Filtern
Dokumenttyp
- Zeitschriftenartikel (36)
- Forschungsdatensatz (7)
- Vortrag (3)
- Sonstiges (2)
- Buchkapitel (1)
Schlagworte
- Mass-Spectrometry (11)
- Cancer (9)
- Mass Spectrometry (9)
- Software (8)
- Metabolomics (7)
- R package (6)
- Mass Spectroscopy (4)
- Tumor metabolism (4)
- Data processing (3)
- Electrochemistry (3)
- Fatty acid metabolism (3)
- Lipidomic profile (3)
- Metabolic stress (3)
- Transformation products (3)
- ABID (2)
- Analytical Chemistry (2)
- Antibody identification (2)
- Collaborative trial (2)
- Fluxomics (2)
- Identity (2)
- MALDI (2)
- MYCN (2)
- Mass spectrometry (2)
- Monoclonal antibody (2)
- Mycotoxins (2)
- Peptide mass fingerprinting (2)
- Reference material (2)
- Renal disease (2)
- Sequencing (2)
- Traceability (2)
- 2,5-dihydroxyacetophenone (1)
- Acidic cleavage (1)
- Antibody (1)
- Antibody light chain (1)
- Antibody subclass (1)
- App (1)
- Arabidopsis (1)
- Aromatic hydrocarbons (1)
- Automation (1)
- Biocides (1)
- Biota (1)
- CE/MC-ICP-MS (1)
- COVID-19 (1)
- Cancer awareness measure (1)
- Cancer cells (1)
- Cancer risk (1)
- Cancer therapy (1)
- Certified reference material (1)
- Cleavage (1)
- Combustion Ion Chromatography (1)
- Construction products (1)
- Corona virus (1)
- DHAP (1)
- Data (1)
- Data Analyses (1)
- Database (1)
- Derivatization (1)
- ECR (1)
- Electrochemical Reactor (1)
- Ergot alkaloids (1)
- Expobome (1)
- Fatty acid desaturation (1)
- Fatty acid synthesis (1)
- Fatty acid uptake (1)
- Fatty acids (1)
- Fertilizer (1)
- Flux Analysis (1)
- General Environmental Science (1)
- Github (1)
- HLA (1)
- HPLC-MS/MS (1)
- HRMS (1)
- Human leukocyte antigen (HLA) (1)
- Hydrazinolysis (1)
- Hydrolysis (1)
- ICP-MS (1)
- ICP-ToF-MS (1)
- Ionophore (1)
- Ionophore antibiotics (1)
- Isotope Labelling (1)
- Isotope ratio (1)
- Isotopologue Distribution (1)
- LC/HRMS (1)
- Lasalocid (1)
- Laser Ablation/Imaging (1)
- Library (1)
- Light chain (1)
- Lipid metabolism (1)
- Lipidomics (1)
- Lysergic acid hydrazide (1)
- MALDI-TOF-MS (1)
- MC-ICP-MS (1)
- Mass Isotopomer Distribution (1)
- Mass-spectrometry (1)
- Massenspektrometrie (1)
- Metabolic Flux (1)
- Method development (1)
- Monensin (1)
- Moxidectin (1)
- Multivariate Statistics (1)
- NIST-mAb 8671 (1)
- Non-target (1)
- Non-targeted analysis (1)
- Nucleocapsid (1)
- Olive oil (1)
- Online software (1)
- Open science (1)
- Peak overlap (1)
- Peptide coverage (1)
- Peptides (1)
- Per- and Polyfluoroalkyl substances (PFAS) (1)
- Programming (1)
- Quality control (1)
- RBD (1)
- Rat/human liver microsomes (1)
- Recombinant antibody (1)
- Reference data (1)
- Reproducibility (1)
- Reproducibility crisis (1)
- Resistance (1)
- SARS-CoV-2 antibody (1)
- Salinomycin (1)
- Sequence coverage (1)
- Sewage sludge (1)
- Shiny-App (1)
- Spectra annotation (1)
- Spike protein (1)
- Statistics (1)
- Substance release (1)
- Sulfuric acid (1)
- Sum Parameter (1)
- Sum Parameter Method (1)
- Suspect and non-target analysis (1)
- Transformation (1)
- Transformation product (1)
- Transient signal (1)
- Truffle Aroma (1)
- Trypsin (1)
- Tryptic digest (1)
- Tuber melanosporum (1)
- UV radiation (1)
- Veterinary drugs (1)
- Water contact (1)
- Zenodo (1)
- species-specific isotope information (1)
Organisationseinheit der BAM
- 1 Analytische Chemie; Referenzmaterialien (48)
- 1.7 Organische Spuren- und Lebensmittelanalytik (48)
- 1.8 Umweltanalytik (11)
- 1.1 Anorganische Spurenanalytik (5)
- 1.5 Proteinanalytik (3)
- VP Vizepräsident (3)
- VP.1 eScience (3)
- 1.6 Anorganische Referenzmaterialien (2)
- 4 Material und Umwelt (2)
- 4.3 Schadstofftransfer und Umwelttechnologien (2)
Eingeladener Vortrag
- nein (3)
ABID
(2022)
In order to automate the spectral comparison for larger libraries of antibodies, we developed the online software ABID 2.0. 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.
The investigation of metabolic fluxes and metabolite distributions within cells by means of tracer molecules is a valuable tool to unravel the complexity of biological systems. Technological advances in mass spectrometry (MS) technology such as atmospheric pressure chemical ionization (APCI) coupled with high resolution (HR), not only allows for highly sensitive analyses but also broadens the usefulness of tracer-based experiments, as interesting signals can be annotated de novo when not yet present in a compound library. However, several effects in the APCI ion source, i.e., fragmentation and rearrangement, lead to superimposed mass isotopologue distributions (MID) within the mass spectra, which need to be corrected during data evaluation as they will impair enrichment calculation otherwise. Here, we present and evaluate a novel software tool to automatically perform such corrections. We discuss the different effects, explain the implemented algorithm, and show its application on several experimental datasets. This adjustable tool is available as an R package from CRAN.
The investigation of metabolic fluxes and metabolite distributions within cells by means of tracer molecules is a valuable tool to unravel the complexity of biological systems. Technological advances in mass spectrometry (MS) technology such as atmospheric pressure chemical ionization (APCI) coupled with high resolution (HR), not only allows for highly sensitive analyses but also broadens the usefulness of tracer‐based experiments, as interesting signals can be annotated de novo when not yet present in a compound library. However, several effects in the APCI ion source, i.e., fragmentation and rearrangement, lead to superimposed mass isotopologue distributions (MID) within the mass spectra, which need to be corrected during data evaluation as they will impair enrichment calculation otherwise. Here, we present and evaluate a novel software tool to automatically perform such corrections. We discuss the different effects, explain the implemented
algorithm, and show its application on several experimental datasets. This adjustable tool is available as an R package from CRAN.
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 35 monoclonal antibodies against SARS-CoV-2 to demonstrate how sequence-independent antibody identification can be achieved by simple means applied to 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 60 min 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 degrees 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. 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.
Towards Unbiased Evaluation of Ionization Performance in LC-HRMS Metabolomics Method Development
(2022)
As metabolomics increasingly finds its way from basic science into applied and regulatory environments, analytical demands on nontargeted mass spectrometric detection methods continue to rise. In addition to improved chemical comprehensiveness, current developments aim at enhanced robustness and repeatability to allow long-term, inter-study, and meta-analyses. Comprehensive metabolomics relies on electrospray ionization (ESI) as the most versatile ionization technique, and recent liquid chromatography-high resolution mass spectrometry (LC-HRMS) instrumentation continues to overcome technical limitations that have hindered the adoption of ESI for applications in the past. Still, developing and standardizing nontargeted ESI methods and instrumental setups remains costly in terms of time and required chemicals, as large panels of metabolite standards are needed to reflect biochemical diversity. In this paper, we investigated in how far a nontargeted pilot experiment, consisting only of a few measurements of a test sample dilution series and comprehensive statistical analysis, can replace conventional targeted evaluation procedures. To examine this potential, two instrumental ESI ion source setups were compared, reflecting a common scenario in practical method development. Two types of feature evaluations were performed, (a) summary statistics solely involving feature intensity values, and (b) analyses additionally including chemical interpretation.
Results were compared in detail to a targeted evaluation of a large metabolite standard panel. We reflect on the advantages and shortcomings of both strategies in the context of current harmonization initiatives in the metabolomics field.
IsoCor
(2022)
Despite numerous advantages offered by hyphenation of chromatography and electrokinetic separation methods with multicollector (MC) ICP-MS for isotope analysis, the main limitation of such systems is the decrease in precision and increase in uncertainty due to generation of short transient signals. To minimize this limitation, most authors compare several isotope ratio calculation methods and establish a multi-step data processing routine based on the precision and accuracy of the methods. However, to the best of our knowledge, there is no universal data processing tool available that incorporates all important steps of the treatment of the transient signals. Thus, we introduce a data processing application (App) IsoCor that facilitates automatic calculation of isotope ratios from transient signals and eases selection of the most suitable method. The IsoCor App performs baseline subtraction, peak detection, mass bias correction, isotope ratio calculation and delta calculation. The feasibility and reliability of the App was proven by reproducing the results from isotope analysis of three elements (neodymium, mercury and sulfur) measured on-line via hyphenated systems. The IsoCor App provides trackability of the results to ensure quality control of the analysis.
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.
The drug salinomycin (SAL) is a polyether antibiotic and used in veterinary Medicine as coccidiostat and growth promoter. Recently, SAL was suggested as a potential anticancer drug.
However, transformation products (TPs) resulting from metabolic and environmental degradation of SAL are incompletely known and structural information is missing. In this study, we therefore systematically investigated the formation and identification of SAL derived TPs using electrochemistry (EC) in an electrochemical reactor and rat and human liver microsome incubation (RLM and HLM) as TP generating methods. Liquid chromatography (LC) coupled to high-resolution mass spectrometry (HRMS) was applied to determine accurate masses in a suspected target analysis to identify TPs and to deduce occurring modification reactions of derived TPs. A total of 14 new, structurally different TPs were found (two EC-TPs, five RLM-TPs, and 11 HLM-TPs). The main modification reactions are decarbonylation for EC-TPs and oxidation (hydroxylation) for RLM/HLM-TPs. Of particular interest are potassium-based TPs identified after liver microsome incubation because these might have been overlooked or declared as oxidated sodium adducts in previous, non-HRMS-based studies due to the small mass difference between K and O + Na of 21 mDa. The MS fragmentation pattern of TPs was used to predict the position of identified modifications in the SAL molecule. The obtained knowledge regarding transformation reactions and novel TPs of SAL will contribute to elucidate SAL-metabolites with regards to structural prediction.
Given the central role of fatty acids in cancer pathophysiology, the exploitation of fatty acid metabolism as a potential antineoplastic therapy has gained much attention. Several natural and synthetic compounds targeting fatty acid metabolism were hitherto identified, and their effectiveness against cancer cell proliferation and survival was determined. This review will discuss the most clinically viable inhibitors or drugs targeting various proteins or enzymes mapped on nine interconnected fatty acid metabolism-related processes. We will discuss the general significance of each of these processes and the effects of their inhibition on cancer cell progression. Moreover, their mechanisms of action, limitations, and future perspectives will be assessed.
Lifestyle modifications could prevent almost one‑third to one‑half of all cancer cases. The awareness of cancer risk factors could motivate people to make such changes in their behaviors and lifestyles. This work aims to investigate the cancer awareness level in the Pakistani population. Telephone interviews of 657 individuals in Pakistan were carried out using the Cancer Awareness Measure (CAM) and Cancer Awareness Measure–MYthical Causes Scale (CAM‑MY). We observed that participants scored significantly better on the CAM scale than the CAM‑MY scale, and CAM scores were negatively associated with CAM‑MY scores. Years of formal education or a biology major at undergraduate or graduate level did not affect our population’s cancer awareness levels. Age displayed a weak but statistically significant negative association with CAM scores. Most participants failed to identify modifiable cancer risk factors, e.g., low physical activity. Efforts should be made to improve awareness of modifiable risk factors. We observed that brief training sessions could markedly improve people’s understanding of cancer risk factors and myths.