106 results found
Driver T, Averbukh V, Frasiński LJ, et al., 2021, Two-dimensional partial covariance mass spectrometry for the top-down analysis of intact proteins., Analytical Chemistry, Vol: 93, Pages: 10779-10788, ISSN: 0003-2700
Two-dimensional partial covariance mass spectrometry (2D-PC-MS) exploits the inherent fluctuations of fragment ion abundances across a series of tandem mass spectra, to identify correlated pairs of fragment ions produced along the same fragmentation pathway of the same parent (e.g., peptide) ion. Here, we apply 2D-PC-MS to the analysis of intact protein ions in a standard linear ion trap mass analyzer, using the fact that the fragment-fragment correlation signals are much more specific to the biomolecular sequence than one-dimensional (1D) tandem mass spectrometry (MS/MS) signals at the same mass accuracy and resolution. We show that from the distribution of signals on a 2D-PC-MS map it is possible to extract the charge state of both parent and fragment ions without resolving the isotopic envelope. Furthermore, the 2D map of fragment-fragment correlations naturally separates the products of the primary decomposition pathways of the molecular ions from those of the secondary ones. We access this spectral information using an adapted version of the Hough transform. We demonstrate the successful identification of highly charged, intact protein molecules bypassing the need for high mass resolution. Using this technique, we also perform the in silico deconvolution of the overlapping fragment ion signals from two co-isolated and co-fragmented intact proteins, demonstrating a viable new method for the concurrent mass spectrometric identification of a mixture of intact protein ions from the same fragment ion spectrum.
Driver T, Bachhawat N, Frasinski L, et al., 2021, Chimera spectrum diagnostics for peptides using two-dimensional partial covariance mass spectrometry, Molecules, Vol: 26, ISSN: 1420-3049
The rate of successful identification of peptide sequences by tandem mass spectrometry (MS/MS) is adversely affected by the common occurrence of co-isolation and co-fragmentation of two or more isobaric or isomeric parent ions. This results in so-called `chimera spectra’, which feature peaks of the fragment ions from more than a single precursor ion. The totality of the fragment ion peaks in chimera spectra cannot be assigned to a single peptide sequence, which contradicts a fundamental assumption of the standard automated MS/MS spectra analysis tools, such as protein database search engines. This calls for a diagnostic method able to identify chimera spectra to single out the cases where this assumption is not valid. Here, we demonstrate that, within the recently developed two-dimensional partial covariance mass spectrometry (2D-PC-MS), it is possible to reliably identify chimera spectra directly from the two-dimensional fragment ion spectrum, irrespective of whether the co-isolated peptide ions are isobaric up to a finite mass accuracy or isomeric. We introduce ‘3-57 chimera tag’ technique for chimera spectrum diagnostics based on 2D-PC-MS and perform numerical simulations to examine its efficiency. We experimentally demonstrate the detection of a mixture of two isomeric parent ions, even under conditions when one isomeric peptide is at one five-hundredth of the molar concentration of the second isomer.
Driver T, Cooper B, Ayers R, et al., 2020, Two-dimensional partial covariance mass spectrometry of large molecules based on fragment correlations, Physical Review X, Vol: 10, Pages: 041004 – 1-041004 – 13, ISSN: 2160-3308
Covariance mapping [L. J. Frasinski, K. Codling, and P. A. Hatherly, Science 246, 1029 (1989)] is a well-established technique used for the study of mechanisms of laser-induced molecular ionization and decomposition. It measures statistical correlations between fluctuating signals of pairs of detected species (ions, fragments, electrons). A positive correlation identifies pairs of products originating from the same dissociation or ionization event. A major challenge for covariance-mapping spectroscopy is accessing decompositions of large polyatomic molecules, where true physical correlations are overwhelmed by spurious signals of no physical significance induced by fluctuations in experimental parameters. As a result, successful applications of covariance mapping have so far been restricted to low-mass systems, e.g., organic molecules of around 50 daltons (Da). Partial-covariance mapping was suggested to tackle the problem of spurious correlations by taking into account the independently measured fluctuations in the experimental conditions. However, its potential has never been realized for the decomposition of large molecules, because in these complex situations, determining and continuously monitoring multiple experimental parameters affecting all the measured signals simultaneously becomes unfeasible. We introduce, through deriving theoretically and confirming experimentally, a conceptually new type of partial-covariance mapping—self-correcting partial-covariance spectroscopy—based on a parameter extracted from the measured spectrum itself. We use the readily available total ion count as the self-correcting partial-covariance parameter, thus eliminating the challenge of determining experimental parameter fluctuations in covariance measurements of large complex systems. The introduced self-correcting partial covariance enables us to successfully resolve correlations of molecules as large as
Berrah N, Sanchez-Gonzalez A, Jurek Z, et al., 2019, Femtosecond-resolved observation of the fragmentation of buckminsterfullerene following X-ray multiphoton ionization (vol 15, pg 1279, 2019), NATURE PHYSICS, Vol: 15, Pages: 1301-1301, ISSN: 1745-2473
Berrah N, Sanchez-Gonzalez A, Jurek Z, et al., 2019, Femtosecond-resolved observation of the fragmentation of buckminsterfullerene following X-ray multiphoton ionization, Nature Physics, Vol: 15, Pages: 1279-1283, ISSN: 1745-2473
X-ray free-electron lasers have, over the past decade, opened up the possibility of understanding the ultrafast response of matter to intense X-ray pulses. In earlier research on atoms and small molecules, new aspects of this response were uncovered, such as rapid sequences of inner-shell photoionization and Auger ionization. Here, we studied a larger molecule, buckminsterfullerene (C60), exposed to 640 eV X-rays, and examined the role of chemical effects, such as chemical bonds and charge transfer, on the fragmentation following multiple ionization of the molecule. To provide time resolution, we performed femtosecond-resolved X-ray pump/X-ray probe measurements, which were accompanied by advanced simulations. The simulations and experiment reveal that despite substantial ionization induced by the ultrashort (20 fs) X-ray pump pulse, the fragmentation of C60 is considerably delayed. This work uncovers the persistence of the molecular structure of C60, which hinders fragmentation over a timescale of hundreds of femtoseconds. Furthermore, we demonstrate that a substantial fraction of the ejected fragments are neutral carbon atoms. These findings provide insights into X-ray free-electron laser-induced radiation damage in large molecules, including biomolecules.
Barillot TR, Matia-Hernando P, Greening D, et al., 2017, Towards XUV pump-probe experiments in the femtosecond to sub-femtosecond regime: New measurement of the helium two-photon ionization cross-section, Chemical Physics Letters, Vol: 683, Pages: 38-42, ISSN: 0009-2614
Non-linear photoionization of molecules in the 10–50 eV range is a prerequisite for pump-probe measurements with sub-femtosecond resolution, but hitherto has been limited to femtosecond resolution, low repetition rate and high photon flux laser systems. We demonstrate two-photon single ionization of helium atoms using 100 pJ, 1.34 fs pulses (main peak FWHM = 680 as) at 1 kHz repetition rate with a central photon energy of 19.6 eV. We obtained an exponent of 2:27 0:21 for the intensity dependence of the signal and a two-photon ionization cross-section of 5:0 0:5 x 10−50 cm4 s. Our work opens the possibility of attosecond pump-probe measurements of ultrafast molecular processes.
Sanchez Gonzalez A, Micaelli P, Olivier C, et al., 2017, Accurate prediction of X-ray pulse properties from a free-electron laser using machine learning, Nature Communications, Vol: 8, ISSN: 2041-1723
Free-electron lasers providing ultra-short high-brightness pulses of X-ray radiation have great potential for a wide impact on science, and are a critical element for unravelling the structural dynamics of matter. To fully harness this potential, we must accurately know the X-ray properties: intensity, spectrum and temporal profile. Owing to the inherent fluctuations in free-electron lasers, this mandates a full characterization of the properties for each and every pulse. While diagnostics of these properties exist, they are often invasive and many cannot operate at a high-repetition rate. Here, we present a technique for circumventing this limitation. Employing a machine learning strategy, we can accurately predict X-ray properties for every shot using only parameters that are easily recorded at high-repetition rate, by training a model on a small set of fully diagnosed pulses. This opens the door to fully realizing the promise of next-generation high-repetition rate X-ray lasers.
Frasinski LJ, 2016, Covariance mapping techniques, Journal of Physics B - Atomic Molecular and Optical Physics, Vol: 49, ISSN: 0953-4075
Recent technological advances in the generation of intense femtosecond pulses have made covariance mapping an attractive analytical technique. The laser pulses available are so intense that often thousands of ionisation and Coulomb explosion events will occur within each pulse. To understand the physics of these processes the photoelectrons and photoions need to be correlated, and covariance mapping is well suited for operating at the high counting rates of these laser sources. Partial covariance is particularly useful in experiments with x-ray free electron lasers, because it is capable of suppressing pulse fluctuation effects. A variety of covariance mapping methods is described: simple, partial (single- and multi-parameter), sliced, contingent and multi-dimensional. The relationship to coincidence techniques is discussed. Covariance mapping has been used in many areas of science and technology: inner-shell excitation and Auger decay, multiphoton and multielectron ionisation, time-of-flight and angle-resolved spectrometry, infrared spectroscopy, nuclear magnetic resonance imaging, stimulated Raman scattering, directional gamma ray sensing, welding diagnostics and brain connectivity studies (connectomics). This review gives practical advice for implementing the technique and interpreting the results, including its limitations and instrumental constraints. It also summarises recent theoretical studies, highlights unsolved problems and outlines a personal view on the most promising research directions.
Sanchez-Gonzalez A, Barillot TR, Squibb RJ, et al., 2015, Auger electron and photoabsorption spectra of glycine in the vicinity of the oxygen K-edge measured with an X-FEL, JOURNAL OF PHYSICS B-ATOMIC MOLECULAR AND OPTICAL PHYSICS, Vol: 48, ISSN: 0953-4075
Zhaunerchyk V, Kaminska M, Mucke M, et al., 2015, Disentangling formation of multiple-core holes in aminophenol molecules exposed to bright X-FEL radiation, Journal of Physics B - Atomic Molecular and Optical Physics, Vol: 48, ISSN: 0953-4075
Competing multi-photon ionization processes, some leading to the formation of double core hole states, have been examined in 4-aminophenol. The experiments used the linac coherent light source (LCLS) x-ray free electron laser, in combination with a time-of-flight magnetic bottle electron spectrometer and the correlation analysis method of covariance mapping. The results imply that 4-aminophenol molecules exposed to the focused x-ray pulses of the LCLS sequentially absorb more than two x-ray photons, resulting in the formation of multiple core holes as well as in the sequential removal of photoelectrons and Auger electrons (so-called PAPA sequences).
Liekhus-Schmaltz CE, Tenney I, Osipov T, et al., 2015, Ultrafast isomerization initiated by X-ray core ionization, Nature Communications, Vol: 6, ISSN: 2041-1723
Rapid proton migration is a key process in hydrocarbon photochemistry. Charge migration and subsequent proton motion can mitigate radiation damage when heavier atoms absorb X-rays. If rapid enough, this can improve the fidelity of diffract-before-destroy measurements of biomolecular structure at X-ray-free electron lasers. Here we study X-ray-initiated isomerization of acetylene, a model for proton dynamics in hydrocarbons. Our time-resolved measurements capture the transient motion of protons following X-ray ionization of carbon K-shell electrons. We Coulomb-explode the molecule with a second precisely delayed X-ray pulse and then record all the fragment momenta. These snapshots at different delays are combined into a ‘molecular movie’ of the evolving molecule, which shows substantial proton redistribution within the first 12 fs. We conclude that significant proton motion occurs on a timescale comparable to the Auger relaxation that refills the K-shell vacancy.
Berrah N, Murphy B, Xiong H, et al., 2015, Femtosecond X-ray-induced fragmentation of fullerenes, Journal of Modern Optics, Vol: 63, Pages: 390-401, ISSN: 1362-3044
A new class of femtosecond, intense, short – wavelength lasers – the free-electron laser – has opened up new opportunities to investigate the structure and dynamics in many scientific areas. These new lasers, whose performance keeps increasing, enable the understanding of physical and chemical changes at an atomic spatial scale and on the time scale of atomic motion which is essential for a broad range of scientific fields. We describe here the interaction of fullerenes in the multiphoton regime with the Linac Coherent Light Source (LCLS) X-ray free-electron laser at SLAC National Laboratory. In particular, we report on new data regarding the ionization of Ho3N@C80 molecules and compare the results with our prior C60 investigation of radiation damage induced by the LCLS pulses. We also discuss briefly the potential impact of newly available instrumentation to physical and chemical sciences when they are coupled with FELs as well as theoretical calculations and modeling.
Mucke M, Zhaunerchyk V, Frasinski LJ, et al., 2015, Covariance mapping of two-photon double core hole states in C2H2 and C2H6 produced by an x-ray free electron laser, New Journal of Physics, Vol: 17, ISSN: 1367-2630
Few-photon ionization and relaxation processes in acetylene (C_2 H_2) and ethane (C_2 H_6) were investigated at the linac coherent light source x-ray free electron laser (FEL) at SLAC, Stanford using a highly efficient multi-particle correlation spectroscopy technique based on a magnetic bottle. The analysis method of covariance mapping has been applied and enhanced, allowing us to identify electron pairs associated with double core hole (DCH) production and competing multiple ionization processes including Auger decay sequences. The experimental technique and the analysis procedure are discussed in the light of earlier investigations of DCH studies carried out at the same FEL and at third generation synchrotron radiation sources. In particular, we demonstrate the capability of the covariance mapping technique to disentangle the formation of molecular DCH states which is barely feasible with conventional electron spectroscopy methods.
Xiong H, Murphy B, Fang L, et al., 2015, Femtosecond x-ray induced fragmentation of Ho3N@C-80, 29th International Conference on Photonic, Electronic, and Atomic Collisions (ICPEAC), Publisher: IOP PUBLISHING LTD, ISSN: 1742-6588
Cooper B, Kolorenc P, Frasinski LJ, et al., 2014, Analysis of a measurement scheme for ultrafast hole dynamics by few femtosecond resolution X-ray pump-probe Auger spectroscopy, Faraday Discussions, Vol: 171, Pages: 93-111, ISSN: 1364-5498
Ultrafast hole dynamics created in molecular systems as a result of sudden ionisation is the focus of much attention in the field of attosecond science. Using the molecule glycine we show through ab initio simulations that the dynamics of a hole, arising from ionisation in the inner valence region, evolves with a timescale appropriate to be measured using X-ray pulses from the current generation of SASE free electron lasers. The examined pump–probe scheme uses X-rays with photon energy below the K edge of carbon (275–280 eV) that will ionise from the inner valence region. A second probe X-ray at the same energy can excite an electron from the core to fill the vacancy in the inner-valence region. The dynamics of the inner valence hole can be tracked by measuring the Auger electrons produced by the subsequent refilling of the core hole as a function of pump–probe delay. We consider the feasibility of the experiment and include numerical simulation to support this analysis. We discuss the potential for all X-ray pump-X-ray probe Auger spectroscopy measurements for tracking hole migration.
Murphy BF, Osipov T, Jurek Z, et al., 2014, Femtosecond X-ray-induced explosion of C-60 at extreme intensity, Nature Communications, Vol: 5, ISSN: 2041-1723
Understanding molecular femtosecond dynamics under intense X-ray exposure is critical to progress in biomolecular imaging and matter under extreme conditions. Imaging viruses and proteins at an atomic spatial scale and on the time scale of atomic motion requires rigorous, quantitative understanding of dynamical effects of intense X-ray exposure. Here we present an experimental and theoretical study of C60 molecules interacting with intense X-ray pulses from a free-electron laser, revealing the influence of processes not previously reported. Our work illustrates the successful use of classical mechanics to describe all moving particles in C60, an approach that scales well to larger systems, for example, biomolecules. Comparisons of the model with experimental data on C60 ion fragmentation show excellent agreement under a variety of laser conditions. The results indicate that this modelling is applicable for X-ray interactions with any extended system, even at higher X-ray dose rates expected with future light sources.
Zhaunerchyk V, Frasinski LJ, Eland JHD, et al., 2014, Theory and simulations of covariance mapping in multiple dimensions for data analysis in high-data-event experiments, Phys. Rev. A
Multi-dimensional covariance analysis and its validity for correlation of processes leading to multiple products are investigated from a theoretical point of view. The need to correct for false correlations induced by experimental parameters which ﬂuctuate from shot to shot, such as the intensity of SASE X-ray Free Electron laser pulses, is emphasized. Three-fold covariance analysis based on simple extension of the two-variable formulation is shown to be valid for variables exhibiting Poisson statistics. In this case false correlations arising from ﬂuctuations in some unstable experimental parameter that scale linearly with signals can be eliminated by three-fold partial covariance analysis, as newly deﬁned here. Four-fold covariance based on the same simple extension is found to be invalid in general. Where ﬂuctuations in an unstable parameter induce non-linear signal variations, a technique of contingent covariance analysis is proposed here to suppress false correlations. In this paper we also show a method to eliminate false correlations associated with ﬂuctuations of several unstable experimental parameters.
Mucke M, Zhaunerchyk V, Squibb RJ, et al., 2014, Mapping the decay of double core hole states of atoms and molecules, 28th International Conference on Photonic, Electronic and Atomic Collisions (ICPEAC), Publisher: IOP PUBLISHING LTD, ISSN: 1742-6588
Oppermann M, Weber SJ, Frasinski LJ, et al., 2013, Multichannel contributions in the nonsequential double ionization of CO2, PHYSICAL REVIEW A, Vol: 88, ISSN: 1050-2947
Kornilov O, Eckstein M, Rosenblatt M, et al., 2013, Coulomb explosion of diatomic molecules in intense XUV fields mapped by partial covariance, Journal of Physics B : Atomic Molecular and Optical Physics, Vol: 46, ISSN: 0953-4075
Single-shot time-of-flight spectra for Coulomb explosion of N2 and I2 molecules have been recorded at the Free electron LASer in Hamburg (FLASH) and have been analysed using a partial covariance mapping technique. The partial covariance analysis unravels a detailed picture of all significant Coulomb explosion pathways, extending up to the N4+-N5+ channel for nitrogen and up to the I8+-I9+ channel for iodine. The observation of the latter channel is unexpected if only sequential ionization processes from the ground state ions are considered. The maximum kinetic energy release extracted from the covariance maps for each dissociation channel shows that Coulomb explosion of nitrogen molecules proceeds much faster than that of the iodine. The N2 ionization dynamics is modelled using classical trajectory simulations in good agreement with the outcome of the experiments. The results suggest that covariance mapping of the Coulomb explosion can be used to measure the intensity and pulse duration of free-electron lasers.
Frasinski LJ, Zhaunerchyk V, Mucke M, et al., 2013, Dynamics of hollow atom formation in intense x-ray pulses probed by partial covariance mapping, Physical Review Letters, Vol: 111, ISSN: 0031-9007
When exposed to ultra-intense X-radiation sources such as Free-Electron Lasers (FELs) the innermost electronic shell can efficiently be emptied creating a transient hollow atom or molecule. Understanding the femtosecond dynamics of such systems is fundamental to achieving atomic resolution in flash diffraction imaging of non-crystallized complex biological samples. We demonstrate the capacity of a correlation method called “partial covariance mapping” to probe the electron dynamics of neon atoms exposed to intense 8 fs pulses of 1062 eV photons. A complete picture of ionization processes competing in hollow atom formation and decay is visualised with unprecedented ease and the map reveals hitherto unobserved non-linear sequences of photoionization and Auger events. The technique is particularly well suited to the high counting rate inherent in FEL experiments.
Zhaunerchyk V, Mucke M, Salén P, et al., 2013, Using Covariance Mapping to Investigate the Dynamics of Multi-Photon Ionization Processes of Ne Atoms Exposed to X-FEL Pulses, Journal of Physics B-Atomic Molecular and Optical Physics
We report on a detailed investigation into the electron emission processes of Ne atoms exposed to intense femtosecond X-ray pulses provided by the Linac Coherent Light Source Free Electron Laser at Stanford. The covariance mapping technique is applied to analyze the data and the capability of this approach to disentangle both linear and non-linear correlation features which may be hidden on coincidence maps of the same data set is demonstrated. Diﬀerent correction techniques which enable improvements on the quality of the spectral features extracted from the covariance maps are explored. Finally, a method for deriving characteristics of the X-ray FEL pulses based on covariance mapping in combination with model simulations is presented.
Weber SJ, Oppermann M, Frasinski LJ, et al., 2013, Dynamical coupling of molecular rotation and Coulomb explosion, Conference on Lasers and Electro-Optics Europe & International Quantum Electronics Conference (CLEO/Europe-IQEC), Publisher: IEEE
Balciunas T, Haessler S, Fan GY, et al., 2013, Toward a "Perfect-Wave" HHG Driving With a Multicolor OPA, 18th International Conference on Ultrafast Phenomena, Publisher: E D P SCIENCES, ISSN: 2100-014X
Oppermann M, Weber SJ, Frasinski LJ, et al., 2013, Controlling ionisation and fragmentation processes in CO2 via inelastic electron recollisions, 18th International Conference on Ultrafast Phenomena, Publisher: E D P SCIENCES, ISSN: 2100-014X
Petrovic VS, Siano M, White JL, et al., 2012, Transient X-Ray Fragmentation: Probing a Prototypical Photoinduced Ring Opening, Physical Review Letters, Vol: 108, Pages: 253006-1-253006-4
We report the ﬁrst study of UV-induced photoisomerization probed via core ionization by an x-ray laser. We investigated x-ray ionization and fragmentation of the cyclohexadiene-hexatriene system at 850 eV during the ring opening. We ﬁnd that the ion-fragmentation patterns evolve over a picosecond, reﬂecting a change in the state of excitation and the molecular geometry: the average kinetic energy per ion fragment and H+ ion count increase as the ring opens and the molecule elongates. We discuss new opportunities for molecular photophysics created by optical pump x-ray probe experiments.
Balciunas T, Haessler S, Andriukaitis G, et al., 2012, Toward "Perfect-Wave" HHG Driving With a Multicolor OPA, Conference on Lasers and Electro-Optics (CLEO), Publisher: IEEE, ISSN: 2160-9020
We study the spectral phase of high-order harmonic emission as an observable for probingultrafast nuclear dynamics after the ionization of a molecule. Using a strong-fieldapproximation theory that includes nuclear dynamics, we relate the harmonic phase to thephase of the overlap integral of the nuclear wavefunctions of the initial neutral molecule andthe molecular ion after an attosecond probe delay. We determine experimentally the groupdelay of the high harmonic emission from D2 and H2 molecules, which allows us to verify therelation between harmonic frequency and the attosecond delay. The small difference in theharmonic phase between H2 and D2 calculated theoretically is consistent with ourexperimental results.
Haessler S, Diveki Z, Boutu W, et al., 2009, Imaging Molecular Orbitals using HHG, 8th Pacific Rim Conference on Lasers and Electro-Optics, Publisher: IEEE, Pages: 1163-1163
Boutu W, Haessler S, Merdji H, et al., 2008, Coherent control of attosecond emission from aligned molecules, NATURE PHYSICS, Vol: 4, Pages: 545-549, ISSN: 1745-2473
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