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This paper describes a wireless mobile prototype able to perform optical measurements by means of a miniaturized spectrometer for low light analysis, e.g. fluorescent sensors.
Evaluations, calculations, calibration management and result display are performed by a computer or a standard tablet. The device was designed primarily to detect traces of oil in drinking or ground water and for the analyses of crude oils. However, it can also address a wide range of fluorescent sensors. The fast and user-friendly inspection of water quality or oil properties, as well as the adaptability and mobility, make the device attractive for a variety of users. Further application areas could be easily implemented by adapting the optics and the software (database, data processing and calibration plots, etc.).
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 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.
Metaproteomics, the study of the collective proteome within a microbial ecosystem, has substantially grown over the past few years. This growth comes from the increased awareness that it can powerfully supplement metagenomics and metatranscriptomics analyses. Although metaproteomics is more challenging than single-species proteomics, its added value has already been demonstrated in various biosystems, such as gut microbiomes or biogas plants. Because of the many challenges, a variety of metaproteomics workflows have been developed, yet it remains unclear what the impact of the choice of workflow is on the obtained results. Therefore, we set out to compare several well-established workflows in the first community-driven, multi-lab comparison in metaproteomics: the critical assessment of metaproteome investigation (CAMPI) study. In this benchmarking study, we evaluated the influence of different workflows on sample preparation, mass spectrometry acquisition, and bioinformatic analysis on two samples: a simplified, lab-assembled human intestinal sample and a complex human fecal sample. We find that the same overall biological meaning can be inferred from the metaproteome data, regardless of the chosen workflow. Indeed, taxonomic and functional annotations were very similar across all sample-specific data sets. Moreover, this outcome was consistent regardless of whether protein groups or peptides, or differences at the spectrum or peptide level were used to infer these annotations. Where differences were observed, those originated primarily from different wet-lab methods rather than from different bioinformatic pipelines. The CAMPI study thus provides a solid foundation for benchmarking metaproteomics workflows, and will therefore be a key reference for future method improvement. [doi:10.25345/C5SX64D9M] [dataset license: CC0 1.0 Universal (CC0 1.0)]
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.
We interpret solving the multi-vehicle routing problem as a team Markov game with partially observable costs. For a given set of customers to serve, the playing agents (vehicles) have the common goal to determine the team-optimal agent routes with minimal total cost. Each agent thereby observes only its own cost. Our multi-agent reinforcement learning approach, the so-called multi-agent Neural Rewriter, builds on the single-agent Neural Rewriter to solve the problem by iteratively rewriting solutions. Parallel agent action execution and partial observability require new rewriting rules for the game. We propose the introduction of a so-called pool in the system which serves as a collection point for unvisited nodes. It enables agents to act simultaneously and exchange nodes in a conflict-free manner. We realize limited disclosure of agent-specific costs by only sharing them during learning. During inference, each agents acts decentrally, solely based on its own cost. First empirical results on small problem sizes demonstrate that we reach a performance close to the employed OR-Tools benchmark which operates in the perfect cost information setting.
MALDI-TOF-MS-based identification of monoclonal murine anti-SARS-CoV-2 antibodies within one hour
(2022)
During the SARS-CoV-2 pandemic, many virus-binding monoclonal antibodies have been developed for clinical and diagnostic purposes. This underlines the importance of antibodies as universal bioanalytical reagents. However, little attention is given to the reproducibility crisis that scientific studies are still facing to date. In a recent study, not even half of all research antibodies mentioned in publications could be identified at all. This should spark more efforts in the search for practical solutions for the traceability of antibodies. For this purpose, we used thirty-five monoclonal antibodies against SARS-CoV-2 to demonstrate how sequence-independent antibody identification can be achieved by simple means applied onto the protein. First, we examined the intact and light chain masses of the antibodies relative to the reference material NIST-mAb 8671. Already half of the antibodies could be identified based solely on these two parameters. In addition, we developed two complementary peptide mass fingerprinting methods with MALDI-TOF-MS that can be performed in 45 minutes and had a combined sequence coverage of over 80%. One method is based on the partial acidic hydrolysis of the protein by 5 mM of sulfuric acid at 99 °C. Furthermore, we established a fast way for a tryptic digest without an alkylation step. We were able to show that the distinction of clones is possible simply by a brief visual comparison of the mass spectra. In this work, two clones originating from the same immunization gave the same fingerprints. Later, a hybridoma sequencing confirmed the sequence identity of these sister clones. In order to automate the spectral comparison for larger libraries of antibodies, we developed the online software ABID 2.0 (https://gets.shinyapps.io/ABID/). This open-source software determines the number of matching peptides in the fingerprint spectra. We propose that publications and other documents critically relying on monoclonal antibodies with unknown amino acid sequences should include at least one antibody fingerprint. By fingerprinting an antibody in question, its identity can be confirmed by comparison with a library spectrum at any time and context.
Probability based taxonomic profiling of viral and microbiome samples using PepGM and Unipept
(2022)
In mass spectrometry based proteomics, protein homology leads to many shared peptides within and between species. This complicates
taxonomic inference in samples of unknown taxonomic origin. PepGM uses a graphical model for taxonomic profiling of viral proteomes and
metaproteomic datasets providing taxonomic confidence scores. To build the graphical model, a list of potentially present taxa needs to be
inferred. To this end, we integrate Unipept, which enables the fast querying of potentially present taxa. Together, they allow for taxonomic
inference with statistically sound confidence scores.
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.