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Organisationseinheit der BAM
- 1 Analytische Chemie; Referenzmaterialien (12)
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- 1.9 Chemische und optische Sensorik (2)
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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%.
This key comparison aims to assess the capabilities of the participants to determine the amount-of-substance fraction oxygen in nitrogen. The GAWG has classified this as a track B comparison, due to the unexpected 50 μmol/mol argon mole fraction content of the transfer standards, which effects the achievable performance of some measurement techniques such a GC-TCD. The separation of oxygen and argon is challenging, and not all systems in use are equally well designed for it. As this analytical challenge due to a substantial fraction of argon in the transfer standards became a reality, the Gas Analysis Working Group (GAWG) decided to qualify this key comparison as a regular key comparison and not as a core comparison, which may be used to support calibration and measurement capabilities (CMCs) for oxygen in nitrogen, or for oxygen in nitrogen mixtures containing argon only (see also the section on support to CMCs).
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.
Lead isotope amount ratios are commonly used in diverse fields such as archaeometry, geochemistry and forensic science. Currently, five reference materials with certified lead isotope amount ratios are available, namely NIST SRM 981, 982 and 983, GBW-04442 and NMIJ 3681-a. Only NIST SRM 981 and NMIJ 3681-a have approximately natural isotopic compositions, and NIST SRM 981 is predominantly used for correcting mass discrimination/mass fractionation in the applied mass spectrometric procedures. Consequently, there is no other certified reference material available to be used for validation and/or quality control of the analytical procedures applied to lead isotope amount ratio measurements. To fill this gap, two new reference materials have been produced and certified for their lead isotope amount ratios. For both certified reference materials, complete uncertainty budgets have been calculated and SI traceability has been established. This provides the users with independent means for validating and verifying their analytical procedures and for conducting quality control measures. ERM-EB400 is a bronze material with a nominal lead mass fraction of 45 mg kg-1 and certified lead isotope amount ratios of n(206Pb)/n(204Pb) = 18.072(17) mol mol-1, n(207Pb)/n(204Pb) = 15.578(18) mol mol-1 and n(208Pb)/n(204Pb) = 38.075(46) mol mol-1 with the associated expanded uncertainties (k = 2) given in brackets. ERM-AE142 is a high-purity solution of lead in 2% nitric acid with a nominal mass fraction of 100 mg kg-1 and certified Pb isotope amount ratios of n(206Pb)/n(204Pb) = 21.114(17) mol mol-1, n(207Pb)/n(204Pb) = 15.944(17) mol mol-1 and n(208Pb)/n(204Pb) = 39.850(44) mol mol-1 with the associated expanded uncertainties (k = 2) given in brackets. Both materials are specifically designed to fall within the natural lead isotopic variation and to assist users with the validation and verification of their analytical procedures. Note that while one of these reference materials requires the chemical separation of Pb from its matrix (ERM-EB400), the other does not (ERM-AE142). As additional information, δ208/206PbNIST SRM981 values are provided for both materials. For ERM-AE142, a delta value of δ208/206PbNIST SRM981 = -28.21(30) ‰ was obtained, and for ERM-EB400, a delta value of δ208/206PbNIST SRM981 = -129.47(38) ‰ was obtained, with the associated expanded uncertainties (k = 2) given in brackets.
Lead (Pb) isotope amount ratios are commonly used in applications ranging from archaeology and forensic sciences to terrestrial and extra-terrestrial geochemistry. Despite their utility and frequency of use, only three certified isotope amount ratio reference materials are currently available for Pb: NIST SRMs 981, 982 and 983. Because SRM 981 has a natural Pb isotopic composition, it is mainly used for correcting instrumental mass discrimination or fractionation. This means that, at present, there are no other certified isotope reference materials with natural Pb isotopic composition that could be used for validating or verifying an analytical procedure involving the measurement of Pb isotope amount ratios.
To fill this gap, two new reference materials, both certified for their Pb isotopic composition, have been produced together with a complete uncertainty assessment. These new reference materials offer SI traceability and an independent means of validating or verifying analytical procedures used to produce Pb isotope amount ratio measurements.
ERM-EB400 is a bronze material containing a nominal Pb mass fraction of 45 mg/kg. ERM-AE142 is a high purity solution of Pb with a nominal mass fraction of 100 mg/kg. Both materials have been specifically produced to assist analysts in verifying or validating their analytical procedures. Note that while one of these reference materials requires the chemical separation of Pb from its matrix (ERM-EB400), the other does not (ERM-AE142). Details on the certification of these isotope reference materials are provided in this report.
The evolution of biological complexity is associated with the emergence of bespoke immune systems that maintain and protect organism integrity. Unlike the well-studied immune systems of cells and individuals, little is known about the origins of immunity during the transition to eusociality, a major evolutionary transition comparable to the evolution of multicellular organisms from single-celled ancestors. We aimed to tackle this by characterizing the immune gene repertoire of 18 cockroach and termite species, spanning the spectrum of solitary, subsocial and eusocial lifestyles. We find that key transitions in termite sociality are correlated with immune gene family contractions. In cross-species comparisons of immune gene expression, we find evidence for a caste-specific social defence system in termites, which appears to operate at the expense of individual immune protection. Our study indicates that a major transition in organismal complexity may have entailed a fundamental reshaping of the immune system optimized for group over individual defence.
To reveal and improve our understanding of the ignition behavior and mechanism, G-G furnace experiments of three typical organic dusts were performed to investigate the minimum ignition temperature (MIT) in O2/N2, O2/ Ar and O2/CO2 atmospheres with oxygen mole fraction from 8.4% to 50%. The experimental results were presented in oxygen-lean and oxy-fuel atmospheres to evaluate the ignition sensitivity of dusts in different atmospheres. It was found that CO2 is the strongest in terms of lowing the ignition sensitivity of the three dusts, and the dust explosion risk increases significantly with increasing O2 mole fraction for the three dusts through a logarithmically and significantly reducing MIT. However, for different dusts, inert gases show different suppression effects. In addition, a modified steady-state homogeneous ignition model was proposed and successfully applied to oxygen-lean atmospheres, and in oxy-fuel atmospheres, this model has also been improved to estimate the ignition mechanism. This ignition mechanism model could be used to successfully predict the minimum ignition temperature of high volatile dust under different inert atmospheres controlled by homogeneous ignition, which will provide a reference for the ignition hazard assessment of dust on hot surfaces.
Exploring the influence of counterpart materials on tribological behaviors of epoxy composites
(2016)
The dependence of the friction and wear of epoxy (EP) composites materials on counterpart materials, such as standard bearing steel, medium carbon steel and chrome-plating (Cr), was investigated. The conventional composite filled with short carbon fiber (SCF) and graphite shows the highest tribological performance when rubbing against Cr, whereas, the hybrid nanocomposite (EP filled with SCF, graphite and silica nanoparticles) exhibits the lowest friction and wear when sliding against the standard bearing steel. The role of nanoparticles in the tribological performance is distinctly different when sliding against with various counterpart materials. It is demonstrated that counterpart materials exert an important influence on material transfer, tribo-oxidation and mechanical mixing of wear products, resulting in the different formation mechanisms of transfer film.
Under the auspices of the Organic Analysis Working Group (OAWG) of the Comité Consultatif pour la Quantité de Matière (CCQM) a key comparison, CCQM K55.a, was coordinated by the Bureau International des Poids et Mesures (BIPM) in 2009/2010. Eleven national measurement institutes and the BIPM participated. Participants were required to assign the mass fraction of estradiol present as the main component in the comparison sample (CCQM-K55.a) which consisted of a bulk estradiol hemihydrate material obtained from a commercial supplier that had been extensively but not exhaustively dried prior to sub-division into the units supplied for the comparison.
Estradiol was selected to be representative of the performance of a laboratory's measurement capability for the purity assignment of organic compounds of medium structural complexity [molar mass range 300500 Da] and low polarity (pKOW < -2) for which related structure impurities can be quantified by capillary gas phase chromatography (GC) or by high performance liquid chromatography (LC).
The majority of participants used a mass balance approach to determine the estradiol content. The key comparison reference value (KCRV) for estradiol in CCQM-K55.a was assigned by combination of KCRVs assigned by consensus from participant results for each orthogonal impurity class. This allowed participants to demonstrate the efficacy (or otherwise) of their implementation of the mass balance approach and to demonstrate that their assigned value for the main component agreed with the KCRV through use of internally consistent contributing methods.
The KCRV for the estradiol content of the material was 984.3 mg/g with a combined standard uncertainty of 0.42 mg/g. The individual participant results showed that a relative expanded uncertainty for the purity assignment of 0.2% is a reasonable estimate of the best achievable result by an individual laboratory for a material of this complexity available in this amount at this level of purity. The relative expanded uncertainties reported by laboratories having results consistent with the KCRV ranged from 0.2% to 0.8%.
The review of results that were biased from the KCRV showed that two major analytical challenges are posed by the material: the measurement of its water content and controlling for related substance artefact formation during the analysis process. The results displaying a positive bias relative to the KCRV (overestimation of estradiol content) were due to underestimation of the water content of the material, while those with a negative bias (underestimation of estradiol) overestimated the total related substance impurities through a failure to detect and control for artefact formation arising from in situ oxidative dimerization of estradiol in neutral solution prior to analysis. There was however good agreement between all participants in the identification and the quantification of the individual related structure impurities actually present in the sample.
The comparison also demonstrated the utility of high-field 1H NMR for both quantitative and qualitative analysis of high purity compounds. It is noted that all the participants who used qNMR as a major or contributing technique and included it as part of, combined it or confirmed it with a conventional 'mass balance' data estimate, obtained results consistent with the KCRV.