Analytical and Bioanalytical Chemistry最新文献

筛选
英文 中文
Quantitative analysis of Δ8- and Δ9-tetrahydrocannabinol metabolites and isomers: a rapid assay in urine by LC-MS/MS.
IF 3.8 2区 化学
Analytical and Bioanalytical Chemistry Pub Date : 2025-01-23 DOI: 10.1007/s00216-025-05738-x
Marco Ballotari, Michael T Truver, Nayana A Sojin, Lauren A Agliano, Rhea Parimoo, Jennifer L Hoyer, Amie J Goodin, Deepthi S Varma, Chris W Chronister, Kay Roussos-Ross, Bruce A Goldberger
{"title":"Quantitative analysis of Δ<sup>8</sup>- and Δ<sup>9</sup>-tetrahydrocannabinol metabolites and isomers: a rapid assay in urine by LC-MS/MS.","authors":"Marco Ballotari, Michael T Truver, Nayana A Sojin, Lauren A Agliano, Rhea Parimoo, Jennifer L Hoyer, Amie J Goodin, Deepthi S Varma, Chris W Chronister, Kay Roussos-Ross, Bruce A Goldberger","doi":"10.1007/s00216-025-05738-x","DOIUrl":"https://doi.org/10.1007/s00216-025-05738-x","url":null,"abstract":"<p><p>An increasing number of cannabis-related products have become available and entered the market, particularly those containing cannabidiol (CBD) and Δ<sup>8</sup>-tetrahydrocannabinol (Δ<sup>8</sup>-THC). Analytical methods for cannabinoids in urine have been described extensively in the literature. However, methods providing good resolution for distinguishing interferences from THC positional isomers are needed. The aim of this project was to develop and validate a liquid chromatography with tandem mass spectrometry (LC-MS/MS) method to quantitate a broad panel of cannabinoids in authentic urine specimens. The method was optimized to quantitate Δ<sup>8</sup>-THC and Δ<sup>9</sup>-THC, 11-OH-Δ<sup>8</sup>-THC and 11-OH-Δ<sup>9</sup>-THC, Δ<sup>8</sup>-THC-COOH and Δ<sup>9</sup>-THC-COOH, CBD, 7-COOH-CBD, CBG, and CBN, and validated with the guidance of the American Academy of Forensic Sciences Standards Board (ASB) Standard 036. The validated assay was then used to evaluate urine samples collected over various time points from female patients (N = 69) enrolled in a study assessing prevalence of marijuana/CBD use during pregnancy from November 2022 to May 2024. Δ<sup>8</sup>- and Δ<sup>9</sup>- isomers were chromatographically resolved and successfully separated. For all analytes, the lower limit of quantitation (LLOQ) was determined to be 10 ng/mL, and the upper limit of quantitation (ULOQ) was 1000 ng/mL. In the authentic samples, the most frequently detected analyte was Δ<sup>9</sup>-THC-COOH, with a median concentration of 278 ng/mL (n = 38). Δ<sup>9</sup>-THC and 11-OH-Δ<sup>9</sup>-THC were detected with a median concentration of 42.4 ng/mL (n = 5) and 65.7 ng/mL (n = 34), respectively. Δ<sup>8</sup>-THC-COOH was detected in n = 3 specimens, with a median concentration of 25.5 ng/mL. The study provided a rapid assay for the analysis of cannabinoids in urine.</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143021701","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Comprehensive quantification of C4 to C26 free fatty acids using a supercritical fluid chromatography-mass spectrometry method in pharmaceutical-grade egg yolk powders intended for total parenteral nutrition use.
IF 3.8 2区 化学
Analytical and Bioanalytical Chemistry Pub Date : 2025-01-23 DOI: 10.1007/s00216-025-05732-3
Mark Dennis Chico Retrato, Anh Vu Nguyen, S J Kumari A Ubhayasekera, Jonas Bergquist
{"title":"Comprehensive quantification of C4 to C26 free fatty acids using a supercritical fluid chromatography-mass spectrometry method in pharmaceutical-grade egg yolk powders intended for total parenteral nutrition use.","authors":"Mark Dennis Chico Retrato, Anh Vu Nguyen, S J Kumari A Ubhayasekera, Jonas Bergquist","doi":"10.1007/s00216-025-05732-3","DOIUrl":"https://doi.org/10.1007/s00216-025-05732-3","url":null,"abstract":"<p><p>Free fatty acids (FFAs) are important energy sources and significant for energy transport in the body. They also play a crucial role in cellular oxidative stress responses, following cell membrane depolarization, making accurate quantification of FFAs essential. This study presents a novel supercritical fluid chromatography-mass spectrometry (SFC-MS) method using selected ion recording in negative electrospray ionization mode, enabling rapid quantification of 31 FFAs within 6 min without derivatization. FFAs are identified and quantified using an HSS C18 SB column and a secondary mobile phase consisting of methanol with formic acid by detecting their [M - H]<sup>-</sup> ions. Calibration curves showed strong linearity (R<sup>2</sup> ≥ 0.9910), spanning 1000-12,000 ng/mL for short-chain FFAs and 50-1200 ng/mL for medium- and long-chain FFAs. The method achieves detection limits as low as 1 ng/µL for short-chain FFAs and 0.05 pg/µL for other FFAs per on-column injection. The method demonstrated high accuracy and precision, with bias and coefficients of variation maintained below 15% across five quality control levels. Freeze-thaw and autosampler stability studies confirmed the behavior of matrix-matched standards under optimal storage conditions. The validated method was applied to the analysis of pharmaceutical-grade egg yolk powders, using 13 deuterated FFAs as internal standards (IS) in comparison with heptadecanoic acid (C17:0). Significant variations in FFA quantification using two different IS approaches underscore the importance of selecting an appropriate IS. In summary, this study introduces a reliable and validated SFC-MS method for analyzing FFAs ranging from C4 to C26, requiring minimal sample preparation.</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143027642","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Certified reference materials for GMO analysis-more than 25 years of GMO CRM production at EC JRC.
IF 3.8 2区 化学
Analytical and Bioanalytical Chemistry Pub Date : 2025-01-23 DOI: 10.1007/s00216-024-05713-y
Stefanie Trapmann, Thomas P J Linsinger, Robert Koeber
{"title":"Certified reference materials for GMO analysis-more than 25 years of GMO CRM production at EC JRC.","authors":"Stefanie Trapmann, Thomas P J Linsinger, Robert Koeber","doi":"10.1007/s00216-024-05713-y","DOIUrl":"https://doi.org/10.1007/s00216-024-05713-y","url":null,"abstract":"<p><p>Certified reference materials (CRMs) play a crucial role in ensuring the quality of analytical measurements. Particularly, the EU labelling legislation on genetically modified organisms (GMOs) in food and feed products explicitly requires CRMs for its implementation. The CRMs are used to calibrate and control the quantitative real-time polymerase chain reaction (qPCR) method and support official control laboratories, such as National Reference Laboratories (NRLs), in maintaining their ISO/IEC 17025 accreditation. The Joint Research Centre of the European Commission (EC JRC) is specialized in the production of reference materials and has been producing GMO CRMs since 1998. Together with a validated event-specific qPCR method, these GMO CRMs form the EU reference system for the quantification of EU-authorized GMO events in food and feed products and ensure a common GMO labelling threshold. This article gives a retrospective view on the more than 25 years of GMO CRM production at JRC. It describes requirements for GMO CRMs in view of an EU market authorization under (EC) No. 1829/2003. The evolution and major improvements of the production of GMO CRMs at JRC are summarized as well as the current understanding of the EU's GMO reference system for GMO quantification and its impact on commutability. It provides insights into GMO CRM sales and their worldwide distribution. This information may be useful for policymakers and researchers in understanding the current EU GMO measurement landscape and to anticipate possible future demands related to GMO events based on new genomic techniques (NGTs).</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143021699","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Carbon nanotubes stabilized in chitosan sponge (CNT-CS) as a new alternative clean-up sorbent for pesticide multiresidue determination in eggplants using QuEChERS and UHPLC-MS/MS 壳聚糖海绵稳定碳纳米管(CNT-CS)作为一种新的清洁吸附剂用于QuEChERS和UHPLC-MS/MS测定茄子中农药多残留。
IF 3.8 2区 化学
Analytical and Bioanalytical Chemistry Pub Date : 2025-01-22 DOI: 10.1007/s00216-025-05736-z
Cleusa F. Zanchin, Luana Floriano, Bruna S. de Farias, Luiz A. A. Pinto, Tito R. S. Cadaval Jr., Osmar D. Prestes, Renato Zanella
{"title":"Carbon nanotubes stabilized in chitosan sponge (CNT-CS) as a new alternative clean-up sorbent for pesticide multiresidue determination in eggplants using QuEChERS and UHPLC-MS/MS","authors":"Cleusa F. Zanchin,&nbsp;Luana Floriano,&nbsp;Bruna S. de Farias,&nbsp;Luiz A. A. Pinto,&nbsp;Tito R. S. Cadaval Jr.,&nbsp;Osmar D. Prestes,&nbsp;Renato Zanella","doi":"10.1007/s00216-025-05736-z","DOIUrl":"10.1007/s00216-025-05736-z","url":null,"abstract":"<div><p>The continuous development and application of pesticides in agriculture require robust multiresidue detection methods to guarantee food safety. This study introduces a novel method for multiresidue determination of pesticides in eggplants using the QuEChERS procedure, incorporating a clean-up step using carbon nanotubes stabilized in chitosan sponge (CNT-CS) and ultra-high performance liquid chromatography with tandem mass spectrometry (UHPLC-MS/MS) for analysis. Upon identifying the optimal extraction conditions, various sorbents were assessed for their efficacy in the dispersive solid-phase extraction (d-SPE). Among these, the biosorbent CNT-CS emerged as the most efficient and cost-effective material, showing the best recovery results from spiked blank samples. The validation demonstrated that the method was adequate for analyzing 111 pesticides in eggplant samples with practical method quantification limits from 5 to 25 µg kg<sup>−1</sup>. When applied to commercial eggplant samples, 27 pesticides were detected, demonstrating the importance of the proposed method. It is noteworthy that the conducted work represents the first report on the use of the biosorbent CNT-CS in the clean-up step of the QuEChERS method. The results obtained in the validation and application steps demonstrate that the proposed method is an excellent alternative for monitoring programs.</p><h3>Graphical Abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":"417 7","pages":"1407 - 1419"},"PeriodicalIF":3.8,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
An effective cell-penetrating peptide-based loading method to extracellular vesicles and enhancement in cellular delivery of drugs. 一种有效的细胞穿透肽基细胞外囊泡装载方法和增强药物的细胞递送。
IF 3.8 2区 化学
Analytical and Bioanalytical Chemistry Pub Date : 2025-01-21 DOI: 10.1007/s00216-025-05742-1
Jin Zhang, Ning Su, Wei Liu, Mengran Li, Haoyang Zheng, Bing Li, Xue Jin, Mingxia Gao, Xiangmin Zhang
{"title":"An effective cell-penetrating peptide-based loading method to extracellular vesicles and enhancement in cellular delivery of drugs.","authors":"Jin Zhang, Ning Su, Wei Liu, Mengran Li, Haoyang Zheng, Bing Li, Xue Jin, Mingxia Gao, Xiangmin Zhang","doi":"10.1007/s00216-025-05742-1","DOIUrl":"https://doi.org/10.1007/s00216-025-05742-1","url":null,"abstract":"<p><p>Extracellular vesicles (EVs) have been demonstrated to own the advantages in evading phagocytosis, crossing biological barriers, and possessing excellent biocompatibility and intrinsic stability. Based on these characteristics, EVs have been used as effective therapeutic carriers for drug delivery, but the low drug loading capacity greatly limits further applications. Herein, we developed a drug loading method based on cell-penetrating peptide (CPP) to enhance the encapsulation of therapeutic reagents in EVs, and EVs-based drug delivery system achieved higher killing efficacy to tumor cells. Urinary EVs and chemotherapy reagent doxorubicin (DOX) were used as model. It is easy to conjugate CPP with DOX (CPP-DOX) through the linker N-succinimidyl 3-maleimidopropionate (SMP). CPP-DOX was incubated with EVs under a mild condition, promoting the encapsulation of DOX into EV cavities. CPP-DOX-EVs showed strong anticancer ability since EVs delivery facilitated the uptake by cancer cells. EVs loading of CPP-DOX exhibited higher drug loading efficiency at 37.18%, presenting about 2.5 times increase in efficiency over EVs loading of DOX through passive incubation. Easy operation and controllable condition further reinforce the advantages compared with other loading methods. CPP-based drug loading method provides an effective strategy for EVs-based drug delivery system.</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998151","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Application of predictive modeling tools for the identification of Ocimum spp. herbal products. 预测建模工具在中药产品鉴别中的应用。
IF 3.8 2区 化学
Analytical and Bioanalytical Chemistry Pub Date : 2025-01-20 DOI: 10.1007/s00216-025-05735-0
Evelyn J Abraham, Sarah J Chamberlain, Wilmer H Perera, R Teal Jordan, Joshua J Kellogg
{"title":"Application of predictive modeling tools for the identification of Ocimum spp. herbal products.","authors":"Evelyn J Abraham, Sarah J Chamberlain, Wilmer H Perera, R Teal Jordan, Joshua J Kellogg","doi":"10.1007/s00216-025-05735-0","DOIUrl":"https://doi.org/10.1007/s00216-025-05735-0","url":null,"abstract":"<p><p>Species identification of botanical products is a crucial aspect of research and regulatory compliance; however, botanical classification can be difficult, especially for morphologically similar species with overlapping genetic and metabolomic markers, like those in the genus Ocimum. Untargeted LC-MS metabolomics coupled with multivariate predictive modeling provides a potential avenue for improving herbal identity investigations, but the current dearth of reference materials for many botanicals limits the applicability of these approaches. This study investigated the potential of using greenhouse-grown authentic Ocimum to build predictive models for classifying commercially available Ocimum products. We found that three species, O. tenuiflorum, O. gratissimum, and O. basilicum, were chemically distinct based on their untargeted UPLC-MS/MS profiles when grown in controlled settings; combined with an orthogonal high-performance thin-layer chromatography (HPTLC) approach, O. tenuiflorum materials revealed two distinct chemotypes which could confound analysis. Three predictive models (partial least squares, LASSO regression, and random forest) were employed to extrapolate these findings to commercially available products; however, the controlled materials were significantly different from external samples, and all three chemometric models were unreliable in classifying external materials. LASSO was the most successful when classifying new greenhouse samples. Overall, this study highlights how growing and processing conditions can influence the complexity of botanical metabolome profiles; further studies are needed to characterize the factors driving herbal products' phytochemistry in conjunction with chemometric predictive modeling.</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998152","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Aptamer-based fluorescence biosensor for rapid detection of chloramphenicol based on pyrene excimer switch. 基于芘准分子开关的配体荧光生物传感器快速检测氯霉素。
IF 3.8 2区 化学
Analytical and Bioanalytical Chemistry Pub Date : 2025-01-20 DOI: 10.1007/s00216-025-05733-2
Jizhao Zhang, Qiang Zhao
{"title":"Aptamer-based fluorescence biosensor for rapid detection of chloramphenicol based on pyrene excimer switch.","authors":"Jizhao Zhang, Qiang Zhao","doi":"10.1007/s00216-025-05733-2","DOIUrl":"https://doi.org/10.1007/s00216-025-05733-2","url":null,"abstract":"<p><p>Chloramphenicol (CAP) is widely used in treating bacteria infection in animals and humans. However, the accumulation of CAP in food and environment caused serious health risk to human. Consequently, sensitive and selective detection of CAP is of great importance in environmental monitoring and food safety. Among various analytical methods, aptamer-based biosensors exhibit great potentials for CAP detection. Here, we developed an aptamer-based biosensor for rapid fluorescence detection of CAP based on pyrene excimer switch by using a newly selected short DNA aptamer with high affinity. The aptamer was labeled with pyrene molecules at both ends. The binding of CAP to the aptamer probe caused two pyrene molecules close to each other and the formation of a pyrene excimer, which induced the increase of the fluorescence signal from the pyrene excimer. CAP detection was achieved by measuring the fluorescence signal changes of the aptamer probes with dual pyrene labels. Under optimized conditions, the developed aptamer biosensor showed a detection limit of 24.4 nmol/L for CAP. The aptamer-based fluorescence sensor could quantify CAP in diluted tap water and lake water, exhibiting potentials for the application in real sample sensing of CAP.</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Full sequencing of 100mer sgRNA via tandem mass spectrometry by targeted RNase H digestion with customized probes. 通过定制探针靶向RNase H酶切,通过串联质谱法对100mer sgRNA进行全测序。
IF 3.8 2区 化学
Analytical and Bioanalytical Chemistry Pub Date : 2025-01-20 DOI: 10.1007/s00216-025-05737-y
Christopher Gawlig, Rebecca Hirschberger, Güngör Hanci, Saskia Schott, Shima Marandi, Ida Ronja Hesse, Michael Rühl
{"title":"Full sequencing of 100mer sgRNA via tandem mass spectrometry by targeted RNase H digestion with customized probes.","authors":"Christopher Gawlig, Rebecca Hirschberger, Güngör Hanci, Saskia Schott, Shima Marandi, Ida Ronja Hesse, Michael Rühl","doi":"10.1007/s00216-025-05737-y","DOIUrl":"https://doi.org/10.1007/s00216-025-05737-y","url":null,"abstract":"<p><p>The use of single-guide RNA (sgRNA) for gene editing using the CRISPR Cas9 system has become a powerful technique in various fields, especially with the growing interest in such molecules as therapeutic options in the last years. An important parameter for the use of these molecules is the verification of the correct sgRNA oligonucleotide sequence. Apart from next-generation sequencing protocols, mass spectrometry (MS) has been proven as a powerful technique for this purpose. The protocol and investigations presented in this work show an optimal digestion and 100% sequence coverage of sgRNA, while top-down approaches or other ribonuclease (RNase) digestion strategies obtain a sequence coverage of up to 80-90% utilizing multiple RNases. The results in this publication were obtained by utilizing DNA-RNA hybrid GAPmer-like probes and RNase H, an enzyme which specifically hydrolyzes RNA in DNA-RNA double strands. We assessed the optimal length of the DNA segment of these hybrid probes to maximize the specificity of the RNase H digestion and to achieve complete sequence confirmation by tandem MS analysis of the resulting digestion products. Furthermore, we showed that the approach is applicable for the identification of common synthesis-related impurities, like truncations and elongations. Despite the fact that the accessibility of this approach for highly modified molecules is limited to nucleotides which are not 2'-O-methylated, the optimized sequence coverage makes it a viable method.</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998158","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Robust discrimination between closely related species of salmon based on DNA fragments. 基于DNA片段的密切相关的鲑鱼物种之间的强大区分。
IF 3.8 2区 化学
Analytical and Bioanalytical Chemistry Pub Date : 2025-01-18 DOI: 10.1007/s00216-024-05724-9
Debra Ellisor, Mary Gregg, Angela Folz, Antonio Possolo
{"title":"Robust discrimination between closely related species of salmon based on DNA fragments.","authors":"Debra Ellisor, Mary Gregg, Angela Folz, Antonio Possolo","doi":"10.1007/s00216-024-05724-9","DOIUrl":"10.1007/s00216-024-05724-9","url":null,"abstract":"<p><p>Closely related species of Salmonidae, including Pacific and Atlantic salmon, can be distinguished from one another based on nucleotide sequences from the cytochrome c oxidase sub-unit 1 mitochondrial gene (COI), using ensembles of fragments aligned to genetic barcodes that serve as digital proxies for the relevant species. This is accomplished by exploiting both the nucleotide sequences and their quality scores recorded in a FASTQ file obtained via Next Generation (NextGen) Sequencing of mitochondrial DNA extracted from Coho salmon caught with hook and line in the Gulf of Alaska. The alignment is done using MUSCLE (Muscle 5.2) [1], applied to multiple versions of each fragment perturbed according to the nucleobase identification error probabilities underlying the quality scores. The Damerau-Levenshtein distance was used to determine the genetic barcode of the candidate species that is closest to each aligned, perturbed fragment. The \"votes\" that the sampled fragments cast for the different candidate species are then pooled and converted into identification probabilities, using weights determined by the entropy of the fragment-specific identification probability distributions. This novel approach to quantify the uncertainty associated with measurements made using NextGen Sequencing can be applied to discriminate closely related species, hence to value-assignment for reference materials supporting determinations of the authenticity of seafood, for example, NIST Reference Materials 8256 and 8257 (Coho salmon) [2].</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998159","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Tools and databases for studying data in the glycosciences 用于研究糖科学数据的工具和数据库。
IF 3.8 2区 化学
Analytical and Bioanalytical Chemistry Pub Date : 2025-01-16 DOI: 10.1007/s00216-025-05730-5
Kiyoko F. Aoki-Kinoshita, Joseph Zaia
{"title":"Tools and databases for studying data in the glycosciences","authors":"Kiyoko F. Aoki-Kinoshita,&nbsp;Joseph Zaia","doi":"10.1007/s00216-025-05730-5","DOIUrl":"10.1007/s00216-025-05730-5","url":null,"abstract":"","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":"417 5","pages":"861 - 863"},"PeriodicalIF":3.8,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998161","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信