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| 4. |
- Kawahara, R., et al.
(författare)
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Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis
- 2021
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Ingår i: Nature Methods. - : Springer Science and Business Media LLC. - 1548-7091 .- 1548-7105. ; 18, s. 1304-1316
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Tidskriftsartikel (refereegranskat)abstract
- Glycoproteomics is a powerful yet analytically challenging research tool. Software packages aiding the interpretation of complex glycopeptide tandem mass spectra have appeared, but their relative performance remains untested. Conducted through the HUPO Human Glycoproteomics Initiative, this community study, comprising both developers and users of glycoproteomics software, evaluates solutions for system-wide glycopeptide analysis. The same mass spectrometrybased glycoproteomics datasets from human serum were shared with participants and the relative team performance for N- and O-glycopeptide data analysis was comprehensively established by orthogonal performance tests. Although the results were variable, several high-performance glycoproteomics informatics strategies were identified. Deep analysis of the data revealed key performance-associated search parameters and led to recommendations for improved 'high-coverage' and 'high-accuracy' glycoproteomics search solutions. This study concludes that diverse software packages for comprehensive glycopeptide data analysis exist, points to several high-performance search strategies and specifies key variables that will guide future software developments and assist informatics decision-making in glycoproteomics. This analysis presents the results of a community-based evaluation of existing software for large-scale glycopeptide data analysis.
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| 5. |
- Aguilar, A., et al.
(författare)
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Double photodetachment from the Cl[-]ion
- 2004
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Ingår i: Physical Review A - Atomic, Molecular, and Optical Physics. - 2469-9926 .- 2469-9934. ; 69:2
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Tidskriftsartikel (refereegranskat)abstract
- The correlated process involving the photodetachment of two electrons from the [Formula Presented] ion has been investigated over the photon energy range 20–45 eV. In the experiment, a beam of photons from the Advanced Light Source (ALS) was collinearly merged with a counterpropagating beam of [Formula Presented] ions from a sputter ion source. The [Formula Presented] ions produced in the interaction region were detected, and the normalized signal was used to monitor the relative cross section for the reaction. An absolute scale for the cross section was established by measuring the spatial overlap of the two beams and by determining the efficiency for collection and detection of the [Formula Presented] ions. The overall magnitude and shape of the measured cross section for this process agrees well with an R-matrix calculation. The calculation identifies the dominant mechanism leading to the production of the [Formula Presented] ion as being a direct nonresonant process involving the ejection of a pair of electrons from the valence shell. Less important is the indirect nonresonant process that involves the production and decay of core-excited and doubly excited states of the Cl atom in an intermediate step. Direct and indirect resonant mechanisms involving the excitation of a single [Formula Presented] core electron or more than one valence electron of the [Formula Presented] ion were found to be insignificant in the energy range studied.
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| 6. |
- Andersson, Pontus, 1971, et al.
(författare)
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Radiative lifetimes of metastable states of negative ions
- 2006
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Ingår i: Physical Review A. Atomic, Molecular, and Optical Physics. - 1050-2947 .- 1094-1622 .- 2469-9926 .- 2469-9934. ; 73, s. 032705-
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Tidskriftsartikel (refereegranskat)abstract
- We present a technique for measuring the radiative lifetimes of metastable states of negative ions that involves the use of a heavy-ion storage ring. The method has been applied to investigate the radiative decay of the np(3) P-2(1/2) levels of Te-(n=5) and Se-(n=4) and the 3p(3) D-2 state of Si- for which the J=3/2 and 5/2 levels were unresolved. All of these states are metastable and decay primarily by emission of E2 and M1 radiation. Multi Configuration Dirac-Hartree-Fock calculations of rates for the transitions in Te- and Se- yielded lifetimes of 0.45 s and 4.7 s, respectively. The measured values agree well with these predicted values. In the case of the D-2 state of Si-, however, our measurement was only able to set a lower limit on the lifetime. The upper limit of the lifetime that can be measured with our apparatus is set by how long the ions can be stored in the ring, a limit determined by the rate of collisional detachment. Our lower limit of 1 min for the lifetime of the D-2 state is consistent with both the calculated lifetimes of 162 s for the D-2(3/2) level and 27.3 h for the D-2(5/2) level reported by O'Malley and Beck and 14.5 h and 12.5 h, respectively, from our Breit-Pauli calculations.
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| 7. |
- Attermeyer, Katrin, et al.
(författare)
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Carbon dioxide fluxes increase from day to night across European streams
- 2021
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Ingår i: Communications Earth & Environment. - : Springer Nature. - 2662-4435. ; 2:1
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Tidskriftsartikel (refereegranskat)abstract
- Globally, inland waters emit over 2 Pg of carbon per year as carbon dioxide, of which the majority originates from streams and rivers. Despite the global significance of fluvial carbon dioxide emissions, little is known about their diel dynamics. Here we present a large-scale assessment of day- and night-time carbon dioxide fluxes at the water-air interface across 34 European streams. We directly measured fluxes four times between October 2016 and July 2017 using drifting chambers. Median fluxes are 1.4 and 2.1mmolm(-2) h(-1) at midday and midnight, respectively, with night fluxes exceeding those during the day by 39%. We attribute diel carbon dioxide flux variability mainly to changes in the water partial pressure of carbon dioxide. However, no consistent drivers could be identified across sites. Our findings highlight widespread day-night changes in fluvial carbon dioxide fluxes and suggest that the time of day greatly influences measured carbon dioxide fluxes across European streams. Diel patterns can greatly impact total stream carbon dioxide emissions, with 39% greater carbon dioxide flux during the night-time relative to the day-time, according to a study of 34 streams across Europe.
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| 8. |
- Bravo, Andrea G., et al.
(författare)
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The interplay between total mercury, methylmercury and dissolved organic matter in fluvial systems : A latitudinal study across Europe
- 2018
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Ingår i: Water Research. - : Elsevier. - 0043-1354 .- 1879-2448. ; 144, s. 172-182
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Tidskriftsartikel (refereegranskat)abstract
- Large-scale studies are needed to identify the drivers of total mercury (THg) and monomethyl-mercury (MeHg) concentrations in aquatic ecosystems. Studies attempting to link dissolved organic matter (DOM) to levels of THg or MeHg are few and geographically constrained. Additionally, stream and river systems have been understudied as compared to lakes. Hence, the aim of this study was to examine the influence of DOM concentration and composition, morphological descriptors, land uses and water chemistry on THg and MeHg concentrations and the percentage of THg as MeHg (%MeHg) in 29 streams across Europe spanning from 41°N to 64°N. THg concentrations (0.06–2.78 ng L−1) were highest in streams characterized by DOM with a high terrestrial soil signature and low nutrient content. MeHg concentrations (7.8–159 pg L−1) varied non-systematically across systems. Relationships between DOM bulk characteristics and THg and MeHg suggest that while soil derived DOM inputs control THg concentrations, autochthonous DOM (aquatically produced) and the availability of electron acceptors for Hg methylating microorganisms (e.g. sulfate) drive %MeHg and potentially MeHg concentration. Overall, these results highlight the large spatial variability in THg and MeHg concentrations at the European scale, and underscore the importance of DOM composition on mercury cycling in fluvial systems.
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| 9. |
- Covington, A. M., et al.
(författare)
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Inner-shell photodetachment from the K- ion
- 2007
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Ingår i: Journal of Physics B-Atomic Molecular and Optical Physics. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 40:5, s. 935-942
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Tidskriftsartikel (refereegranskat)
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| 10. |
- Davis, V. T., et al.
(författare)
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Photo-double detachment from the F- ion
- 2005
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Ingår i: Journal of Physics B-Atomic Molecular and Optical Physics. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 38:14, s. 2579-2589
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Tidskriftsartikel (refereegranskat)
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| 11. |
- Ellmann, A, et al.
(författare)
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Radiative lifetime of a bound excited state of Te-
- 2004
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 92:25, s. 253002-
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Tidskriftsartikel (refereegranskat)abstract
- We report on the first experimental study of the lifetime of a bound excited state of a negative ion. A new experimental technique was developed and used to measure the radiative lifetime of the 5p(5) P-2(1/2) level of Te-. The experiment was performed in a magnetic storage ring, where a laser beam was applied along one of the straight sections. In the experiment the population of the excited J=1/2 level was probed each time the Te- ions passed through the laser field. A decay curve was built up by sampling the population of the excited level of the Te- ions as a function of time after injection into the ring. A multiconfiguration Dirac-Hartree-Fock calculation was performed in conjunction with the experiment. The calculation yielded a radiative lifetime of 0.45 s, in excellent agreement with the measured value of 0.42(5) s.
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| 12. |
- Lindahl, Anton, 1982, et al.
(författare)
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Experimental studies of partial photodetachment cross sections in K- below the K(7 2P) threshold
- 2012
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Ingår i: Physical Review A. - : American Physical Society. - 1050-2947. ; 85:3
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Tidskriftsartikel (refereegranskat)abstract
- A collinear beams apparatus has been used to determine photodetachment cross sections for K− in the photon energy range 4.250–4.360 eV. State-selective detection, utilizing a resonance ionization scheme, was applied to measure partial cross sections for those channels which leave the residual K atoms in the excited 7 2S, 5 2F, and 5 2G states. The energy region studied encompassed the openings of the aforementioned channels, as well as the channel that leaves the K atom in the 7 2P state. Two previously unobserved resonances were seen in all three partial cross sections between the K(5 2G) and K(7 2P) thresholds. It is shown that a more reliable determination of resonance parameters can be made if the same resonances are observed in several channels. In the region below the K(5 2F) threshold, three previously observed resonances were investigated [Kiyan et al. Phys. Rev. Lett. 84 5979 (2000)]. A greatly increased modulation of the signal was obtained by detecting in the K(7 2S) channel instead of the K(5 2S) channel used in the previous study. Furthermore, the shapes of the cross sections in the threshold regions are discussed. A detailed description of the apparatus and the experimental procedure employed is presented in the paper.
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| 13. |
- Lindahl, Anton, 1982, et al.
(författare)
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Observation of thresholds and overlapping resonances below the 10(2)P(1/2) and P-2(3/2) thresholds in the photodetachment of Cs
- 2013
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Ingår i: Physical Review A. - 1050-2947. ; 88:5
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Tidskriftsartikel (refereegranskat)abstract
- A collinear beam apparatus has been used to study photodetachment of Cs-. Partial cross sections were measured using state-selective detection based on a resonance ionization scheme. Several resonances were observed in the Cs(10(2)S), Cs(6 2F), Cs(6 2G), and Cs(6 2H) final-state channels below the Cs(10(2)P3/2) channel opening. A model was developed to account for the interference between overlapping resonances. This model is essentially a generalization of the Fano [U. Fano, Phys. Rev. 124, 1866 (1961)] and Shore [B. W. Shore, Phys. Rev. 171, 43 (1968)] parametrizations for single resonances. Resonance parameters were extracted by fitting the model to the data sets. The openings of the Cs(10(2)S) and Cs(6 2F) channels, where the polarizabilities of the atomic states are large and positive, showed rapid onsets. In the case of the Cs(6(2)G) and Cs(6(2)H) channels, on the other hand, the photodetachment cross sections increased slowly with energy. For the Cs(6(2)H) channel this is the expected behavior, since it is the result of a large and negative polarizability of the 6(2)H state. In addition, the excitation of the Cs(6(2)H) state with respect to the Cs ground state was found to be 28 356.3(2) cm(-1), in agreement with a previous experiment.
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| 14. |
- Lindahl, Anton, 1982, et al.
(författare)
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Threshold behaviour in photodetachment of K-
- 2012
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Ingår i: Journal of Physics: Conference Series (XXVII International Conference on Photonic, Electronic and Atomic Collisions (ICPEAC 2011)). - : IOP Publishing. - 1742-6588 .- 1742-6596. ; 388:PART 2
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Konferensbidrag (refereegranskat)abstract
- A photodetachment experiment has been performed with the formation of atoms in highly excited states of high positive and negative polarizabilities. A semiclassical model has been developed to describe the effect of the repulsive polarization potential in the vicinity of the photoreaction threshold.
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| 15. |
- Lindahl, Anton, 1982, et al.
(författare)
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Threshold Photodetachment in a Repulsive Potential
- 2012
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Ingår i: Physical Review Letters. - : American Physical Society. - 0031-9007. ; 108:3
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Tidskriftsartikel (refereegranskat)abstract
- We report on the first experimental observation of a new threshold behavior observed in the 5 2G partial channel in photodetachment of K-. It arises from the repulsive polarization interaction between the detached electron and the residual K(5 2G) atom, which has a large negative dipole polarizability. In order to account for the observation in the K(5 2G) channel, we have developed a semiclassical model that predicts an exponential energy dependence for the cross section. The measurements were made with collinear laser-ion beams and a resonance ionization detection scheme.
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| 19. |
- Windelius, Olle, 1972, et al.
(författare)
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A collinear angle-resolved photoelectron spectrometer
- 2017
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Ingår i: Nuclear Instruments and Methods in Physics Research, Section B: Beam Interactions with Materials and Atoms. - : Elsevier BV. - 0168-583X. ; 410, s. 144-152
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Tidskriftsartikel (refereegranskat)abstract
- In the present paper we describe a newly designed collinear photoelectron spectrometer for angular distribution measurements. We will henceforth refer to this instrument by the acronym PEARLS (PhotoElectron Angle-Resolved Linear Spectrometer). The design was motivated by the desire to collect electrons emitted from an extended linear source consisting of collinear photon and ion beams at a synchrotron radiation site. The electrons could be produced in either photoionization or photodetachment events. The primary advantage of a collinear beams geometry is that the effective interaction volume can be made much larger than that obtainable with a crossed beams geometry, which has been used in many earlier photoelectron spectroscopic studies. The present apparatus is capable of collecting electrons over a beam source length of 22 cm. The electrons are detected using Channel Electron Multipliers (CEMs). There are 4 detector planes placed perpendicular to the direction of the beam source, where each plane contains 4 CEMs. The use of all 4 detector planes with a total of 16 CEMs enhances the photoelectron signal, which is important at a synchrotron radiation site where the photon flux is typically low. If photoelectrons of different energies are emitted, the design allows for electrostatic energy analyzers to be placed in front of the CEMs. We have performed a photodetachment experiment to demonstrate the functionality of the PEARLS apparatus using a pulsed laser as the photon source. In particular, we have measured the angular distribution of photoelectrons ejected from Ag- at two different photon energies. © 2017 Elsevier B.V.
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