Frontiers in analytical science最新文献

{"title":"Why do we need to go beyond overall biological variability assessment in metabolomics?","authors":"J. Boccard, Serge Rudaz","doi":"10.3389/frans.2023.1112390","DOIUrl":"https://doi.org/10.3389/frans.2023.1112390","url":null,"abstract":"Unlike other systems such as plants, microorganisms or fungi, human cells are not proficient in eliciting the production of defense compounds in response to external stresses and threats. Human metabolism is essentially based on a set of primary metabolites that participate in the various regulatory events of cells and tissues. The challenge is therefore to maintain homeostasis and allow the survival of the individual through the modulation of existing endogenous metabolic pathways with a relatively stable set of ubiquitous compounds. Since these complex regulatory phenomena are potentially subject to multiple influences, assessing their overall variability, as achieved by most conventional approaches, is not sufficiently informative. The experimental evaluation of several factors acting simultaneously on the metabolome is paramount. Because metabolomics involves the characterization of multivariate metabolic phenotypes, such a methodology requires specific data analysis tools to fully exploit the relevant information considering the different factors, as well as their respective impact on metabolite levels. The investigation of high-dimensional multifactorial data in metabolomics opens new challenges and requires the development of innovative experimental strategies involving structured designs of experiments to assess cause-effect associations and offer deeper insight into relevant biological information. In the future, key outputs should not only consider lists of metabolites, but also include their specific variation related to each effect that can be identified and/or quantified, thus allowing accurate biochemical and functional relationships to be highlighted.","PeriodicalId":73063,"journal":{"name":"Frontiers in analytical science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42948818","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Challenges and perspectives in MS-based omics approaches for ecotoxicology studies: An insight on Gammarids sentinel amphipods","authors":"Valentina Calabrese, A. Salvador, Y. Clément, Thomas Brunet, A. Espeyte, A. Chaumot, O. Geffard, D. Degli-Esposti, S. Ayciriex","doi":"10.3389/frans.2023.1118494","DOIUrl":"https://doi.org/10.3389/frans.2023.1118494","url":null,"abstract":"The aquatic environment is one of the most complex biosystems, as organism at all trophic levels may be exposed to a multitude of pollutants. As major goals, ecotoxicology typically investigates the impact of toxic pollutants on the ecosystems through the study of sentinel organisms. Over the past decades, Mass Spectrometry (MS)-based omics approaches have been extended to sentinel species both in laboratory and field exposure conditions. Single-omics approaches enable the discovery of biomarkers mirroring the health status of an organism. By covering a restricted set of the molecular cascade, they turn out to only partially satisfy the understanding of complex ecotoxicological effects. In contrast, a more complete understanding of the ecotoxicity pathways can be accessed through multi-omics approaches. In this perspective, we provide a state-of-the-art and a critical evaluation on further developments in MS-based single and multi-omics studies in aquatic ecotoxicology. As case example, literature regarding Gammarids freshwater amphipods, non-model sentinel organisms sensitive to pollutants and environmental changes and crucial species for downstream ecosystems, will be reviewed.","PeriodicalId":73063,"journal":{"name":"Frontiers in analytical science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44898061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recent methodological developments in data-dependent analysis and data-independent analysis workflows for exhaustive lipidome coverage","authors":"Marie Valmori, Vincent Marie, F. Fenaille, B. Colsch, D. Touboul","doi":"10.3389/frans.2023.1118742","DOIUrl":"https://doi.org/10.3389/frans.2023.1118742","url":null,"abstract":"Untargeted lipidomics applied to biological samples typically involves the coupling of separation methods to high-resolution mass spectrometry (HRMS). Getting an exhaustive coverage of the lipidome with a high confidence in structure identification is still highly challenging due to the wide concentration range of lipids in complex matrices and the presence of numerous isobaric and isomeric species. The development of innovative separation methods and HRMS(/MS) acquisition workflows helped improving the situation but issues still remain regarding confident structure characterization. To overcome these issues, thoroughly optimized MS/MS acquisition methods are needed. For this purpose, different methodologies have been developed to enable MS and MS/MS acquisition in parallel. Those methodologies, derived from the proteomics, are referred to Data Dependent Acquisition (DDA) and Data Independent Acquisition (DIA). In this context, this perspective paper presents the latest developments of DDA- and DIA-based lipidomic workflows and lists available bioinformatic tools for the analysis of resulting spectral data.","PeriodicalId":73063,"journal":{"name":"Frontiers in analytical science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45903694","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Promoting transparency in forensic science by integrating categorical and evaluative reporting through decision theory","authors":"M. Sigman, Mary R. Williams","doi":"10.3389/frans.2023.1105642","DOIUrl":"https://doi.org/10.3389/frans.2023.1105642","url":null,"abstract":"Forensic science standards often require the analyst to report in categorical terms. Categorical reporting without reference to the strength of the evidence, or the strength threshold that must be met to sustain or justify the decision, obscures the decision-making process, and allows for inconsistency and bias. Standards that promote reporting in probabilistic terms require the analyst to report the strength of the evidence without offering a conclusive interpretation of the evidence. Probabilistic reporting is often based on a likelihood ratio which depends on calibrated probabilities. While probabilistic reporting may be more objective and less open to bias than categorical reporting, the report can be difficult for a lay jury to interpret. These reporting methods may appear disparate, but the relationship between the two is easily understood and visualized by a simple decision theory construct known as the receiver operating characteristic (ROC) curve. Implementing ROC-facilitated reporting through an expanded proficiency testing regime may provide transparency in categorical reporting and potentially obviate some of the lay jury interpretation issues associated with probabilistic reporting.","PeriodicalId":73063,"journal":{"name":"Frontiers in analytical science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42627878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-cell metabolome profiling for phenotyping parasitic diseases in phytoplankton","authors":"M. Vallet, Filip Kaftan, A. Buaya, M. Thines, L. Guillou, A. Svatoš, G. Pohnert","doi":"10.3389/frans.2022.1051955","DOIUrl":"https://doi.org/10.3389/frans.2022.1051955","url":null,"abstract":"Bloom-forming phytoplankton are key players in aquatic ecosystems, fixing carbon dioxide and forming the base of the marine food web. Diverse stresses, such as nutrient depletion, temperature increase, and pathogen emergence can influence the health and dynamics of algal populations. While population responses to these stressors are well-documented in the aquatic ecosystems, little is known about the individual cellular adaptations. These are however the key to an in-depth physiological understanding of microbiome dynamics in the plankton. Finding solutions to disease control in aquaculture also depends on knowledge of infection dynamics and physiology in algae. Single-cell metabolomics can give insight into infection processes by providing a snapshot of small molecules within a biological system. We used a single-cell metabolome profiling workflow to track metabolic changes of diatoms and dinoflagellates subjected to parasite infection caused by the oomycete Lagenisma coscinodisci and the alveolate Parvilucifera spp. We accurately classified the healthy phenotype of bloom-forming phytoplankton, including the diatoms Coscinodiscus granii and Coscinodiscus radiatus, and the toxic dinoflagellate Alexandrium minutum. We discriminated the infection of the toxic dinoflagellate A. minutum with the alveolate parasitoids Parvilucifera infectans and P. rostrata down to the single-cell resolution. Strain and species-specific responses of the diatom hosts Coscinodiscus spp. Infected with the oomycete pathogen Lagenisma coscinodisci could be recognized. LC-HRMS and fragmentation pattern analysis enabled the structure elucidation of metabolic predictors of infection (guanine, xanthine, DMSP, and pheophorbide). The purine salvage pathway and DMSP lysis could be assigned as regulated processes during host invasion. The findings establish single-cell metabolome profiling with LDI-HRMS coupled with classification analysis as a reliable diagnostic tool to track metabolic changes in algae.","PeriodicalId":73063,"journal":{"name":"Frontiers in analytical science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41433264","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In-depth structural proteomics integrating mass spectrometry and polyacrylamide gel electrophoresis","authors":"Nobuaki Takemori, Ayako Takemori","doi":"10.3389/frans.2022.1107183","DOIUrl":"https://doi.org/10.3389/frans.2022.1107183","url":null,"abstract":"The establishment of a highly sensitive method for obtaining structural information on proteins and protein complexes in vivo has long been a technological challenge in structural biology. In recent years, protein structure analysis approaches using top-down mass spectrometry, native mass spectrometry, and cross-linking mass spectrometry, among others, have been developed, and these techniques have emerged as the most promising methods for obtaining comprehensive structural information on the cellular proteome. However, information obtained by MS alone is derived mainly from protein components that are abundant in vivo, with insufficient data on low abundance components. For the detection of those low abundance components, sample fractionation prior to mass spectrometry is highly effective because it can reduce the complexity of the sample. Polyacrylamide gel electrophoresis (PAGE), which is widely used in biochemical experiments, is an excellent technique for protein separation in a simple straightforward procedure and is also a promising fractionation tool for structural proteomics. The difficulty of recovering proteins in gels has been an obstacle, thus far limiting its application to structural mass spectrometry. With the breakthrough of PEPPI-MS, an exceptionally efficient passive extraction method for proteins in gels that appeared in 2020, various PAGE-based proteome fractionation workflows have been developed, resulting in the rapid integration of structural mass spectrometry and PAGE. In this paper, we describe a simple and inexpensive PAGE-based sample preparation strategy that accelerates the broad use of structural mass spectrometry in life science research, and discuss future prospects for achieving in-depth structural proteomics using PAGE.","PeriodicalId":73063,"journal":{"name":"Frontiers in analytical science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48053346","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sterilization of micronized indomethacin","authors":"Karyna Krupianskaya, B. Croonenborghs, Annick Gillet, Bernard Appeltans, A. Meyers, Aaron DeMent, G. Van den Mooter, A. Van Schepdael, E. Haghedooren","doi":"10.3389/frans.2022.1028752","DOIUrl":"https://doi.org/10.3389/frans.2022.1028752","url":null,"abstract":"Sterilization is a pivotal topic in the pharmaceutical industry, whereby the nomenclature of “sterile” refers to the absence of viable microorganisms. Since microorganisms can reproduce in the body and cause potentially fatal infections, it is critical to sterilize parenteral products to prevent this. In recent years, 70%–90% of potential drugs and 40% of marketed drugs have demonstrated a low solubility. Micronization is a widely spread approach to increase the dissolution rate. A subset of micronized products require sterilization, but published studies on the effects of sterilization on micronized products are currently lacking. The effect of sterilization on the micronized active pharmaceutical ingredient indomethacin was explored in this study. The sterilization methods in scope were one photon-based method using gamma irradiation and one gas-based method with nitrogen dioxide gas. Indomethacin was micronized using two micronization techniques, cryomilling and spray drying. Different conditions were used for cryomilling where the number of grinding balls in the ball mill and the degree of filling were varied. The solid state of all samples was evaluated after micronization, and only the effectively micronized samples were selected for sterilization with gamma rays and nitrogen dioxide. Gamma irradiation was performed with the active pharmaceutical ingredient stored at −80°C at a commonly used industry standard target dose of 25 kGy. Nitrogen dioxide sterilization took place at 21°C, a concentration of 10 mg/L, a relative humidity of 30% and using two NO2 pulses. Before and after sterilization, all samples were analyzed by high performance liquid chromatography with UV detection, whereby the assay of indomethacin was examined as well as the peak purity and the formation of impurities. In comparison to the non-micronized reference, both sterilization methods demonstrate a significant decrease of content of micronized samples and an increase of the impurity profile. The non-micronized sample showed no significant difference after sterilization. It could be observed that micronized indomethacin samples demonstrate more degradation and are subsequently more susceptible to degradation upon sterilization with gamma rays and nitrogen dioxide gas, driving towards the need for assessment of the micronization impact combined with sterilization approach.","PeriodicalId":73063,"journal":{"name":"Frontiers in analytical science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45526866","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hydrogen Deuterium Exchange and other Mass Spectrometry-based Approaches for Epitope Mapping.","authors":"Prashant N Jethva, Michael L Gross","doi":"10.3389/frans.2023.1118749","DOIUrl":"10.3389/frans.2023.1118749","url":null,"abstract":"<p><p>Antigen-antibody interactions are a fundamental subset of protein-protein interactions responsible for the \"survival of the fittest\". Determining the interacting interface of the antigen, called an epitope, and that on the antibody, called a paratope, is crucial to antibody development. Because each antigen presents multiple epitopes (unique footprints), sophisticated approaches are required to determine the target region for a given antibody. Although X-ray crystallography, Cryo-EM, and nuclear magnetic resonance can provide atomic details of an epitope, they are often laborious, poor in throughput, and insensitive. Mass spectrometry-based approaches offer rapid turnaround, intermediate structural resolution, and virtually no size limit for the antigen, making them a vital approach for epitope mapping. In this review, we describe in detail the principles of hydrogen deuterium exchange mass spectrometry in application to epitope mapping. We also show that a combination of MS-based approaches can assist or complement epitope mapping and push the limit of structural resolution to the residue level. We describe in detail the MS methods used in epitope mapping, provide our perspective about the approaches, and focus on elucidating the role that HDX-MS is playing now and in the future by organizing a discussion centered around several improvements in prototype instrument/applications used for epitope mapping. At the end, we provide a tabular summary of the current literature on HDX-MS-based epitope mapping.</p>","PeriodicalId":73063,"journal":{"name":"Frontiers in analytical science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10512744/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41124674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Toward the analysis of functional proteoforms using mass spectrometry-based stability proteomics.","authors":"Ji Kang, Meena Seshadri, Kellye A Cupp-Sutton, Si Wu","doi":"10.3389/frans.2023.1186623","DOIUrl":"10.3389/frans.2023.1186623","url":null,"abstract":"<p><p>Functional proteomics aims to elucidate biological functions, mechanisms, and pathways of proteins and proteoforms at the molecular level to examine complex cellular systems and disease states. A series of stability proteomics methods have been developed to examine protein functionality by measuring the resistance of a protein to chemical or thermal denaturation or proteolysis. These methods can be applied to measure the thermal stability of thousands of proteins in complex biological samples such as cell lysate, intact cells, tissues, and other biological fluids to measure proteome stability. Stability proteomics methods have been popularly applied to observe stability shifts upon ligand binding for drug target identification. More recently, these methods have been applied to characterize the effect of structural changes in proteins such as those caused by post-translational modifications (PTMs) and mutations, which can affect protein structures or interactions and diversify protein functions. Here, we discussed the current application of a suite of stability proteomics methods, including thermal proteome profiling (TPP), stability of proteomics from rates of oxidation (SPROX), and limited proteolysis (LiP) methods, to observe PTM-induced structural changes on protein stability. We also discuss future perspectives highlighting the integration of top-down mass spectrometry and stability proteomics methods to characterize intact proteoform stability and understand the function of variable protein modifications.</p>","PeriodicalId":73063,"journal":{"name":"Frontiers in analytical science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11281393/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45767880","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Perspective on the potential of tandem-ion mobility /mass spectrometry methods for structural proteomics applications.","authors":"Tyler C Cropley,&nbsp;Mengqi Chai,&nbsp;Fanny C Liu,&nbsp;Christian Bleiholder","doi":"10.3389/frans.2023.1106752","DOIUrl":"https://doi.org/10.3389/frans.2023.1106752","url":null,"abstract":"<p><p>Cellular processes are usually carried out collectively by the entirety of all proteins present in a biological cell, i.e. the proteome. Mass spectrometry-based methods have proven particularly successful in identifying and quantifying the constituent proteins of proteomes, including different molecular forms of a protein. Nevertheless, protein sequences alone do not reveal the function or dysfunction of the identified proteins. A straightforward way to assign function or dysfunction to proteins is characterization of their structures and dynamics. However, a method capable to characterize detailed structures of proteins and protein complexes in a large-scale, systematic manner within the context of cellular processes does not yet exist. Here, we discuss the potential of <i>tandem</i>-ion mobility / mass spectrometry (tandem-IM/MS) methods to provide such ability. We highlight the capability of these methods using two case studies on the protein systems ubiquitin and avidin using the tandem-TIMS/MS technology developed in our laboratory and discuss these results in the context of other developments in the broader field of tandem-IM/MS.</p>","PeriodicalId":73063,"journal":{"name":"Frontiers in analytical science","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10273136/pdf/nihms-1885000.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10065758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}