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Applying data-driven AI systems makes it possible to extract patterns from given data, generate predictions and helps making decisions. Material research and testing holds a plethora of AI-based applications, for example, for the automatized search and synthesis of new materials, the detection of materials defects, or the prediction of process and materials parameters (inverse problems). However, AI algorithms can often only be as good as the training data from which the corresponding models are learned. Therefore, it is also indispensable to develop measures for the standardization and quality assurance of such data.
For this purpose, we develop and implement methods from transferring data from various sources into a homogeneous data repository with uniform data descriptions. Through the standardization and corresponding machine-readable interfaces, research data can be made usable and reusable for further data analyses. In addition to the technical implementation of integrative platforms, it is crucial that quality-assured research data management is recognized and implemented as an integral part of daily scientific work. Finally, we provide a vision of how the Federal Institute for Materials Research and Testing can benefit from data-driven AI systems. We discuss early applications and take a peek at future research.
Metaproteomics has substantially grown over the past years and supplements other omics approaches by bringing valuable functional information, enabling genotype- phenotype linkages and connections to metabolic outputs. Currently, a wide variety of metaproteomic workflows is available, yet their impact on the results remains to be thoroughly assessed.
Here, we carried out the first community-driven, multi-lab comparison in metaproteomics: the critical assessment of metaproteome investigation (CAMPI) study. Based on well-established workflows, we evaluated the influence of sample preparation, mass spectrometry acquisition, and bioinformatic analysis using two samples: a simplified, lab-assembled human intestinal model and a human fecal sample.
Although bioinformatic pipelines contributed to variability in peptide identification, wet-lab workflows were the most important source of differences between analyses. Overall, these peptide-level differences largely disappeared at the protein group level. Differences were observed between peptide- and protein-centric approaches for the predicted community composition but similar functional profiles were found across workflows.
The CAMPI findings demonstrate the robustness of current metaproteomics research and provide a perspective for future benchmarking studies.
In diesem Vortrag wird die Perspektive einer digitalen Qualitätsinfrastruktur (QI) auf informatischer Seite vorgestellt. Eine zu entwickelnde QI-Cloud ist die Grundlage einer verteilten IT-Plattform über die digitalisierte Prozesse der QI abgewickelt, Daten sicher vorgehalten und ausgetauscht sowie digitale Zertifikate ausgestellt werden können.
Dazu werden Methoden wie die Distributed Ledger Technologie sowie Smart Standards beschrieben, die das Potential haben, essentielle technologische Bestandteile einer digital transformierten QI zu werden.
In mass spectrometry based proteomics, protein homology leads to
many shared peptides within and between species. This complicates
taxonomic inference. inference. We introduce PepGM, a graphical model for taxonomic profiling of viral proteomes and metaproteomic datasets.
Using the graphical model, our approach computes statistically sound
scores for taxa based on peptide scores from a previous database
search, eliminating the need for commonly used heuristics. heuristics.
In mass spectrometry based proteomics, protein homology leads to
many shared peptides within and between species. This complicates
taxonomic inference. inference. We introduce PepGM, a graphical model for taxonomic profiling of viral proteomes and metaproteomic datasets.
Using the graphical model, our approach computes statistically sound
scores for taxa based on peptide scores from a previous database
search, eliminating the need for commonly used heuristics.
Glow discharge optical emission spectroscopy (GD-OES) is a technique for the analysis of solids such as metals, semiconductors, and ceramics. A low-pressure glow discharge plasma is applied in this system, which ‘sputters’ and promotes the sample atoms to a higher energy state. When the atoms return to their ground state, they emit light with characteristic wavelengths, which a spectrometer can detect. Thus, GD-OES combines the advantages of ICP-OES with solid sampling techniques, which enables it to determine the bulk elemental composition and depth profiles. However, direct solid sampling methods such as glow-discharge spectroscopy require reference materials for calibration due to the strong matrix effect.
Reference materials are essential when the accuracy and reliability of measurement results need to be guaranteed to generate confidence in the analysis. These materials are frequently used to determine measurement uncertainty, validate methods, suitability testing, and quality assurance. In addition, they guarantee that measurement results can be compared to recognized reference values. Unfortunately, the availability of certified reference materials suited to calibrate all elements in different matrix materials is limited. Therefore various calibration strategies and the preparation of traceable matrix-matched calibration standards will be discussed.
Machine learning is an essential component of the growing field of data science. Through statistical methods, algorithms are trained to make classifications or predictions, uncovering key insights within data mining projects. Therefore, it was tried in our work to combine GD-OES with machine learning strategies to establish a new and robust calibration model, which can be used to identify the elemental composition and concentration of metals from a single spectrum. For this purpose, copper reference materials from different manufacturers, which contain various impurity elements, were investigated using GD-OES. The obtained spectra information are evaluated with different algorithms (e.g., gradient boosting and artificial neural networks), and the results are compared and discussed in detail.
Driven by recent technological advances and the need for improved viral diagnostic applications, mass spectrometry-based proteomics comes into play for detecting viral pathogens accurately and efficiently. However, the lack of specific algorithms and software tools presents a major bottleneck for analyzing data from host-virus samples. For example, accurate species- and strain-level classification of a priori unidentified organisms remains a very challenging task in the setting of large search databases. Another prominent issue is that many existing solutions suffer from the protein inference issue, aggravated because many homologous proteins are present across multiple species. One of the contributing factors is that existing bioinformatic algorithms have been developed mainly for single-species proteomics applications for model organisms or human samples. In addition, a statistically sound framework was lacking to accurately assign peptide identifications to viral taxa. In this presentation, an overview is given on current bioinformatics developments that aim to overcome the above-mentioned issues using algorithmic and statistical methods. The presented methods and software tools aim to provide tailored solutions for both discovery-driven and targeted proteomics for viral diagnostics and taxonomic sample profiling. Furthermore, an outlook is provided on how the bioinformatic developments might serve as a generic toolbox, which can be transferred to other research questions, such as metaproteomics for profiling microbiomes and identifying bacterial pathogens.
In view of the increasing digitization of research and the use of data-intensive measurement and analysis methods, research institutions and their staff are faced with the challenge of documenting a constantly growing volume of data in a comprehensible manner, archiving them for the long term, and making them available for discovery and re-use by others in accordance with the FAIR principles. At BAM, we aim to facilitate the integration of research data management (RDM) strategies during the whole research cycle from the creation and standardized description of materials datasets to their publication in open repositories. To this end, we present the BAM Data Store, a central system for internal RDM that fulfills the heterogenous demands of materials science and engineering labs. The BAM Data Store is based on openBIS, an open-source software developed by the ETH Zurich that has originally been created for life science laboratories but that has since been deployed in a variety of research domains. The software offers a browser-based user interface for the digital representation of lab inventory entities (e.g., samples, chemicals, instruments, and protocols) and an electronic lab notebook for the standardized documentation of experiments and analyses.
To investigate whether openBIS is a suitable framework for the BAM Data Store, we carried out a pilot phase during which five research groups with employees from 16 different BAM divisions were introduced to the software. The pilot groups were chosen to represent a diverse array of domain use cases and RDM requirements (e.g., small vs big data volume, heterogenous vs structured data types) as well as varying levels of prior IT knowledge on the users’ side.
Overall, the results of the pilot phase are promising: While the creation of custom data structures and metadata schemas can be time-intensive and requires the involvement of domain experts, the system offers specific benefits in the form of a simplified documentation and automation of research processes, as well as constituting a basis for data-driven analysis. In this way, heterogeneous research workflows in various materials science research domains could be implemented, from the synthesis and characterization of nanomaterials to the monitoring of engineering structures. In addition to the technical deployment and the development of domain-specific metadata standards, the pilot phase also highlighted the need for suitable institutional infrastructures, processes, and role models. An institute-wide rollout of the BAM Data Store is currently being planned.
Die Angabe von Unsicherheiten bei zertifizierten Werten von Referenzmaterialien ist von entscheidender Bedeutung. Die korrekte Einbindung der Unsicherheiten zur Berechnung von Verfahrensmessunsicherheiten ist wesentlich für die Gewährleistung der Genauigkeit und Zuverlässigkeit von Messungen. In diesem Vortrag werden die verschiedenen Einflussfaktoren auf die Unsicherheit zertifizierter Werte gemäß ISO Guide 35 dargestellt. Dabei werden insbesondere die Charakterisierung, Homogenität und Stabilität als entscheidende Faktoren für die Bestimmung der Unsicherheit eines Referenzmaterials betrachtet. Abschließend wird das Konzept anhand eines konkreten Beispiels veranschaulicht, um die praktische Anwendung und die Auswirkungen auf die Berechnung von Verfahrensmessunsicherheiten zu verdeutlichen.