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 - TY - JOUR A1 - Vogel, Christian A1 - Roesch, Philipp A1 - Wittwer, Philipp A1 - Piechotta, Christian A1 - Lisec, Jan A1 - Sommerfeld, Thomas A1 - Kluge, Stephanie A1 - Herzel, Hannes A1 - Huthwelker, T. A1 - Borca, C. A1 - Simon, Franz-Georg T1 - Levels of per- and polyfluoroalkyl substances (PFAS) in various wastewater-derived fertilizers - Analytical investigations from different perspectives N2 - Solid wastewater-based fertilizers were screened for per- and polyfluoroalkyl substances (PFAS) by the extractable organic fluorine (EOF) sum parameter method. The EOF values for ten sewage sludges from Germany and Switzerland range from 154 to 7209 mg kg−1. For thermal treated sewage sludge and struvite the EOF were lower with values up to 121 mg kg−1. Moreover, the application of PFAS targeted and suspect screening analysis of selected sewage sludge samples showed that only a small part of the EOF sum parameter values can be explained by the usually screened legacy PFAS. The hitherto unknown part of EOF sum parameter contains also fluorinated pesticides, pharmaceutical and aromatic compounds. Because these partly fluorinated compounds can degrade to (ultra-)short PFAS in wastewater treatment plants they should be considered as significant sources of organic fluorine in the environment. The combined results of sum parameter analysis and suspect screening reveal the need to update current regulations, such as the German fertilizer ordinance, to focus not solely on a few selected PFAS such as perfluorooctane sulfonic acid (PFOS) and perfluorooctanoic acid (PFOA) but consider an additional sum parameter approach as a more holistic alternative. Moreover, diffusion gradient in thin-films (DGT) passive samplers were utilized as an alternative simplified extraction method for PFAS in solid wastewater-based fertilizers and subsequently quantified via combustion ion chromatography. However, the DGT method was less sensitive and only comparable to the EOF values of the fertilizers in samples with >150 mg kg−1, because of different diffusion properties for various PFAS, but also kinetic exchange limitations. KW - Combustion ion chromatography KW - Per- and polyfluoroalkyl substances (PFAS) KW - Sewage sludge KW - Fertilizer PY - 2023 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-583429 DO - https://doi.org/10.1039/d3va00178d SN - 2754-7000 VL - 2 IS - 10 SP - 1436 EP - 1445 PB - Royal Society of Chemistry (RSC) CY - London AN - OPUS4-58342 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Russo, Francesco F. A1 - Nowatzky, Yannek A1 - Jaeger, Carsten A1 - Parr, Maria K. A1 - Benner, Philipp A1 - Muth, Thilo A1 - Lisec, Jan T1 - Machine learning methods for compound annotation in non‐targeted mass spectrometry—A brief overview of fingerprinting, in silico fragmentation and de novo methods N2 - Non‐targeted screenings (NTS) are essential tools in different fields, such as forensics, health and environmental sciences. NTSs often employ mass spectrometry (MS) methods due to their high throughput and sensitivity in comparison to, for example, nuclear magnetic resonance–based methods. As the identification of mass spectral signals, called annotation, is labour intensive, it has been used for developing supporting tools based on machine learning (ML). However, both the diversity of mass spectral signals and the sheer quantity of different ML tools developed for compound annotation present a challenge for researchers in maintaining a comprehensive overview of the field.In this work, we illustrate which ML‐based methods are available for compound annotation in non‐targeted MS experiments and provide a nuanced comparison of the ML models used in MS data analysis, unravelling their unique features and performance metrics. Through this overview we support researchers to judiciously apply these tools in their daily research. This review also offers a detailed exploration of methods and datasets to show gaps in current methods, and promising target areas, offering a starting point for developers intending to improve existing methodologies. KW - Mass Spectrometry KW - Spectra annotation KW - Machine learning PY - 2024 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-608732 DO - https://doi.org/10.1002/rcm.9876 VL - 38 IS - 20 SP - 1 EP - 15 PB - Wiley AN - OPUS4-60873 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Peter, Elisa K. A1 - Jaeger, Carsten A1 - Lisec, Jan A1 - Peters, R. Sven A1 - Mourot, Rey A1 - Rossel, Pamela E. A1 - Tranter, Martyn A1 - Anesio, Alexandre M. A1 - Benning, Liane G. T1 - Endometabolic profiling of pigmented glacier ice algae: the impact of sample processing N2 - Introduction Glacier ice algae, mainly Ancylonema alaskanum and Ancylonema nordenskiöldi, bloom on Greenland Ice Sheet bare ice surfaces. They significantly decrease surface albedo due to their purple-brown pigmentation, thus increasing melt. Little is known about their metabolic adaptation and factors controlling algal growth dynamics and pigment formation. A challenge in obtaining such data is the necessity of melting samples, which delays preservation and introduces bias to metabolomic analysis. There is a need to evaluate the physiological response of algae to melting and establish consistent sample processing strategies for metabolomics of ice microbial communities. Objectives To address the impact of sample melting procedure on metabolic characterization and establish a processing and analytical workflow for endometabolic profiling of glacier ice algae. Methods We employed untargeted, high-resolution mass spectrometry and tested the effect of sample melt temperature (10, 15, 20 °C) and processing delay (up to 49 h) on the metabolome and lipidome, and complemented this approach with cell counts (FlowCam), photophysiological analysis (PAM) and diversity characterization. Results and Conclusion We putatively identified 804 metabolites, with glycerolipids, glycerophospholipids and fatty acyls being the most prominent superclasses ( 50% of identified metabolites). Among the polar metabolome, carbohydrates and amino acid-derivatives were the most abundant. We show that 8% of the metabolome is affected by melt duration, with a pronounced decrease in betaine membrane lipids and pigment precursors, and an increase in phospholipids. Controlled fast melting at 10 °C resulted in the highest consistency, and is our recommendation for future supraglacial metabolomics studies. KW - Metabolic profiling KW - Mass Spectrometry KW - Ice algae PY - 2024 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-607921 DO - https://doi.org/10.1007/s11306-024-02147-6 VL - 20 IS - 5 SP - 1 EP - 15 PB - Springer Science and Business Media LLC AN - OPUS4-60792 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 - Development of an Online Isotope Dilution CE/ICP–MS Method for the Quantification of Sulfur in Biological Compounds N2 - We report an analytical methodology for the quantification of sulfur in biological molecules via a speciesunspecific postcolumn isotope dilution (online ID) approach using capillary electrophoresis (CE) coupled online with inductively coupled plasma−mass spectrometry (online ID CE/ICP−MS). The method was optimized using a mixture of standard compounds including sulfate, methionine, cysteine, cystine, and albumin, yielding compound recoveries between 98 and 105%. The quantity of sulfur is further converted to the quantity of the compounds owing to the prior knowledge of the sulfur content in the molecules. The limit of detection and limit of quantification of sulfur in the compounds were 1.3−2.6 and 4.1−8.4 mg L−1, respectively, with a correlation coefficient of 0.99 within the concentration range of sulfur of 5−100 mg L−1. The capability of the method was extended to quantify albumin in its native matrix (i.e., in serum) using experimentally prepared serum spiked with a pure albumin standard for validation. The relative expanded uncertainty of the method for the quantification of albumin was 6.7% (k = 2). Finally, we tested the applicability of the method on real samples by the analysis of albumin in bovine and human sera. For automated data assessment, a software application (IsoCor) which was developed by us in a previous work was developed further for handling of online ID data. The method has several improvements compared to previously published setups: (i) reduced adsorption of proteins onto the capillary wall owing to a special capillary-coating procedure, (ii) baseline separation of the compounds in less than 30 min via CE, (iii) quantification of several sulfur species within one run by means of the online setup, (iv) SI traceability of the quantification results through online ID, and (v) facilitated data processing of the transient signals using the IsoCor application. Our method can be used as an accurate approach for quantification of proteins and other biological molecules via sulfur analysis in complex matrices for various fields, such as environmental, biological, and pharmaceutical studies as well as clinical diagnosis. Sulfur is an essential element in living organisms, where it plays important roles in various biological processes, such as protein synthesis, enzyme activity, and antioxidant defense. However, the biological effects of different sulfur species can vary widely, and imbalances in sulfur speciation have been observed in a range of diseases, including cancer, Alzheimer’s disease, and diabetes.1−3 The accurate quantification of sulfur and its species in biological samples requires sensitive and selective analytical techniques. In recent years, separation techniques coupled online with inductively coupled plasma−mass spectrometry (ICP−MS) have emerged as powerful online analytical tools complementary to molecular spectrometric methods for speciation analysis of biological compounds. External calibration4−9 and isotope dilution (ID)10−15 are common calibration approaches applied for online quantification of sulfur species in complex samples. The ID analysis is advantageous over. KW - Analytical Chemistry KW - CE/MC-ICP-MS KW - species-specific isotope information PY - 2024 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-594736 DO - https://doi.org/10.1021/acs.analchem.3c03553 SN - 0003-2700 SP - 1 EP - 8 PB - American Chemical Society (ACS) AN - OPUS4-59473 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CHAP A1 - Lisec, Jan A1 - Jaeger, C. ED - Antonio, C. T1 - Statistical and Multivariate Analysis of MS-Based Plant Metabolomics Data N2 - Raw data from metabolomics experiments are initially subjected to peak identification and signal deconvolution to generate raw data matrices m × n, where m are samples and n are metabolites. We describe here simple statistical procedures on such multivariate data matrices, all provided as functions in the programming environment R, useful to normalize data, detect biomarkers, and perform sample classification. KW - Mass-Spectrometry KW - Multivariate Statistics PY - 2018 SN - 978-1-4939-7819-9 SN - 978-1-4939-7818-2 DO - https://doi.org/10.1007/978-1-4939-7819-9_20 SN - 1064-3745 SN - 1940-6029 VL - 1778 SP - Chapter 20, 285 EP - 296 PB - Springer-Verlag AN - OPUS4-45492 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Lisec, Jan T1 - CorMID - Correct Mass Isotopologue Distribution Vectors 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 - Software KW - R package KW - Mass Isotopomer Distribution KW - Flux Analysis PY - 2022 UR - https://github.com/cran/CorMID/ PB - GitHub CY - San Francisco, CA, USA AN - OPUS4-56442 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Adamus, A. A1 - Ali, I. A1 - Vasileiadis, V. A1 - Al-Hileh, L. A1 - Lisec, Jan A1 - Frank, M. A1 - Seitz, G. A1 - Engel, N. T1 - Vincetoxicum arnottianum modulates motility features and metastatic marker expression in pediatric rhabdomyosarcoma by stabilizing the actin cytoskeleton N2 - Background: Prevention of metastatic invasion is one of the main challenges in the treatment of alveolar rhabdomyosarcoma. Still the therapeutic options are limited. Therefore, an anti-tumor screening was initiated focusing on the anti-metastatic and anti-invasion properties of selected medicinal plant extracts and phytoestrogens, already known to be effective in the prevention and treatment of different cancer entities. Methods: Treatment effects were first evaluated by cell viability, migration, invasion, and colony forming assays on the alveolar rhabdomyosarcoma cell line RH-30 in comparison with healthy primary cells. Results: Initial anti-tumor screenings of all substances analyzed in this study, identified the plant extract of Vincetoxicum arnottianum (VSM) as the most promising candidate, harboring the highest anti-metastatic potential. Those significant anti-motility properties were proven by a reduced ability for migration (60%), invasion (99%) and colony formation (61%) under 48 h exposure to 25 μg/ml VSM. The restricted motility features were due to an induction of the stabilization of the cytoskeleton – actin fibers were 2.5-fold longer and were spanning the entire cell. Decreased proliferation (PCNA, AMT, GCSH) and altered metastasis (e. g. SGPL1, CXCR4, stathmin) marker expression on transcript and protein level confirmed the significant lowered tumorigenicity under VSM treatment. Finally, significant alterations in the cell metabolism were detected for 25 metabolites, with levels of uracil, N-acetyl serine and propanoyl phosphate harboring the greatest alterations. Compared to the conventional therapy with cisplatin, VSM treated cells demonstrated a similar metabolic shutdown of the primary cell metabolism. Primary control cells were not affected by the VSM treatment. Conclusions: This study revealed the VSM root extract as a potential, new migrastatic drug candidate for the putative treatment of pediatric alveolar rhabdomyosarcoma with actin filament stabilizing properties and accompanied by a marginal effect on the vitality of primary cells. KW - Mass Spectroscopy KW - Metabolomics KW - Cancer PY - 2021 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-533530 DO - https://doi.org/10.1186/s12906-021-03299-x VL - 21 IS - 1 PB - Springer Nature AN - OPUS4-53353 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -