergo Pathway A to form the K ion series. It is proposed that this rearrangement (migration of a substituted benzyl group) proceeds by way of a gas-phase intramolecular S(N)2 reaction. Second, a gas phase intramolecular S(N)Ar type rearrangement mechanism is proposed to explain the formation of the F ion series from protonated and lithium-cationized 5 (or 6). This skeletal rearrangement reaction competes with the S(N)2 reaction of the Pathway A, which produces the K ion series, in IRMPD of protonated 5 and 6. Third, the formation pathway of the W ion series is explained by a gas phase Cope type rearrangement mechanism.     

2D FT-ICR MS of Calmodulin: A Top-Down and Bottom-Up Approach

Two-dimensional Fourier transform ion cyclotron resonance mass spectrometry (2D FT-ICR MS) allows data-independent fragmentation of all ions in a sample and correlation of fragment ions to their precursors through the modulation of precursor ion cyclotron radii prior to fragmentation. Previous results show that implementation of 2D FT-ICR MS with infrared multi-photon dissociation (IRMPD) and electron capture dissociation (ECD) has turned this method into a useful analytical tool. In this work, IRMPD tandem mass spectrometry of calmodulin (CaM) has been performed both in one-dimensional and two-dimensional FT-ICR MS using a top-down and bottom-up approach. 2D IRMPD FT-ICR MS is used to achieve extensive inter-residue bond cleavage and assignment for CaM, using its unique features for fragment identification in a less time- and sample-consuming experiment than doing the same thing using sequential MS/MS experiments.

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Structural characterization of the GM1 ganglioside by infrared multiphoton dissociation, electron capture dissociation, and electron detachment dissociation electrospray ionization FT-ICR MS/MS

Gangliosides play important biological roles and structural characterization of both the carbohydrate and the lipid moieties is important. The FT-ICR MS/MS techniques of electron capture dissociation (ECD), electron detachment dissociation (EDD), and infrared multiphoton dissociation (IRMPD) provide extensive fragmentation of the protonated and deprotonated GM1 ganglioside. ECD provides extensive structural information, including identification of both halves of the ceramide and cleavage of the acetyl moiety of the N-acetylated sugars. IRMPD provides similar glycan fragmentation but no cleavage of the acetyl moiety. Cleavage between the fatty acid and the long-chain base of the ceramide moiety is seen in negative-ion IRMPD but not in positive-ion IRMPD of GM1. Furthermore, this extent of fragmentation requires a range of laser powers, whereas all information is available from a single ECD experiment. However, stepwise fragmentation by IRMPD may be used to map the relative labilities for a series of cleavages. EDD provides the alternative of electron-induced fragmentation for negative ions with extensive fragmentation, but suffers from low efficiency as well as complication of data analysis by frequent loss of hydrogen atoms. We also show that analysis of MS/MS data for glycolipids is greatly simplified by classification of product ion masses to specific regions of the ganglioside based solely on mass defect graphical analysis.     

Infrared spectroscopy of gas-phase Cr+ coordination complexes: determination of binding sites and electronic states

Infrared spectra were recorded for a series of gas-phase Cr+ complexes using infrared multiphoton dissociation (IRMPD) in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. The functionalized aromatic ligands (acetophenone, anisole, aniline, and dimethyl aniline) offer a choice of either aromatic ring-pi or n-donor-base binding sites. Use of the FELIX free electron laser light source allowed convenient, rapid scanning of the chemically informative wavelength range from approximately 500 to 1800 cm(-1), which in many cases characterized the preferred site of metal binding, as well as the electronic spin state of the complex. Mono-complex ions, Cr+(ligand), for anisole, aniline, and dimethyl aniline and bis-complex ions, Cr+(ligand)(2), for anisole, aniline, and acetophenone were produced by ligand attachment to laser-desorbed Cr+ ions in the FT-ICR cell. The photodissociation yields plotted as a function of wavelength were interpreted as approximations to the infrared absorption spectra and were compared with computed spectra of different possible geometries and spin states. Clear-cut diagnostic features in the spectra of the acetophenone, anisole, and aniline complexes showed the sites of Cr+ attachment to be the carbonyl oxygen site for acetophenone (bis-complex) and the ring-pi site for anisole and aniline (both mono- and bis-complexes). The bis-complexes of aniline and anisole are low-spin (probably doublet) states, while the mono-complexes of these same ligands are high-spin (sextet) states. The dimethyl aniline complex gave a cluttered spectrum in poor agreement with calculations, which may reflect a mixture of binding-site isomers in this case.     

Characterization of orphan monooxygenases by rapid substrate screening using FT-ICR mass spectrometry

Characterization of orphan enzymes, for which the catalytic functions and actual substrates are still not elucidated, is a significant challenge in the postgenomic era. Here, we describe a general strategy for exploring the catalytic potentials of orphan monooxygenases based on direct infusion analysis by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR/MS). Eight cytochromes P450 from Bacillus subtilis were recombinantly expressed in Escherichia coli and subjected to a reconstitution system containing appropriate electron transfer components and many potential substrates. The reaction mixtures were directly analyzed using FT-ICR/MS, and substrates of the putative enzymes were readily identified from the mass spectral data. This allowed identification of previously unreported CYP109B1 substrates and the functional assignment of two putative cytochromes P450, CYP107J1 and CYP134A1. The FT-ICR/MS-based approach can be easily applied to large-scale screening with the aid of the extremely high mass resolution and accuracy.     

Reaction of hydrogen gas with C60 at elevated pressure and temperature: hydrogenation and cage fragmentation

Products of the reaction of C(60) with H(2) gas have been monitored by high-resolution atmospheric pressure photoionization Fourier transform ion cyclotron resonance mass spectrometry (APPI FT-ICR MS), X-ray diffraction, and IR spectroscopy as a function of hydrogenation period. Samples were synthesized at 673 K and 120 bar hydrogen pressure for hydrogenation periods between 300 and 5000 min, resulting in the formation of hydrofullerene mixtures with hydrogen content ranging from 1.6 to 5.3 wt %. Highly reduced C(60)H(x) (x > 36-40) and products of their fragmentation were identified in these samples by APPI FT-ICR MS. A sharp change in structure was observed for samples with at least 5.0 wt % of hydrogen. Low-mass (300-500 Da) hydrogenation products not observed by prior field desorption (FD) FT-ICR MS were detected by APPI FT-ICR MS and their elemental compositions obtained for the first time. Synthetic and analytical fragmentation pathways are discussed.     

Direct screening of a dynamic combinatorial library using mass spectrometry

A dynamic combinatorial library (DCL) screening approach is described that permits direct identification of the effective (from ineffective) combination of building blocks in the equilibrating DCL. The approach uses Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) together with sustained off-resonance irradiation collision activated dissociation (SORI-CAD) to detect noncovalent protein-DCL ligand complexes under native conditions. It was shown that in a single, rapid experiment one could concurrently identify all the ligands of interest from the DCL against a background of inactive DCL ligands while still in the presence of the target protein. This result has demonstrated that mass spectrometry may provide a fast preliminary screening approach to identify DCL candidates for later verification with more traditional but time-consuming analysis. The MS/MS enables DCL mixtures to be effectively deconvoluted without the need for either chromatography, synthesis of DCL sub-libraries, conversion of the DCL to a static library, or disruption of the protein-ligand complexes before analysis--all typically necessary for the current screening method for DCLs.     

Fragmentation study of peptides using Fourier transform ion cyclotron resonance with infrared multiphoton dissociation: experiment and simulation

In this study, the fragmentation of gas-phase protonated Angiotensin II is investigated using electrospray ionization (ESI), Fourier-transform ion cyclotron resonance (FT-ICR), and mass spectrometry (MS) with a laser cleavage infrared multiphoton dissociation (IRMPD) technique. The experimental results show that the spectra peaks for the photoproducts are y2/b6- and y7-type ions, corresponding to the cleavage of His-Pro and Asp-Arg in the parent amino acid sequence. The fragmentation of the peptide under collision-free vacuum conditions is modeled using molecular dynamics simulations (MD). The binding energy for the peptide bonds (C'-N bond) of Angiotensin II is estimated from ab initio calculations. The calculations are directed at predicting experimental measurements of the product ions from the photodissociation of the peptide. The product distributions simulated by the MD dissociation trajectories include predominantly y7/b1 and y2/b6 pair ions.     

Infrared multiphoton dissociation of the siderophore enterobactin and its Fe(III) complex. Influence of Fe(III) binding on dissociation kinetics and relative energetics

The dissociation pathways of the siderophore enterobactin and its complex with Fe(III) were examined using infrared multiphoton dissociation (IRMPD). Under experimental conditions (pH = 3.5), both compounds' electrospray spectra exhibited exclusively singly-charged anions. The compositions of the dissociation products were characterized by accurate mass measurements using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). The primary dissociation channel for both species was determined to be the loss of one serine group from the precursor molecules. To further investigate the influence of Fe(III) binding on the intramolecular interactions, dissociation kinetics and relative energetics for the loss of this serine group were determined using the focused radiation for gaseous multiphoton energy-transfer (FRAGMENT) method. From the kinetic data, it was found that enterobactin was approximately seven times more reactive than its Fe(III) complex over the range of laser intensities investigated. The relative activation energies, however, exhibited similar values, approximately 7 kcal.mol(-1). These results suggest that at pH = 3.5, Fe(III) interacts with only two of the three serine groups. The results from the present work are believed to be valuable for the characterization of novel siderophores as well as their associated metabolites and synthetic analogues.     

Affinity capture using chimeric membrane proteins bound to magnetic beads for rapid ligand screening by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry

The rapid and specific detection of therapeutically important ligands in complex mixtures, that may bind to membrane proteins, remains challenging for many research laboratories and pharmaceutical industries. Through its use in the development of screening assays, mass spectrometry (MS) is currently experiencing a period of tremendous expansion. In the study presented here, we took advantage of the remarkable stability properties of a bacterial membrane protein, the KcsA K⁺ channel, produced in E. coli and purified as a tetrameric protein in the presence of a detergent. This membrane protein can subserve as a molecular template to display the pore‐forming region of human K⁺ channels, which are considered as targets in the search for inhibitory ligands. The engineered chimeric proteins were linked to metal‐bound magnetic beads, for the screening of complex peptide mixtures, such as that of scorpion venoms. The affinity‐captured scorpion toxins were eluted prior to matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOFMS), and to nano‐electrospray ionization tandem mass QqTOF mass spectrometry (MS/MS) analysis. The de novo sequence of the toxins was deduced by combining the MS/MS fragmentation of the reduced form (up to the 33 first residues) and the trypsin digest peptides of the native toxins. This affinity‐capture screening assay led to the isolation and characterization of potent and specific ligands of the human K⁺ channel, Kv1.3. The affinity‐capture procedure is fast and reproducible. When linked to magnetic beads, the chimeric membrane protein can be re‐used several times without losing any of its selectivity or specificity. This assay also benefits from the fact that it requires minimal amounts of animal venoms or complex mixtures, which can be expensive or difficult to procure. Copyright © 2009 John Wiley & Sons, Ltd.