automRm: An R Package for Fully Automatic LC-QQQ-MS Data Preprocessing Powered by Machine Learning

Preprocessing of liquid chromatography-mass spectrometry (LC-MS) raw data facilitates downstream statistical and biological data analyses. In the case of targeted LC-MS data, consistent recognition of chromatographic peaks is a main challenge, in particular, for low abundant signals. Fully automatic preprocessing is faster than manual peak review and does not depend on the individual operator. Here, we present the R package automRm for fully automatic preprocessing of LC-MS data recorded in MRM mode. Using machine learning (ML) for detection of chromatographic peaks and quality control of reported results enables the automatic recognition of complex patterns in raw data. In addition, this approach renders automRm generally applicable to a wide range of analytical methods including hydrophilic interaction liquid chromatography (HILIC), which is known for sample-to-sample variations in peak shape and retention time. We demonstrate the impact of the choice of training data set, of the applied ML algorithm, and of individual peak characteristics on automRm’s ability to correctly report chromatographic peaks. Next, we show that automRm can replicate results obtained by manual peak review on published data. Moreover, automRm outperforms alternative software solutions regarding the variation in peak integration among replicate measurements and the number of correctly reported peaks when applied to a HILIC-MS data set. The R package is freely available from gitlab (https://gitlab.gwdg.de/joerg.buescher/automrm)

Targeted LC-MS/MS-based metabolomics and lipidomics on limited hematopoietic stem cell numbers

Metabolism is important for the regulation of hematopoietic stem cells (HSCs) and drives cellular fate. Due to the scarcity of HSCs, it has been technically challenging to perform metabolome analyses gaining insight into HSC metabolic regulatory networks. Here, we present two targeted liquid chromatography–mass spectrometry approaches that enable the detection of metabolites after fluorescence-activated cell sorting when sample amounts are limited. One protocol covers signaling lipids and retinoids, while the second detects tricarboxylic acid cycle metabolites and amino acids. For complete details on the use and execution of this protocol, please refer to Schönberger et al. (2022)

Polarized Proton Beams from Laser-induced Plasmas

We report on the concept of an innovative source to produce polarized proton/deuteron beams of a kinetic energy up to several GeV from a laser-driven plasma accelerator. Spin effects have been implemented into the PIC simulation code VLPL to make theoretical predictions about the behavior of proton spins in laser-induced plasmas. Simulations of spin-polarized targets show that the polarization is conserved during the acceleration process. For the experimental realization, a polarized HCl gas-jet target is under construction using the fundamental wavelength of a Nd:YAG laser system to align the HCl bonds and simultaneously circular polarized light of the fifth harmonic to photo-dissociate, yielding nuclear polarized H atoms. Subsequently, their degree of polarization is measured with a Lamb-shift polarimeter. The final experiments, aiming at the first observation of a polarized particle beam from laser-generated plasmas, will be carried out at the 10 PW laser system SULF at SIOM/Shanghai.Comment: 7 pages, 7 figure

The ABC Effect in Double-Pionic Nuclear Fusion and a pn Resonance as its Possible Origin

The ABC effect -- a long-standing puzzle in double-pionic fusion -- has been reexamined by the first exclusive and kinematically complete measurements of solid statistics for the fusion reactions $pn \to d\pi^0\pi^0$, $pd \to ^3$He$\pi\pi$ and $dd \to ^4$He$\pi\pi$ using the WASA detector, first at CELSIUS and recently at COSY -- the latter with a statistics increased by another two orders of magnitude. In all cases we observe a huge low-mass enhancement in the $\pi\pi$-invariant mass accompanied by a pronounced $\Delta\Delta$ excitation. For the most basic fusion reaction, the $pn \to d\pi^0\pi^0$ reaction, we observe in addition a very pronounced resonance-like energy dependence in the total cross section with a maximum 90 MeV below the $\Delta\Delta$ mass and a width of only 50 MeV, which is five times smaller than expected from a conventional $t$-channel $\Delta\Delta$ excitation. This reveals the ABC effect to be the consequence of a s-channel resonance with the formfactor of this dibaryonic state being reflected in the low-mass enhancement of the $\pi\pi$-invariant mass. From the fusion reactions to $^3$He and $^4$He we learn that this resonance is robust enough to survive even in nuclei.Comment: conference proceedings PANIC 0

Phenomenological analysis of K+ meson production in proton-nucleus collisions

Total and differential cross sections from literature, on the production of K+ mesons in pA interactions at projectile energies between T=0.8 and 2.9 GeV, covering the transition across the free nucleon-nucleon threshold at 1.58 GeV, have been investigated. From the target-mass dependence of the production cross sections no evidence for the expected change of the dominant reaction mechanism from two-step to direct kaon production was found. At T=1.0 GeV the A dependences of the total cross sections and of the most recent data from COSY-Juelich, differential cross sections measured under forward angles, are strongly different. The invariant K+ production cross sections show an overall exponential scaling behavior with the squared four-momentum transfer between the beam proton and the produced K+ meson for t< -0.05 GeV^2 independent of the beam energy and emission angle. The data from COSY-Juelich reveal a strongly different t dependence in the region of t>0 GeV^2. Further data at forward angles and different beam energies should be taken in order to explore this region of kinematically extreme conditions.Comment: 9 Pages, 11 Figure

Shape Isomerism at N = 40: Discovery of a Proton Intruder in 67Co

The nuclear structure of 67Co has been investigated through 67Fe beta-decay. The 67Fe isotopes were produced at the LISOL facility in proton-induced fission of 238U and selected using resonant laser ionization combined with mass separation. The application of a new correlation technique unambiguously revealed a 496(33) ms isomeric state in 67Co at an unexpected low energy of 492 keV. A 67Co level scheme has been deduced. Proposed spin and parities suggest a spherical (7/2-) 67Co ground state and a deformed first excited (1/2-) state at 492 keV, interpreted as a proton 1p-2h prolate intruder state.Comment: 4 pages, 5 figures, preprint submitted to Physical Review Letter

Eta and eta-prime meson production in the reaction pn -> dM near threshold

The two-step model with pi-, rho- and omega- exchanges taken into account is applied to investigate the reactions pn -> d eta and pn -> d eta-prime. The existing experimental data on the reaction pn -> d eta are analysed and predictions for the cross section of the reaction pn -> d eta-prime are presented. It is found that pi- as well as rho exchange yield significant contributions in both reactions. The effect of the final state interaction is also studied.Comment: 15 pages, 4 figure

The tactical mimicry of social enterprise strategies: acting ‘as if’ in the everyday life of third sector organizations

Using England as a paradigmatic case of the „enterprising up ‟ of the third sector through social enterprise policies and programs, this article sheds light on resistance as enacted through dramaturgical identification with government strategies. Drawing from a longitudinal qualitative research study, which is interpreted via Michel de Certeau‟s theory of the everyday, we present the case study of Teak, a charitable regeneration company, to illustrate how its Chief Executive Liam „acted as ‟ a social entrepreneur in order to gain access to important resources. We establish „tactical mimicry ‟ as a sensitizing concept to suggest that third sector practitioners ‟ identification with the normative premises of „social enterprise ‟ is part of a parasitical prosaics geared toward appropriating public money. While tactical mimicry conforms to strategies only in order to exploit them, its ultimate aim is to increase potentials of collective agency outside the direct influence of power. The contribution we make is threefold: first, we extend the recent debate on productive resistance by highlighting how „playing the game ‟ without changing existing relations of power can nevertheless produce largely favorable outcomes. Second, we suggest that recognition of the productive potential of tactical mimicry requires methodologies which pay attention to the spatial and temporal dynamics of resistance. And third, we argue that explaining „social enterprise‟ without consideration of the non-discursive, mainly financial resources made available to those who identify with it, necessarily risks overlooking a crucial element of the dramaturgical dynamic of discourse

Subthreshold antiproton production in proton-carbon reactions

Data from KEK on subthreshold antiproton as well as on pi(+-) and K(+-) production in proton-nucleus reactions are described at projectile energies between 3.5 and 12.0 GeV. We use a model which considers a hadron-nucleus reaction as an incoherent sum over collisions of the projectile with a varying number of target nucleons. It samples complete events and allows thus for the simultaneous consideration of all particle species measured. The overall reproduction of the data is quite satisfactory. It is shown that the contributions from the interaction of the projectile with groups of several target nucleons are decisive for the description of subthreshold production. Since the collective features of subthreshold production become especially significant far below the threshold, the results are extrapolated down to COSY energies. It is concluded that an antiproton measurement at ANKE-COSY should be feasible, if the high background of other particles can be efficiently suppressed.Comment: 15 pages, 5 figures, gzipped tar file, submitted to J. Phys. G v2: Modification of text due to demands of referee