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Mass spectrometry-based proteomics provides a holistic snapshot of the entire protein set of living cells on a molecular level. Currently, only a few deep learning approaches exist that involve peptide fragmentation spectra, which represent partial sequence information of proteins. Commonly, these approaches lack the ability to characterize less studied or even unknown patterns in spectra because of their use of explicit domain knowledge. Here, to elevate unrestricted learning from spectra, we introduce ‘ad hoc learning of fragmentation’ (AHLF), a deep learning model that is end-to-end trained on 19.2 million spectra from several phosphoproteomic datasets. AHLF is interpretable, and we show that peak-level feature importance values and pairwise interactions between peaks are in line with corresponding peptide fragments. We demonstrate our approach by detecting post-translational modifications, specifically protein phosphorylation based on only the fragmentation spectrum without a database search. AHLF increases the area under the receiver operating characteristic curve (AUC) by an average of 9.4% on recent phosphoproteomic data compared with the current state of the art on this task. Furthermore, use of AHLF in rescoring search results increases the number of phosphopeptide identifications by a margin of up to 15.1% at a constant false discovery rate. To show the broad applicability of AHLF, we use transfer learning to also detect cross-linked peptides, as used in protein structure analysis, with an AUC of up to 94%.
We report the results of a Versailles Project on Advanced Materials and Standards (VAMAS) interlaboratory study on the measurement of the shell thickness and chemistry of nanoparticle coatings. Peptide-coated gold particles were supplied to laboratories in two forms: a colloidal suspension in pure water and particles dried onto a silicon wafer. Participants prepared and analyzed these samples using either X-ray photoelectron spectroscopy (XPS) or low energy ion scattering (LEIS). Careful data analysis revealed some significant sources of discrepancy, particularly for XPS. Degradation during transportation, storage, or sample preparation resulted in a variability in thickness of 53%. The calculation method chosen by XPS participants contributed a variability of 67%. However, variability of 12% was achieved for the samples deposited using a single method and by choosing photoelectron peaks that were not adversely affected by instrumental transmission effects. The study identified a need for more consistency in instrumental transmission functions and relative sensitivity factors since this contributed a variability of 33%. The results from the LEIS participants were more consistent, with variability of less than 10% in thickness, and this is mostly due to a common method of data analysis. The calculation was performed using a model developed for uniform, flat films, and some participants employed a correction factor to account for the sample geometry, which appears warranted based upon a simulation of LEIS data from one of the participants and comparison to the XPS results.
In additive manufacturing (AM) Laser Metal Deposition (LMD), parts are built by welding layers of powder feedstock onto a substrate. Applications for steel powders include forging tools and structural components for various industries. For large parts, the choice of tool-paths influences the build-rate, the part performance and the distortions in a highly geometry-dependent manner. With weld-path lengths in the range of hundreds of meters, a reliable, automated tool path generation is essential for the usability of LMD processes.
In this contribution, automated tool-path generation approaches are shown and their results are discussed for arbitrary geometries. The investigated path strategies are the classical approaches: “Zig-zag-” and “contour-parallel-strategies”. After generation, the tool-paths are automatically formatted into g-code for experimental build-up and ASCII for a numerical simulation model. Finally, the tool paths are discussed in regards to volume-fill, microstructure and porosity for the experimental samples.
This work presents a part of the IGF project 18737N “Welding distortion simulation” (FOSTA P1140)
The Gibbs free energy of a grain boundary is a complex thermodynamic function of temperature, pressure, and composition. These complexities add to the intrinsic crystallographic and chemical constraints imposed by the adjacent bulk phase. Recently we have proposed a density-based model for assessing grain boundary thermodynamics that enables a CALPHAD-informed description of the grain boundary. As such, the Gibbs free energy of the grain boundary is directly linked with available CALPHAD thermodynamic data. In this talk, new aspects of interfacial segregation and phase transformation are revealed by benchmarking the current model for various experimental cases, including several steels, high-entropy alloys and aluminum alloys. The effects of elastic interactions on the grain boundary segregation and the application of the model to a nanocrystalline Pt-Au alloy, with numerous grain boundaries of various characters, will be discussed.
This study describes an interlaboratory comparison (ILC) among nine (9) laboratories to evaluate and validate the standard operation procedure (SOP) for single-particle (sp) ICP-TOFMS developed within the context of the Horizon 2020 project ACEnano. The ILC was based on the characterization of two different Pt nanoparticle (NP) suspensions in terms of particle mass, particle number concentration, and isotopic composition. The two Pt NP suspensions were measured using icpTOF instruments (TOFWERK AG, Switzerland).
Two Pt NP samples were characterized and mass equivalent spherical sizes (MESSs) of 40.4 ± 7 nm and 58.8 ± 8 nm were obtained, respectively. MESSs showed <16% relative standard deviation (RSD) among all participating labs and <4% RSD after exclusion of the two outliers. A good agreement was achieved between the different participating laboratories regarding particle mass, but the particle number concentration results were more scattered, with <53% RSD among all laboratories, which is consistent with results from previous ILC studies conducted using ICP-MS instrumentation equipped with a sequential mass spectrometer. Additionally, the capabilities of sp-ICP-TOFMS to determine masses on a particle basis are discussed with respect to the potential for particle density determination. Finally, because quasi-simultaneous multi-isotope and multielement determinations are a strength of ICP-TOFMS instrumentation, the precision and trueness of isotope ratio determinations were assessed. The average of 1000 measured particles yielded a precision of below ±1% for intensity ratios of the most abundant Pt isotopes, i.e. 194Pt and 195Pt, while the accuracy of isotope ratios with the lower abundant isotopes was limited by counting statistics.
The dynamics of laser-induced plasma plume splitting is investigated using spatiotemporal plasma imaging and spectrometry in this paper. Plasma plume splitting into fast and slow components is clearly observed using plasma optical emission as time evolves. The spatial resolved plasma spectra are used to investigate the plasma species distribution, which reveals that the charged copper ions, which radiate at wavelength range 485 nm - 504 nm, are merely present in the fast component. In order to further interpret the mechanism, the pressure-dependent and laser energy-dependent plume splitting are analyzed. Based on the results, the charge separation field is proposed to explain this phenomenon. This work can be of importance for such areas as laser induced breakdown spectroscopy, laser-induced ion source formation, pulse laser deposition, film growth, and nanoscale synthesis.
The present work provides a comparative study on the interface and adhesion properties of surface modified single glass fibers embedded in an acrylate matrix. To facilitate a covalent bonding at the fibermatrix interface, the fibers are functionalized with selected organosilanes that comprise either passive (unsaturated C¼C bonds of methacrylate moieties) or photoactive functionalities (photocleavable bis(acyl)phosphane oxide groups). Immobilization of the functional silanes is carried out by a classic silanization reaction involving a condensation reaction across the surface hydroxyl groups of the inorganic glass fibers. The change of the physico-chemical properties of the fibers due to desizing and subsequent surface modification is monitored by X-ray photoelectron spectroscopy and zeta potential measurements. In addition, scanning electron microscopy is used to follow the changes in surface morphology. After the modification step, the desized and modified single fibers are embedded in a photocurable acrylate resin formulation. By performing single fiber pull-out tests, maximum pull-out force, friction strength and apparent interfacial shear strength are determined as a function of the coupled silanes. The results reveal that the attached organosilanes lead to a significant increase in adhesion strength, whilst the performance of the photo-cleavable organosilane is superior to the passive methacryl-functional derivative.
CCQM key comparison K-129 for the quantitative analysis of Cu(In,Ga)Se2 (CIGS) films has been performed by the Surface Analysis Working Group (SAWG) of the Consultative Committee for Amount of Substance (CCQM). The objective of this key comparison is to compare the equivalency of the National Metrology Institutes (NMIs) and Designated Institutes (DIs) for the measurement of mole fractions of Cu, In, Ga and Se in a thin CIGS film. The measurand of this key comparison is the average mole fractions of Cu, In, Ga and Se of a test CIGS alloy film in the unit of mole fraction (mol/mol). Mole fraction with the metrological unit of mol/mol can be practically converted to atomic fraction with the unit of at%.
In this key comparison, a CIGS film with certified mole fractions was supplied as a reference specimen to determine the relative sensitivity factors (RSFs) of Cu, In, Ga and Se. The mole fractions of the reference specimen were certified by isotope dilution - inductively coupled plasma/mass spectrometry (ID-ICP/MS) and are traceable to the SI. A total number counting (TNC) method was recommended as a method to determine the signal intensities of the constituent elements acquired in the depth profiles by Secondary Ion Mass Spectrometry (SIMS), X-ray Photoelectron Spectroscopy (XPS) and Auger Electron Spectroscopy (AES). Seven NMIs and one DI participated in this key comparison. The mole fractions of the CIGS films were measured by depth profiling based-SIMS, AES and XPS. The mole fractions were also measured by non-destructive X-Ray Fluorescence (XRF) Analysis and Electron Probe Micro Analysis (EPMA) with Energy Dispersive X-ray Spectrometry (EDX).
In this key comparison, the average degrees of equivalence uncertainties for Cu, In, Ga and Se are 0.0093 mol/mol, 0.0123 mol/mol, 0.0047 mol/mol and 0.0228 mol/mol, respectively. These values are much smaller than that of Fe in a Fe-Ni alloy film in CCQM K-67 (0.0330 mol/mol). This means that the quantification of multi-element alloy films is possible by depth profiling analysis using the TNC method.
A pilot study for the quantitative surface analysis of multi-element alloy films has been performed by the Surface Analysis Working Group (SAWG) of the Consultative Committee for Amount of Substance (CCQM). The aim of this pilot study is to ensure the equivalency in the measurement capability of national metrology institutes for the quantification of multi-element alloy films. A Cu(In,Ga)Se2 (CIGS) film with non-uniform depth distribution was chosen as a representative multi-element alloy film. The atomic fractions of the reference and the test CIGS films were certified by isotope dilution - inductively coupled plasma/mass spectrometry. A total number counting (TNC) method was used as a method to determine the signal intensities of the constituent elements, which are compared with their certified atomic fractions. The atomic fractions of the CIGS films were measured by various methods, such as Secondary Ion Mass Spectrometry (SIMS), Auger Electron Spectroscopy (AES), X-ray Photoelectron Spectroscopy (XPS), X-Ray Fluorescence (XRF) analysis and Electron Probe Micro Analysis (EPMA) with Energy Dispersive X-ray Spectrometry (EDX). Fifteen laboratories from eight National Metrology Institutes (NMIs), one Designated Institute (DI) and six non-NMIs participated in this pilot study. Although the average atomic fractions of 18 data sets showed rather poor relative standard deviations of about 5.5 % to 6.8 %, they were greatly improved to about 1.5 % to 2.2 % by excluding 5 strongly deviating data sets from the average atomic fractions. In this pilot study, the average expanded uncertainties of SIMS, XPS, AES, XRF and EPMA were 3.84%, 3.68%, 3.81%, 2.88% and 2.90%, respectively. These values are much better than those in the key comparison K-67 for composition of a Fe-Ni alloy film. As a result, the quantification of CIGS films using the TNC method was found to be a good candidate as a subject for a CCQM key comparison.
A pilot study for the thickness measurement of HfO2 films was performed by the Surface Analysis Working Group (SAWG) of the Consultative Committee for Amount of Substance (CCQM). The aim of this pilot study was to ensure the equivalency in the measurement capability of national metrology institutes for the thickness measurement of HfO2 films. In this pilot study, the thicknesses of six HfO2 films with nominal thickness from 1 nm to 4 nm were measured by X-ray Photoelectron Spectroscopy (XPS), X-ray Reflectometry(XRR), X-ray Fluorescence Analysis (XRF), Transmission Electron Spectroscopy (TEM), Spectroscopic Ellipsometry (SE) and Rutherford Backscattering Spectrometry (RBS). The reference thicknesses were determined by mutual calibration of a zero-offset method (Medium Energy Ion Scattering Spectroscopy (MEIS) of KRISS) and a method traceable to the length unit (the average thicknesses of three XRR data except the thinnest film). These reference thicknesses are traceable to the length unit because they are based on the traceability of XRR. For the thickness measurement by XPS, the effective attenuation length of Hf 4f electrons was determined. In the cases of XRR and TEM, the offset values were determined from a linear fitting between the reference thicknesses and the individual data by XRR and TEM. The amount of substance of HfO2, expressed as thickness of HfO2 films (in both linear and areal density units), was found to be a good subject for a CCQM key comparison.
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The final report has been peer-reviewed and approved for publication by the CCQM.