TY - JOUR A1 - Feord, Helen K. A1 - Trautwein-Schult, Anke A1 - Keuschnig, Christoph A1 - Ostrzinski, Anne A1 - Peter, Elisa K. A1 - Jaeger, Carsten A1 - Lisec, Jan A1 - Mourot, Rey A1 - Peters, Ravi Sven A1 - Çiftçi, Ozan A1 - Tranter, Martyn A1 - Anesio, Alexandre M. A1 - Becher, Dörte A1 - Benning, Liane G. T1 - Algae-dominated metaproteomes uncover cellular adaptations to life on the Greenland Ice Sheet N2 - Eukaryotic algae-dominated microbiomes thrive on the Greenland Ice Sheet (GrIS) in harsh environmental conditions, including low temperatures, high light, and low nutrient availability. Chlorophyte algae bloom on snow, while streptophyte algae dominate bare ice surfaces. Empirical data about the cellular mechanisms responsible for their survival in these extreme conditions are scarce. This knowledge gap was addressed by quantifying proteins for both algal taxa from samples on the southern margin of the GrIS. We show that the streptophyte glacier ice algae have a relative enrichment in proteins involved in environmental signaling and nutrient transport, indicative of cellular readiness to dynamically respond to extreme GriS environmental cues, linked, for example, to photoprotection and the rapid update of scarce nutrients. In contrast, the chlorophyte snow algae have a high abundance of proteins linked to lipid and nitrogen metabolisms, providing evidence for the biological processes sustaining the cellular carbon and nitrogen stores necessary for survival in an oligotrophic environment. We also identify proteins in both taxa linked to the synthesis and breakdown of key cellular pigments. Our study gives novel insights into the cellular biology of these algae and their adaptation to extreme environments. KW - Metabolic profiling KW - Mass spectrometry KW - Ice algae PY - 2025 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-641037 DO - https://doi.org/10.1038/s41522-025-00770-2 SN - 2055-5008 VL - 11 IS - 1 SP - 1 EP - 11 PB - Springer Science and Business Media LLC AN - OPUS4-64103 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Schoknecht, Ute A1 - Mathies, Helena A1 - Lisec, Jan T1 - Leaching and transformation of film preservatives in paints induced by combined exposure to ultraviolet radiation and water contact under controlled laboratory conditions N2 - Stormwater from urban areas can transport biocidally active substances and related transformation products from buildings into the environment. The occurrence of these substances in urban runoff depends on the availability of water, and on ultraviolet radiation exposure that causes photolytic reactions. In a systematic laboratory study, painted test specimens were exposed to either ultraviolet radiation, water contact, or a combination of both. Leaching of the biocidally active substances carbendazim, diuron, octylisothiazolinone, terbutryn, and selected transformation products of terbutryn and diuron were observed under various exposure conditions. Remaining concentrations of these substances in the paint were quantified. It was demonstrated that the distribution of active substances and transformation products in eluates and in the coatings themselves differs with exposure conditions. Strategies for environmental monitoring of biocide emissions need to consider the most relevant transformation products. However, environmental concentrations of biocidally active substances and transformation products depend on earlier exposure conditions. As a consequence, monitoring data cannot describe emission processes and predict expected leaching of biocidally active substances from buildings if the data are collected only occasionally. KW - Substance release KW - Construction products KW - Biocides KW - Transformation KW - UV radiation KW - Water contact PY - 2021 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-532114 DO - https://doi.org/10.3390/w13172390 SN - 2073-4441 VL - 13 IS - 17 SP - 1 EP - 16 PB - MDPI CY - Basel AN - OPUS4-53211 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Langenhan, Jennifer A1 - Jaeger, Carsten A1 - Baum, K. A1 - Simon, M. A1 - Lisec, Jan T1 - A Flexible Tool to Correct Superimposed Mass Isotopologue Distributions in GC‐APCI‐MS Flux Experiments N2 - 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. KW - Mass Spectrometry KW - Isotopologue Distribution KW - Metabolic Flux KW - R package PY - 2022 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-547318 DO - https://doi.org/10.3390/metabo12050408 VL - 12 IS - 5 SP - 1 EP - 10 PB - MDPI AN - OPUS4-54731 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Tscheuschner, Georg A1 - Kaiser, Melanie N. A1 - Lisec, Jan A1 - Beslic, D. A1 - Muth, Thilo A1 - Krüger, M. A1 - Mages, H. W. A1 - Dorner, B. G. A1 - Knospe, J. A1 - Schenk, J. A. A1 - Sellrie, F. A1 - Weller, Michael G. T1 - MALDI-TOF-MS-Based Identification of Monoclonal Murine Anti-SARS-CoV-2 Antibodies within One Hour N2 - 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. KW - Reproducibility KW - Quality control KW - Traceability KW - Peptides KW - Peptide mass fingerprinting KW - Monoclonal antibody KW - Recombinant antibody KW - Identity KW - Antibody identification KW - Sequencing KW - Light chain KW - Mass spectrometry KW - Software KW - Open science KW - Library KW - COVID-19 KW - Corona virus KW - Sequence coverage KW - NIST-mAb 8671 KW - Reference material KW - RBD KW - Spike protein KW - Nucleocapsid KW - Cleavage KW - Tryptic digest KW - MALDI KW - DHAP KW - 2,5-dihydroxyacetophenone KW - Github KW - Zenodo KW - ABID PY - 2022 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-547347 DO - https://doi.org/10.3390/antib11020027 VL - 11 IS - 2 SP - 1 EP - 22 PB - MDPI CY - Basel AN - OPUS4-54734 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Jaeger, Carsten A1 - Lisec, Jan T1 - Towards Unbiased Evaluation of Ionization Performance in LC-HRMS Metabolomics Method Development N2 - 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. KW - Mass Spectrometry KW - Non-targeted analysis KW - Method development PY - 2022 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-548065 DO - https://doi.org/10.3390/metabo12050426 VL - 12 IS - 5 SP - 1 EP - 13 PB - MDPI AN - OPUS4-54806 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Munir, R. A1 - Noureen, N. A1 - Bashir, M. A1 - Shoaib, N. A1 - Ashraf, A. A1 - Lisec, Jan A1 - Zaidi, N. T1 - Cancer Awareness Measure (CAM) and Cancer Awareness Measure MYthical Causes Scale (CAM‑MY) scores in Pakistani population N2 - 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. KW - Cancer KW - Cancer awareness measure KW - Cancer risk PY - 2022 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-548960 DO - https://doi.org/10.1038/s41598-022-13012-8 SN - 2045-2322 VL - 12 IS - 1 SP - 1 EP - 10 PB - Nature Publishing Group CY - London AN - OPUS4-54896 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Tukhmetova, Dariya A1 - Lisec, Jan A1 - Vogl, Jochen A1 - Meermann, Björn T1 - Data processing made easy: standalone tool for automated calculation of isotope ratio from transient signals – IsoCor N2 - 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. KW - Isotope ratio KW - Transient signal KW - MC-ICP-MS KW - Data processing KW - App PY - 2022 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-559068 DO - https://doi.org/10.1039/D2JA00208F VL - 37 IS - 11 SP - 2401 EP - 2409 PB - Royal Society of Chemistry AN - OPUS4-55906 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Orf, I. A1 - Tenenboim, H. A1 - Omranian, N. A1 - Nikoloski, Z. A1 - Fernie, A. R. A1 - Lisec, Jan A1 - Brotman, Y. A1 - Bromke, M. A. T1 - Transcriptomic and Metabolomic Analysis of a Pseudomonas-Resistant versus a Susceptible Arabidopsis Accession N2 - Accessions of one plant species may show significantly different levels of susceptibility to stresses. The Arabidopsis thaliana accessions Col-0 and C24 differ significantly in their resistance to the pathogen Pseudomonas syringae pv. tomato (Pst). To help unravel the underlying mechanisms contributing to this naturally occurring variance in resistance to Pst, we analyzed changes in transcripts and compounds from primary and secondary metabolism of Col-0 and C24 at different time points after infection with Pst. Our results show that the differences in the resistance of Col-0 and C24 mainly involve mechanisms of salicylic-acid-dependent systemic acquired resistance, while responses of jasmonic-acid-dependent mechanisms are shared between the two accessions. In addition, arginine metabolism and differential activity of the biosynthesis pathways of aliphatic glucosinolates and indole glucosinolates may also contribute to the resistance. Thus, this study highlights the difference in the defense response strategies utilized by different genotypes. KW - Mass Spectrometry KW - Arabidopsis KW - Resistance PY - 2022 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-559549 DO - https://doi.org/10.3390/ijms232012087 VL - 23 IS - 20 SP - 1 EP - 27 PB - MDPI AN - OPUS4-55954 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Munir, R. A1 - Lisec, Jan A1 - Jaeger, Carsten A1 - Zaidi, N. T1 - Abundance, fatty acid composition and saturation index of neutral lipids in colorectal cancer cell lines N2 - Lipid droplets, the dynamic organelles that store Triglycerides (TG) and cholesterol esters (CE), are highly accumulated in colon cancer cells. This work studies the TG and CE subspecies profile in colon carcinoma cell lines, SW480 derived from primary tumor, and SW620 derived from a metastasis of the same tumor. It was previously reported that the total TG and CE content is dramatically higher in SW620 cells; however, TG and CE subspecies profile has not been investigated in detail. The work presented here confirms that the total TG and CE Content is significantly higher in the SW620 cells. Moreover, the fatty acid (FA) composition of TG is significantly altered in the SW620 cells, with significant decrease in the abundance of saturated triglycerides. This resulted in a significantly decreased TG saturation index in the SW620 cells. The saturation index of CE was also significantly decreased in the SW620 cells. KW - Mass Spectroscopy KW - Metabolomics KW - Cancer PY - 2021 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-533504 DO - https://doi.org/10.18388/abp.2020_5465 VL - 68 IS - 1 SP - 1 EP - 4 PB - ABP Acta Biochimica Polonica AN - OPUS4-53350 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Noureen, N. A1 - Shah, F. A. A1 - Lisec, Jan A1 - Usman, H. A1 - Khalid, M. A1 - Munir, R. A1 - Zaidi, N. T1 - Revisiting the association between human leukocyte antigen and end-stage renal disease N2 - Multiple works have studied possible associations between human leukocyte antigen (HLA) alleles and end stage renal disease (ESRD) showing, however, contradictory and inconsistent results. Here, we revisit the association between ESRD and HLA antigens, comparing HLA polymorphism (at HLA-A, -B, -C, -DRB1, -DQB1 and DQA1 loci) in ESRD patients (n = 497) and controls (n = 672). Our data identified several HLA alleles that displayed a significant positive or negative association with ESRD. We also determined whether heterozygosity or homozygosity of the ESRD-associated HLA alleles at different loci could modify the prevalence of the disease. Few HLA allele combinations displayed significant associations with ESRD, among which A*3_26 combination showed the highest strength of association (OR = 4.488, P≤ 0.05) with ESRD. Interestingly, the age of ESRD onset was not affected by HLA allele combinations at different loci. We also performed an extensive literature analysis to determine whether the association of HLA to ESRD can be similar across different ethnic groups. Our analysis showed that at least certain HLA alleles, HLA-A*11, HLA-DRB1*11, and HLA-DRB1*4, display a significant association with ESRD in different ethnic groups. The findings of our study will help in determining possible protective or susceptible roles of various HLA alleles in ESRD. KW - Cancer KW - Human leukocyte antigen (HLA) KW - Renal disease PY - 2020 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-512651 DO - https://doi.org/10.1371/journal.pone.0238878 SN - 1932-6203 VL - 15 IS - 9 SP - e0238878 AN - OPUS4-51265 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -