Enabling MALDI-FTICR-MS/MS for high-performance proteomics through combination of infrared and collisional activation

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is a central tool for proteomic analysis, yet the singly protonated tryptic peptide ions produced by MALDI are significantly more difficult to dissociate for tandem mass spectrometry (MS/MS) than the corresponding multiply protonated ions. In order to overcome this limitation, current proteomic approaches using MALDI-MS/MS involve high-energy collision-induced dissociation (CID). Unfortunately, the use of high-energy CID complicates product ion spectra with a significant proportion of irrelevant fragments while also reducing mass accuracy and mass resolution. In order to address the lack of a high-resolution, high mass accuracy MALDI-MS/MS platform for proteomics, Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and a recently developed MS/MS technique termed CIRCA (for combination of infrared and collisional activation) have been applied to proteomic analysis. Here, CIRCA is shown to be suitable for dissociating singly protonated tryptic peptides, providing greater sequence coverage than either CID or infrared multiphoton dissociation (IRMPD) alone. Furthermore, the CIRCA fragmentation spectra are of sufficient quality to allow protein identification based on the MS/MS spectra alone or in concert with the peptide mass fingerprint (PMF). This is accomplished without compromising mass accuracy or mass resolution. As a result, CIRCA serves to enable MALDI-FTICR-MS/MS for high-performance proteomics experiments.     

Fragmentation of protonated peptide ions via interaction with metastable atoms

Fragmentation of protonated peptide ions via interaction with low kinetic energy electronicallyexcited metastable argon atoms was studied in a linear trap-time-of-flight mass spectrometer. Metastable argon atoms were generated using a glow discharge-type source. Protonated peptide ions of substance P, bradykinin, fibrinopetide A, and insulin oxidized chain B were produced by electrospray ionization and trapped in a quadrupole ion guide for 100-400 ms. Intensive series of c- and z-ions were observed in all cases. The kinetic measurements of the fragmentation rates are consistent with calculations of the reaction cross section based on the Landau-Zener approximation.     

Measurements of collisional broadening coefficients by infrared polarization spectroscopy

We present measurements of collisional broadening coefficients, obtained at atmospheric pressure, by polarization spectroscopy. Using tunable single mode laser radiation at approximately 2 microm, high-resolution infrared polarization spectra were recorded for CO2-Ar and CO2-He binary mixtures. The recorded polarization spectra were fitted with a Lorentzian cubed function form to obtain the broadening coefficients. The full-width at half-maxima (FWHM) collisional broadening rates of CO2 by Ar and He, for the R14 (12 degrees1<--00 degrees0) line, have been determined to be 0.161+/-0.018 cm-1 atm-1 and 0.1823+/-0.0032 cm-1 atm-1, respectively.     

Relative dissociation energies of protonated peptides by electrospray ionization/surface-induced dissociation

Relative dissociation energies (RDEs) are obtained for the major fragment ions produced by electrospray ionization/surface-induced dissociation of singly protonated triglycine, tetraglycine, leucine enkephalin, and leucine enkephalin arginine. A previously described data analysis method (Lim, H.; et al. J. Phys. Chem. B 1998, 102, 4753) is employed to analyze the energy-resolved mass spectra by subtracting out the distribution of energy transferred to the surface, integrating over the distribution of the incident ion energy, and taking into account the precursor ion initial internal energy and kinetic energy distributions. These variables are optimized by anchoring the RDE for the lowest energy fragment of a given precursor ion to its literature values and then using these optimized parameters to obtain the other RDEs. The RDEs of the four major fragments of triglycine vary from 2.4 eV for the b(2) fragment ion to 6.0 eV for the a(2) ion. The RDEs of the four major fragments of tetraglycine vary from 3.2 eV for the y(2) ion to 5.7 eV for the a(2) ion. The leucine enkephalin RDEs range from 1.1 eV for the b(4) ion to 2.1 eV for the b(2) ion. The leucine enkephalin arginine RDEs all lay between 2.5 and 3.5 eV. The overall trend of fragmentation order for all peptides is (y(n), b(n)) < a(n) and is consistent with the results from other experiments. The peptide RDEs presented here are only as accurate as the literature values to which they are anchored. Determination of absolute dissociation energies from SID data will require further refinement of the data analysis method.     

Efficient infrared upconversion via a ladder-type atomic configuration

We have demonstrated experimentally that infrared light at 1529.4?nm can be converted into the visible at 780?nm with 54% efficiency through a ladder-type atomic configuration in ⁸⁵Rb. Specifically we theoretically analyze that high efficiency is due to the large nonlinear dispersion of the index of refraction from the off-resonant enhancement in a four-wave mixing (FWM) process. By using two perpendicular polarized pump fields, the coherence of two FWM processes in this configuration is verified.     

Identification of bacteriophage MS2 coat protein from E. coli lysates via ion trap collisional activation of intact protein ions

Collisional activation of the intact MS2 viral capsid protein with subsequent ion/ion reactions has been used to identify the presence of this virus in E. coli lysates. Tandem ion trap mass spectrometry experiments on the +7, +8, and +9 charge states, followed by ion/ion reactions, provided the necessary sequence tag information (and molecular weight data) needed for protein identification via database searching. The most directly informative structural information is obtained from those charge states that produce a series of product ions arising from fragmentation at adjacent residues. The formation of these product ions via dissociation at adjacent amino acid residues depends greatly on the charge state of the parent ion. Database searching of the charge-state-specific sequence tags was performed by two different search engines: the ProteinInfo program from the Protein information Retrieval On-line World Wide Web Lab or PROWL and the TagIdent program from the ExPASy molecular biology server. These search engines were used in conjunction with the sequence tag information generated via collisional activation of the intact viral coat protein. These programs were used to evaluate the feasibility of generating sequence tags from collisional activation of intact multiply charged protein ions in a quadrupole ion trap.     

Surface-induced dissociation of protonated peptides: implications of initial kinetic energy spread.

Surface-induced dissociation (SID) has been used to produce daughter ion spectra of small protonated peptides generated by fast atom bombardment (FAB). The relative abundances of daughter ions depends critically upon the energy of the ion/surface collision. A wide array of decomposition processes may be observed using ELAB collision energies in the range 10-20 eV. At approximately 13-eV collision energy, the variety of decomposition processes is maximized for the small peptides studied; hence, maximum structural information may be deduced. Collisionally-activated dissociations (CAD) using argon gas and the identical protonated peptides could not produce as large an array of daughter ions in a constant condition experiment. An apparent contradiction is thereby posed because SID is known to produce a narrow distribution of ion internal energies relative to CAD. This apparent contradiction is resolved by considering the rather large kinetic energy spread of ions leaving the FAB source. For the SID process, this large initial kinetic energy distribution is converted into a significantly wider spread in center-of-mass collision energy, leading to a broader variety of decomposition processes (high and low energy) compared to CAD.     

Fragmentation of peptides in MALDI in-source decay mediated by hydrogen radicals

In-source decay (ISD) in matrix-assisted laser desorption/ionization (MALDI) shares some similarities with the novel fragmentation technique electron capture dissociation (ECD). In both reactions, the otherwise strong N-C(alpha) bond is cleaved, forming fragment ions of the c and z types, while labile posttranslational modifications are preserved. Therefore, it is tempting to assume that ISD and ECD have some mechanistic aspects in common. Because electrons are present in the MALDI plume, we investigated the previously suggested possibility that ISD is a variation of ECD. However, experiments with peptides with only one site for efficient protonation revealed that ISD is not caused by electron capture. Instead, ICD seems to be induced by hydrogen atoms generated by a photochemical reaction of the matrix. We provide evidence for this reaction by hydrogen/deuterium exchange experiments with peptides containing a minimal number of exchangeable hydrogen atoms. The hydrogen atom model in ECD is indirectly supported by the proposed fragmentation mechanism for ISD, because our data suggest that hydrogen radicals can induce fragmentation by cleavage of the N-C(alpha) bond, independent from their origin.     

Supplemental activation method for high-efficiency electron-transfer dissociation of doubly protonated peptide precursors

Electron-transfer dissociation (ETD) delivers the unique attributes of electron capture dissociation to mass spectrometers that utilize radio frequency trapping-type devices (e.g., quadrupole ion traps). The method has generated significant interest because of its compatibility with chromatography and its ability to: (1) preserve traditionally labile post-translational modifications (PTMs) and (2) randomly cleave the backbone bonds of highly charged peptide and protein precursor ions. ETD, however, has shown limited applicability to doubly protonated peptide precursors, [M + 2H]2+, the charge and type of peptide most frequently encountered in "bottom-up" proteomics. Here we describe a supplemental collisional activation (CAD) method that targets the nondissociated (intact) electron-transfer (ET) product species ([M + 2H]+*) to improve ETD efficiency for doubly protonated peptides (ETcaD). A systematic study of supplementary activation conditions revealed that low-energy CAD of the ET product population leads to the near-exclusive generation of c- and z-type fragment ions with relatively high efficiency (77 +/- 8%). Compared to those formed directly via ETD, the fragment ions were found to comprise increased relative amounts of the odd-electron c-type ions (c+*) and the even-electron z-type ions (z+). A large-scale analysis of 755 doubly charged tryptic peptides was conducted to compare the method (ETcaD) to ion trap CAD and ETD. ETcaD produced a median sequence coverage of 89%-a significant improvement over ETD (63%) and ion trap CAD (77%).     

Identification of c-type heme-containing peptides using nonactivated immobilized metal affinity chromatography resin enrichment and higher-energy collisional dissociation

The c-type cytochromes play essential roles in many biological activities of both prokaryotic and eukaryotic cells, including electron transfer, enzyme catalysis, and induction of apoptosis. We report a novel enrichment strategy for identifying c-type heme-containing peptides that uses nonactivated IMAC resin. The strategy demonstrated at least 7-fold enrichment for heme-containing peptides digested from a cytochrome c protein standard, and quantitative linear performance was also assessed for heme-containing peptide enrichment. Heme-containing peptides extracted from the periplasmic fraction of Shewanella oneidensis MR-1 were further identified using higher-energy collisional dissociation tandem mass spectrometry. The results demonstrated the applicability of this enrichment strategy to identify c-type heme-containing peptides from a highly complex biological sample and, at the same time, confirmed the periplasmic localization of heme-containing proteins during suboxic respiration activities of S. oneidensis MR-1.     

Rapidly alternating transmission mode electron-transfer dissociation and collisional activation for the characterization of polypeptide ions

Cation transmission/electron-transfer reagent anion storage mode electron-transfer ion/ion reactions and beam-type collisional activation of the polypeptide ions are performed in rapid succession in the high-pressure collision cell (Q2) of a quadrupole/time-of-flight tandem mass spectrometer (QqTOF), where the electron-transfer reagent anions are accumulated. Duty cycles for both electron-transfer dissociation (ETD) and collision-induced dissociation (CID) experiments are improved relative to ion trapping approaches since there are no discrete ion storage and reaction steps for ETD experiments and no discrete ion storage step and frequency tuning for CID experiments. For this technique, moderately high resolution and mass accuracy are also obtained due to mass analysis via the TOF analyzer. This relatively simple approach has been demonstrated with a triply charged tryptic peptide, a triply charged tryptic phosphopeptide, and a triply charged tryptic N-linked glycopeptide. For the tryptic peptide, the sequence is identified with more certainty than would be available from a single method alone due to the complementary information provided by these two dissociation methods. Because of the complementary information derived from both ETD and CID dissociation methods, peptide sequence and post-translational modification (PTM) sites for the phosphopeptide are identified. This combined ETD and CID approach is particularly useful for characterizing glycopeptides because ETD generates information about both peptide sequence and locations of the glycosylation sites, whereas CID provides information about the glycan structure.     

Electron-transfer ion/ion reactions of doubly protonated peptides: effect of elevated bath gas temperature

In this study, the electron-transfer dissociation (ETD) behavior of cations derived from 27 different peptides (22 of which are tryptic peptides) has been studied in a 3D quadrupole ion trap mass spectrometer. Ion/ion reactions between peptide cations and nitrobenzene anions have been examined at both room temperature and in an elevated temperature bath gas environment to form ETD product ions. From the peptides studied, the ETD sequence coverage tends to be inversely related to peptide size. At room temperature, very high sequence coverage (approximately 100%) was observed for small peptides (< or =7 amino acids). For medium-sized peptides composed of 8-11 amino acids, the average sequence coverage was 46%. Larger peptides with 14 or more amino acids yielded an average sequence coverage of 23%. Elevated-temperature ETD provided increased sequence coverage over room-temperature experiments for the peptides of greater than 7 residues, giving an average of 67% for medium-sized peptides and 63% for larger peptides. Percent ETD, a measure of the extent of electron transfer, has also been calculated for the peptides and also shows an inverse relation with peptide size. Bath gas temperature does not have a consistent effect on percent ETD, however. For the tryptic peptides, fragmentation is localized at the ends of the peptides suggesting that the distribution of charge within the peptide may play an important role in determining fragmentation sites. A triply protonated peptide has also been studied and shows behavior similar to the doubly charged peptides. These preliminary results suggest that for a given charge state there is a maximum size for which high sequence coverage is obtained and that increasing the bath gas temperature can increase this maximum.     

A mechanistic investigation of the enhanced cleavage at histidine in the gas-phase dissociation of protonated peptides

Enhanced gas-phase cleavage of peptides adjacent to histidine was investigated. The peptides examined were angiotensins III (RVYIHPF) and IV (VYIHPF) as well as synthetic peptide analogues with altered key residues ((R)VYI-X-Z-F; X = F or H and Z = A, P, or Sar) or a fixed charge M3P(+)CH(2)C(O)-VYIHPF. While all singly protonated peptide ions containing both histidine and arginine fragment nonselectively, the doubly protonated peptide ions with arginine and histidine, and the singly protonated peptides containing histidine but not arginine, cleave in a selective manner. In particular, dominant complementary b+/y+ product ions resulting from cleavage between the HP amide bond are observed. For the fixed-charge derivative, selective cleavage occurs only if a proton is added to produce a doubly charged precursor. The results are consistent with involvement of a protonated histidine in the selective cleavage. The ratio of b+/y+ is determined by the identity of the residue C-terminal to histidine and by the ability of protonated histidine to transfer a proton to the C-terminal leaving fragment. This was probed further by systematically changing the residue C-terminal to histidine and by alkylating histidine. The results indicate that while b+/y+ complementary ion pairs dominate in doubly protonated RVYIHPF, b5(2+) and b6(2+) product ions dominate the spectra of doubly protonated RVYIHAF. Also, dominant b5(2+) product ions are observed when the histidine side chain is alkylated (H) in doubly protonated RVYIHPF. Based on all of the results, a selective fragmentation mechanism for enhanced cleavage at histidine involving an atypical b ion structure is proposed.     

Charge-state-dependent sequence analysis of protonated ubiquitin ions via ion trap tandem mass spectrometry

One of the major factors governing the "top-down" sequence analysis of intact multiply protonated proteins by tandem mass spectrometry is the effect of the precursor ion charge state on the formation of product ions. To more fully understand this effect, electrospray ionization coupled to a quadrupole ion trap mass spectrometer, collision-induced dissociation, and gas-phase ion/ion reactions have been employed to examine the fragmentation of the [M + 12H]12+ to [M + H]+ ions of bovine ubiquitin. At low charge states (+1 to +6), loss of NH3 or H2O from the protonated precursor and directed cleavage at aspartic acid residues was observed. At intermediate charge states, (+7, +8, and +9), extensive nonspecific fragmentation of the protein backbone was observed, with 50% sequence coverage obtained from the [M + 8H]8+ ion alone. At high charge states, (+10, +11, +12), the single dominant channel that was observed was the preferential fragmentation of a single proline residue. These data can be readily explained in terms of the current model for intramolecular proton mobilization, that is, the "mobile proton model", the mechanisms for amide bond dissociation developed for protonated peptides, as well as the structures of the multiply charged ions of ubiquitin in the gas phase, examined by ion mobility and hydrogen/deuterium exchange measurements.     

Direct sub-micrometer patterning of nanostructured conducting polymer films via a low-energy infrared laser

Despite the many attractive properties of conjugated polymers, their practical applications are often limited by the lack of a simple, scalable, and nondisruptive patterning method. Here, a direct, scalable, high-resolution patterning technique for conducting polymers is demonstrated that does not involve photoresists, masks, or postprocessing treatment. Complex, well-defined patterns down to sub-micrometer scales can be created from nanofibrous films of a wide variety of conducting polymers by photothermally welding the nanofibers using a low-energy infrared laser. The welding depth, structural robustness, and optical properties of the films are readily controlled. In addition, the electrical properties such as conductivity can be precisely tuned over a 7-order of magnitude range, while maintaining the characteristic tunable electronic properties in the nonwelded polyaniline regions.     

Electron-Impact-Induced Fragmentation of a Glutamine Molecule

Technical Physics Letters - The formation of ionized products upon single and dissociative ionization of a glutamine (C5H10N2O3) molecule by electron impact at low (70 eV) and high (11.5 MeV)...     

Optimizing maintenance and repair policies via a combination of genetic algorithms and Monte Carlo simulation

In this paper we present an optimization approach based on the combination of a Genetic Algorithms maximization procedure with a Monte Carlo simulation. The approach is applied within the context of plant logistic management for what concerns the choice of maintenance and repair strategies. A stochastic model of plant operation is developed from the standpoint of its reliability/availability behavior, i.e. of the failure/repair/maintenance processes of its components. The model is evaluated by Monte Carlo simulation in terms of economic costs and revenues of operation. The flexibility of the Monte Carlo method allows us to include several practical aspects such as stand-by operation modes, deteriorating repairs, aging, sequences of periodic maintenances, number of repair teams available for different kinds of repair interventions (mechanical, electronic, hydraulic, etc.), components priority rankings. A genetic algorithm is then utilized to optimize the components maintenance periods and number of repair teams. The fitness function object of the optimization is a profit function which inherently accounts for the safety and economic performance of the plant and whose value is computed by the above Monte Carlo simulation model. For an efficient combination of Genetic Algorithms and Monte Carlo simulation, only few hundreds Monte Carlo histories are performed for each potential solution proposed by the genetic algorithm. Statistical significance of the results of the solutions of interest (i.e. the best ones) is then attained exploiting the fact that during the population evolution the fit chromosomes appear repeatedly many times. The proposed optimization approach is applied on two case studies of increasing complexity.     

Electron transfer ion/ion reactions in a three-dimensional quadrupole ion trap: reactions of doubly and triply protonated peptides with SO2*-

Ion-ion reactions between a variety of peptide cations (doubly and triply charged) and SO2 anions have been studied in a 3-D quadrupole ion trap, resulting in proton and electron transfer. Electron transfer dissociation (ETD) gives many c- and z-type fragments, resulting in extensive sequence coverage in the case of triply protonated peptides with SO2*-. For triply charged neurotensin, in which a direct comparison can be made between 3-D and linear ion trap results, abundances of ETD fragments relative to one another appear to be similar. Reactions of doubly protonated peptides with SO2*- give much less structural information from ETD than triply protonated peptides. Collision-induced dissociation (CID) of singly charged ions formed in reactions with SO2*- shows a combination of proton and electron transfer products. CID of the singly charged species gives more structural information than ETD of the doubly protonated peptide, but not as much information as ETD of the triply protonated peptide.