The Role of Momentum Partitioning in Covariance Ion Imaging Analysis.

We present results from a covariance ion imaging study, which employs extensive filtering, on the relationship between fragment momenta to gain deeper insight into photofragmentation dynamics. A new data analysis approach is introduced that considers the momentum partitioning between the fragments of the breakup of a molecular polycation to disentangle concurrent fragmentation channels, which yield the same ion species. We exploit this approach to examine the momentum exchange relationship between the products, which provides direct insight into the dynamics of molecular fragmentation. We apply these techniques to extensively characterize the dissociation of 1-iodopropane and 2-iodopropane dications prepared by site-selective ionization of the iodine atom using extreme ultraviolet intense femtosecond laser pulses with a photon energy of 95 eV. Our assignments are supported by classical simulations, using parameters largely obtained directly from the experimental data.

Efficient prediction of attosecond two-colour pulses from an X-ray free-electron laser with machine learning.

X-ray free-electron lasers are sources of coherent, high-intensity X-rays with numerous applications in ultra-fast measurements and dynamic structural imaging. Due to the stochastic nature of the self-amplified spontaneous emission process and the difficulty in controlling injection of electrons, output pulses exhibit significant noise and limited temporal coherence. Standard measurement techniques used for characterizing two-coloured X-ray pulses are challenging, as they are either invasive or diagnostically expensive. In this work, we employ machine learning methods such as neural networks and decision trees to predict the central photon energies of pairs of attosecond fundamental and second harmonic pulses using parameters that are easily recorded at the high-repetition rate of a single shot. Using real experimental data, we apply a detailed feature analysis on the input parameters while optimizing the training time of the machine learning methods. Our predictive models are able to make predictions of central photon energy for one of the pulses without measuring the other pulse, thereby leveraging the use of the spectrometer without having to extend its detection window. We anticipate applications in X-ray spectroscopy using XFELs, such as in time-resolved X-ray absorption and photoemission spectroscopy, where improved measurement of input spectra will lead to better experimental outcomes.

Compact single-shot soft X-ray photon spectrometer for free-electron laser diagnostics.

The photon spectrum from free-electron laser (FEL) light sources offers valuable information in time-resolved experiments and machine optimization in the spectral and temporal domains. We have developed a compact single-shot photon spectrometer to diagnose soft X-ray spectra. The spectrometer consists of an array of off-axis Fresnel zone plates (FZP) that act as transmission-imaging gratings, a Ce:YAG scintillator, and a microscope objective to image the scintillation target onto a two-dimensional imaging detector. This spectrometer operates in segmented energy ranges which covers tens of electronvolts for each absorption edge associated with several atomic constituents: carbon, nitrogen, oxygen, and neon. The spectrometer's performance is demonstrated at a repetition rate of 120 Hz, but our detection scheme can be easily extended to 200 kHz spectral collection by employing a fast complementary metal oxide semiconductor (CMOS) line-scan camera to detect the light from the scintillator. This compact photon spectrometer provides an opportunity for monitoring the spectrum downstream of an endstation in a limited space environment with sub-electronvolt energy resolution.

Time-Resolved X-ray Photoelectron Spectroscopy: Ultrafast Dynamics in CS2 Probed at the S 2p Edge.

Recent developments in X-ray free-electron lasers have enabled a novel site-selective probe of coupled nuclear and electronic dynamics in photoexcited molecules, time-resolved X-ray photoelectron spectroscopy (TRXPS). We present results from a joint experimental and theoretical TRXPS study of the well-characterized ultraviolet photodissociation of CS2, a prototypical system for understanding non-adiabatic dynamics. These results demonstrate that the sulfur 2p binding energy is sensitive to changes in the nuclear structure following photoexcitation, which ultimately leads to dissociation into CS and S photoproducts. We are able to assign the main X-ray spectroscopic features to the CS and S products via comparison to a first-principles determination of the TRXPS based on ab initio multiple-spawning simulations. Our results demonstrate the use of TRXPS as a local probe of complex ultrafast photodissociation dynamics involving multimodal vibrational coupling, nonradiative transitions between electronic states, and multiple final product channels.

Identification of Cofragmented Combinatorial Peptide Isomers by Two-Dimensional Partial Covariance Mass Spectrometry.

Combinatorial post-translational modifications (PTMs), such as those forming the so-called "histone code", have been linked to cell differentiation, embryonic development, cellular reprogramming, aging, cancers, neurodegenerative disorders, etc. Nevertheless, a reliable mass spectral analysis of the combinatorial isomers represents a considerable challenge. The difficulty stems from the incompleteness of information that could be generated by the standard MS to differentiate cofragmented isomeric sequences in their naturally occurring mixtures based on the fragment mass-to-charge ratio and relative abundance information only. Here we show that fragment-fragment correlations revealed by two-dimensional partial covariance mass spectrometry (2D-PC-MS) allow one to solve the combinatorial PTM puzzles that cannot be tackled by the standard MS as a matter of principle. We introduce 2D-PC-MS marker ion correlation approach and demonstrate experimentally that it can provide the missing information enabling identification of cofragmentated combinatorially modified isomers. Our in silico study shows that the marker ion correlations can be used to unambiguously identify 5 times more cofragmented combinatorially acetylated tryptic peptides and 3 times more combinatorially modified Glu-C peptides of human histones than is possible using standard MS methods.

Disentangling sequential and concerted fragmentations of molecular polycations with covariant native frame analysis.

We present results from an experimental ion imaging study into the fragmentation dynamics of 1-iodopropane and 2-iodopropane following interaction with extreme ultraviolet intense femtosecond laser pulses with a photon energy of 95 eV. Using covariance imaging analysis, a range of observed fragmentation pathways of the resulting polycations can be isolated and interrogated in detail at relatively high ion count rates (∼12 ions shot-1). By incorporating the recently developed native frames analysis approach into the three-dimensional covariance imaging procedure, contributions from three-body concerted and sequential fragmentation mechanisms can be isolated. The angular distribution of the fragment ions is much more complex than in previously reported studies for triatomic polycations, and differs substantially between the two isomeric species. With support of simple simulations of the dissociation channels of interest, detailed physical insights into the fragmentation dynamics are obtained, including how the initial dissociation step in a sequential mechanism influences rovibrational dynamics in the metastable intermediate ion and how signatures of this nuclear motion manifest in the measured signals.

The time-resolved atomic, molecular and optical science instrument at the Linac Coherent Light Source.

The newly constructed time-resolved atomic, molecular and optical science instrument (TMO) is configured to take full advantage of both linear accelerators at SLAC National Accelerator Laboratory, the copper accelerator operating at a repetition rate of 120 Hz providing high per-pulse energy as well as the superconducting accelerator operating at a repetition rate of about 1 MHz providing high average intensity. Both accelerators power a soft X-ray free-electron laser with the new variable-gap undulator section. With this flexible light source, TMO supports many experimental techniques not previously available at LCLS and will have two X-ray beam focus spots in line. Thereby, TMO supports atomic, molecular and optical, strong-field and nonlinear science and will also host a designated new dynamic reaction microscope with a sub-micrometer X-ray focus spot. The flexible instrument design is optimized for studying ultrafast electronic and molecular phenomena and can take full advantage of the sub-femtosecond soft X-ray pulse generation program.

Attosecond coherent electron motion in Auger-Meitner decay.

In quantum systems, coherent superpositions of electronic states evolve on ultrafast time scales (few femtoseconds to attoseconds; 1 attosecond = 0.001 femtoseconds = 10-18 seconds), leading to a time-dependent charge density. Here we performed time-resolved measurements using attosecond soft x-ray pulses produced by a free-electron laser, to track the evolution of a coherent core-hole excitation in nitric oxide. Using an additional circularly polarized infrared laser pulse, we created a clock to time-resolve the electron dynamics and demonstrated control of the coherent electron motion by tuning the photon energy of the x-ray pulse. Core-excited states offer a fundamental test bed for studying coherent electron dynamics in highly excited and strongly correlated matter.

Proteomic Database Search Engine for Two-Dimensional Partial Covariance Mass Spectrometry.

We present a protein database search engine for the automatic identification of peptide and protein sequences using the recently introduced method of two-dimensional partial covariance mass spectrometry (2D-PC-MS). Because the 2D-PC-MS measurement reveals correlations between fragments stemming from the same or consecutive decomposition processes, the first-of-its-kind 2D-PC-MS search engine is based entirely on the direct matching of the pairs of theoretical and the experimentally detected correlating fragments, rather than of individual fragment signals or their series. We demonstrate that the high structural specificity afforded by 2D-PC-MS fragment correlations enables our search engine to reliably identify the correct peptide sequence, even from a spectrum with a large proportion of contaminant signals. While for peptides, the 2D-PC-MS correlation-matching procedure is based on complementary and internal ion correlations, the identification of intact proteins is entirely based on the ability of 2D-PC-MS to spatially separate and resolve the experimental correlations between complementary fragment ions.

Multi-resolution electron spectrometer array for future free-electron laser experiments.

The design of an angular array of electron time-of-flight (eToF) spectrometers is reported, intended for non-invasive spectral, temporal, and polarization characterization of single shots of high-repetition rate, quasi-continuous, short-wavelength free-electron lasers (FELs) such as the LCLS II at SLAC. This array also enables angle-resolved, high-resolution eToF spectroscopy to address a variety of scientific questions on ultrafast and nonlinear light-matter interactions at FELs. The presented device is specifically designed for the time-resolved atomic, molecular and optical science endstation (TMO) at LCLS II. In its final version, the spectrometer comprises up to 20 eToF spectrometers aligned to collect electrons from the interaction point, which is defined by the intersection of the incoming FEL radiation and a gaseous target. The full composition involves 16 spectrometers forming a circular equiangular array in the plane normal to the X-ray propagation and four spectrometers at 54.7° angle relative to the principle linear X-ray polarization axis with orientations in the forward and backward direction of the light propagation. The spectrometers are capable of independent and minimally chromatic electrostatic lensing and retardation, in order to enable simultaneous angle-resolved photo- and Auger-Meitner electron spectroscopy with high energy resolution. They are designed to ensure an energy resolution of 0.25 eV across an energy window of up to 75 eV, which can be individually centered via the adjustable retardation to cover the full range of electron kinetic energies relevant to soft X-ray methods, 0-2 keV. The full spectrometer array will enable non-invasive and online spectral-polarimetry measurements, polarization-sensitive attoclock spectroscopy for characterizing the full time-energy structure of SASE or seeded LCLS II pulses, and support emerging trends in molecular-frame spectroscopy measurements.

Chimera Spectrum Diagnostics for Peptides Using Two-Dimensional Partial Covariance Mass Spectrometry.

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.

Two-Dimensional Partial Covariance Mass Spectrometry for the Top-Down Analysis of Intact Proteins.

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.

Time-resolved pump-probe spectroscopy with spectral domain ghost imaging.

An atomic-level picture of molecular and bulk processes, such as chemical bonding and charge transfer, necessitates an understanding of the dynamical evolution of these systems. On the ultrafast timescales associated with nuclear and electronic motion, the temporal behaviour of a system is often interrogated in a 'pump-probe' scheme. Here, an initial 'pump' pulse triggers dynamics through photoexcitation, and after a carefully controlled delay a 'probe' pulse initiates projection of the instantaneous state of the evolving system onto an informative measurable quantity, such as electron binding energy. In this paper, we apply spectral ghost imaging to a pump-probe time-resolved experiment at an X-ray free-electron laser (XFEL) facility, where the observable is spectral absorption in the X-ray regime. By exploiting the correlation present in the shot-to-shot fluctuations in the incoming X-ray pulses and measured electron kinetic energies, we show that spectral ghost imaging can be applied to time-resolved pump-probe measurements. In the experiment presented, interpretation of the measurement is simplified because spectral ghost imaging separates the overlapping contributions to the photoelectron spectrum from the pump and probe pulse.

Multi-channel photodissociation and XUV-induced charge transfer dynamics in strong-field-ionized methyl iodide studied with time-resolved recoil-frame covariance imaging.

The photodissociation dynamics of strong-field ionized methyl iodide (CH3I) were probed using intense extreme ultraviolet (XUV) radiation produced by the SPring-8 Angstrom Compact free electron LAser (SACLA). Strong-field ionization and subsequent fragmentation of CH3I was initiated by an intense femtosecond infrared (IR) pulse. The ensuing fragmentation and charge transfer processes following multiple ionization by the XUV pulse at a range of pump-probe delays were followed in a multi-mass ion velocity-map imaging (VMI) experiment. Simultaneous imaging of a wide range of resultant ions allowed for additional insight into the complex dynamics by elucidating correlations between the momenta of different fragment ions using time-resolved recoil-frame covariance imaging analysis. The comprehensive picture of the photodynamics that can be extracted provides promising evidence that the techniques described here could be applied to study ultrafast photochemistry in a range of molecular systems at high count rates using state-of-the-art advanced light sources.

Attosecond transient absorption spooktroscopy: a ghost imaging approach to ultrafast absorption spectroscopy.

The recent demonstration of isolated attosecond pulses from an X-ray free-electron laser (XFEL) opens the possibility for probing ultrafast electron dynamics at X-ray wavelengths. An established experimental method for probing ultrafast dynamics is X-ray transient absorption spectroscopy, where the X-ray absorption spectrum is measured by scanning the central photon energy and recording the resultant photoproducts. The spectral bandwidth inherent to attosecond pulses is wide compared to the resonant features typically probed, which generally precludes the application of this technique in the attosecond regime. In this paper we propose and demonstrate a new technique to conduct transient absorption spectroscopy with broad bandwidth attosecond pulses with the aid of ghost imaging, recovering sub-bandwidth resolution in photoproduct-based absorption measurements.

Negative Ion Mode Collision-Induced Dissociation for Analysis of Protein Arginine Methylation.

Arginine methylation is a common protein post-translational modification (PTM) that plays a key role in eukaryotic cells. Three distinct types of this modification are found in mammals: asymmetric Nη1Nη1-dimethylarginine (aDMA), symmetric Nη1Nη2-dimethylarginine (sDMA), and an intermediate Nη1-monomethylarginine (MMA). Elucidation of regulatory mechanisms of arginine methylation in living organisms requires precise information on both the type of the modified residues and their location inside the protein amino acid sequences. Despite mass spectrometry (MS) being the method of choice for analysis of multiple protein PTMs, unambiguous characterization of protein arginine methylation may not be always straightforward. Indeed, frequent internal basic residues of Arg methylated tryptic peptides hamper their sequencing under positive ion mode collision-induced dissociation (CID), the standardly used tandem mass spectrometry method, while the relative stability of the aDMA and sDMA side chains under alternative non-ergodic electron-based fragmentation techniques, electron-capture and electron transfer dissociations (ECD and ETD), may impede differentiation between the isobaric residues. Here, for the first time, we demonstrate the potential of the negative ion mode collision-induced dissociation MS for analysis of protein arginine methylation and present data revealing that the negative polarity approach can deliver both an unambiguous identification of the arginine methylation type and extensive information on the modified peptide sequences.