Analytical and Bioanalytical Chemistry最新文献_第2页

Comparative analysis of glycoproteomic software using a tailored glycan database.

IF 3.8 2区化学

Analytical and Bioanalytical Chemistry Pub Date : 2025-04-01 Epub Date: 2025-03-18 DOI: 10.1007/s00216-025-05780-9

Reuben A Hogan, Lauren E Pepi, Nicholas M Riley, Robert J Chalkley

{"title":"Comparative analysis of glycoproteomic software using a tailored glycan database.","authors":"Reuben A Hogan, Lauren E Pepi, Nicholas M Riley, Robert J Chalkley","doi":"10.1007/s00216-025-05780-9","DOIUrl":"10.1007/s00216-025-05780-9","url":null,"abstract":"Glycoproteomics is a rapidly developing field, and data analysis has been stimulated by several technological innovations. As a result, there are many software tools from which to choose; and each comes with unique features that can be difficult to compare. This work presents a head-to-head comparison of five modern analytical software: Byonic, Protein Prospector, MSFraggerGlyco, pGlyco3, and GlycoDecipher. To enable a meaningful comparison, parameter variables were minimized. One potential confounding variable is the glycan database that informs glycoproteomic searches. We performed glycomic profiling of the samples and used the output to construct matched glycan databases for each software. Up to 17,000 glycopeptide spectra were identified across three replicates of wild-type SH-SY5Y cells. There was overlap among all software for glycoproteins identified, locations of glycosites, and glycans; but there was no clear winner. Incorporation of several comparative criteria was critically important for learning the most information in this study and should be used more broadly when assessing software. A single criterion, such as number of glycopeptide spectra found, is not sufficient. We present evidence that suggests Byonic reports many spurious results at the glycoprotein and glycosite level. Overall, our results indicate that glycoproteomic searches should involve more than one software, excluding the current version of Byonic, to generate confidence by consensus. It may be useful to consider software with peptide-first approaches and with glycan-first approaches.","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":"1985-2001"},"PeriodicalIF":3.8,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143646737","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

Differentiating between normal and inflammatory blood serum samples using spectrochemical analytical techniques and chemometrics.

IF 3.8 2区化学

Analytical and Bioanalytical Chemistry Pub Date : 2025-04-01 Epub Date: 2025-03-06 DOI: 10.1007/s00216-025-05802-6

Rania M Abdelazeem, Zienab Abdel-Salam, Mohamed Abdel-Harith

{"title":"Differentiating between normal and inflammatory blood serum samples using spectrochemical analytical techniques and chemometrics.","authors":"Rania M Abdelazeem, Zienab Abdel-Salam, Mohamed Abdel-Harith","doi":"10.1007/s00216-025-05802-6","DOIUrl":"10.1007/s00216-025-05802-6","url":null,"abstract":"Inflammation detection in blood serum samples is commonly performed using clinical analyzers, which are expensive and complex and require specific labels or markers. Spectrochemical analytical techniques, such as laser-induced breakdown spectroscopy (LIBS) and laser-induced fluorescence (LIF), have emerged as alternative methods for qualitative and non-destructive analysis in various fields. This study explores applying LIBS and LIF techniques for label-free discrimination between normal and inflammatory blood serum samples. In the LIBS analysis, the serum samples are deposited on ashless filter paper and exposed to a high-power Nd:YAG laser source to induce plasma emission. The emitted light is dispersed in a spectrometer and an ICCD camera that captures the spectral lines. The LIF technique utilizes a diode-pumped solid-state laser source to excite the blood serum sample placed in a quartz cuvette. The resulting emission spectra are collected and analyzed using a spectrometer equipped with a CCD detector. The obtained spectroscopic data from both techniques is subjected to principal component analysis (PCA) and graph theory for classification and clustering. The PCA classified the two classes with a data variance of 85.4% and 92.8% based on the first two principal components (PCs) for LIBS and LIF spectra. The graph theory clustered the two classes with an accuracy of 76% and 100% based on LIBS and LIF spectra. The statistical methods effectively discriminate between normal and inflammatory serum samples, providing satisfactory results. The proposed spectrochemical methods offer several advantages over traditional clinical analyzers. They are cost-effective and rapid, making them suitable for the fast and reliable identification of serum samples in laboratories. The non-destructive nature of these techniques eliminates the need for specific labels or markers, further streamlining the analysis process.","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":"2133-2142"},"PeriodicalIF":3.8,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143565569","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

Alkaline persulfate oxidation as an intermediate step for the development of a wet chemical oxidation interface for compound-specific δ¹⁵N analysis by LC-IRMS.

IF 3.8 2区化学

Analytical and Bioanalytical Chemistry Pub Date : 2025-04-01 Epub Date: 2025-02-22 DOI: 10.1007/s00216-025-05795-2

Daniel Köster, Tobias Hesse, Felix Niemann, Maik A Jochmann, Torsten C Schmidt

{"title":"Alkaline persulfate oxidation as an intermediate step for the development of a wet chemical oxidation interface for compound-specific δ15N analysis by LC-IRMS.","authors":"Daniel Köster, Tobias Hesse, Felix Niemann, Maik A Jochmann, Torsten C Schmidt","doi":"10.1007/s00216-025-05795-2","DOIUrl":"10.1007/s00216-025-05795-2","url":null,"abstract":"For the measurement of compound-specific isotope ratios by liquid chromatography isotope ratio mass spectrometry (LC-IRMS), complete mineralization of organic compounds to a single species of measurement gas is required so that isotopic fractionation can be minimized and corrected by identical treatment with standards. The established use of peroxydisulfate in an acidic environment has its limitations, especially when it comes to the complete oxidation of nitrogen-containing compounds with aromatic ring systems. Under acidic oxidation conditions, ammonium and nitrate were identified as the main nitrogen containing mineralization products of the oxidation of different model compounds. In contrast to the oxidation in an acidic environment, alkaline peroxydisulfate oxidation leads to nitrate as a final mineralization product. The concept of alkaline oxidation was transferred from large-scale batch experiments to a commercially available oxidation reactor used in LC-IRMS systems. The obtained nitrate recoveries indicate that alkaline oxidation could be a promising step towards the measurement of compound-specific nitrogen isotope ratios by LC-IMRS. In our work, we show that alkaline peroxydisulfate oxidation allows faster and more complete mineralization of nitrogen-containing compounds. For several model compounds, 63 to 100% of the initially present nitrogen was converted to nitrate within a reaction time of 43 s.","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":"2085-2096"},"PeriodicalIF":3.8,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476072","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

Single compound data supplementation to enhance transferability of fermentation specific Raman spectroscopy models.

IF 3.8 2区化学

Analytical and Bioanalytical Chemistry Pub Date : 2025-04-01 Epub Date: 2025-02-06 DOI: 10.1007/s00216-025-05768-5

Maarten Klaverdijk, Marcel Ottens, Marieke E Klijn

{"title":"Single compound data supplementation to enhance transferability of fermentation specific Raman spectroscopy models.","authors":"Maarten Klaverdijk, Marcel Ottens, Marieke E Klijn","doi":"10.1007/s00216-025-05768-5","DOIUrl":"10.1007/s00216-025-05768-5","url":null,"abstract":"Raman spectroscopy is a valuable analytical tool for real-time analyte quantification in fermentation processes. Quantification is performed with chemometric models that translate Raman spectra into concentration values, which are typically calibrated with process data from multiple comparable fermentations. However, process-specific models underperform for minor process variation(s) or different operation modes due to the integration of cross-correlations, resulting in low target analyte specificity. Thus, model transferability is poor and labor-intensive (re-)calibration of models is required for related processes. In this work, partial least-squares models for glucose, ethanol, and biomass were calibrated with Saccharomyces cerevisiae batch fermentation data and subsequently transferred to a fed-batch operation. To enhance model transferability without additional process runs, single compound data supplementation was performed. The supplemented models increased overall target analyte specificity and demonstrated sufficient prediction accuracy for the fed-batch process (root-mean-square errors of prediction (RMSEP) of 3.06 mM, 8.65 mM, and 0.99 g/L for glucose, ethanol, and biomass), while maintaining high prediction accuracy for the batch process (RMSEP of 1.71 mM, 4.20 mM, and 0.17 g/L for glucose, ethanol, and biomass). This work showcases that process data in combination with single compound spectra is a fast and efficient strategy to apply Raman spectroscopy for real-time process monitoring across related processes.","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":"1873-1884"},"PeriodicalIF":3.8,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11914363/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143254046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Species-specific optimization of oxylipin ionization in LC-MS: a design of experiments approach to improve sensitivity.

IF 3.8 2区化学

Analytical and Bioanalytical Chemistry Pub Date : 2025-04-01 Epub Date: 2025-02-01 DOI: 10.1007/s00216-025-05759-6

Louis Schmidt, Ulrike Garscha

{"title":"Species-specific optimization of oxylipin ionization in LC-MS: a design of experiments approach to improve sensitivity.","authors":"Louis Schmidt, Ulrike Garscha","doi":"10.1007/s00216-025-05759-6","DOIUrl":"10.1007/s00216-025-05759-6","url":null,"abstract":"Oxylipins are diverse bioactive signaling molecules, which occur in very low concentrations in complex matrices, posing challenges in achieving consistent and sensitive analysis. UHPLC-MS/MS is the preferred technique to separate and quantify these molecules, often optimized using a time-consuming trial-and-error approach. In this study, we applied the design of experiments (DoE) approach to systematically investigate the ionization properties of multiple oxylipin species. Fractional factorial and central composite designs were employed to detect relevant instrument parameters and optimize signal intensity in ESI-MS/MS analysis. Response surface modeling revealed distinct ionization and fragmentation behaviors between polar and apolar oxylipins, driven by their responses to interface temperature and collision-induced dissociation (CID) gas pressure. Particularly, prostaglandins and lipoxins benefit from higher CID gas pressure and lower temperatures compared to the lipophilic HODEs and HETEs to achieve optimal intensity in multiple reaction monitoring analysis. While global source parameters were optimized, analyte-specific entrance/exit potentials and collision energies required individual adjustments. The final method was applied to analyze seven oxylipin classes including leukotrienes, prostaglandins, lipoxins, resolvins, HETEs, HODES, and HoTrEs. Although improvements in lower limits of quantification were modest (< 1 pg on-column), signal-to-noise ratios increased two-fold for lipoxins and resolvins and three- to four-fold for leukotrienes and HETEs, enhancing detection at trace levels. This DoE-guided strategy provides a powerful tool to improve UHPLC-MS/MS analysis of oxylipins across various instrument vendors, guiding the way towards inter-laboratory comparability.","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":"1807-1818"},"PeriodicalIF":3.8,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11913994/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143073376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Quantitation of antibiotics in fresh fermentation medium by hydrophilic interaction chromatography mass spectrometry.

IF 3.8 2区化学

Analytical and Bioanalytical Chemistry Pub Date : 2025-04-01 Epub Date: 2025-02-21 DOI: 10.1007/s00216-025-05775-6

Nadia Marcon, Mathias Rüdt, Joachim Klein, Saša M Miladinović

引用次数: 0

Cost-effective, user-friendly detection and preconcentration of thrombin on a sustainable paper-based electrochemical platform.

IF 3.8 2区化学

Analytical and Bioanalytical Chemistry Pub Date : 2025-04-01 Epub Date: 2025-02-01 DOI: 10.1007/s00216-025-05764-9

Ada Raucci, Giuseppina Sorrentino, Sima Singh, Nicola Borbone, Giorgia Oliviero, Gennaro Piccialli, Monica Terracciano, Stefano Cinti

{"title":"Cost-effective, user-friendly detection and preconcentration of thrombin on a sustainable paper-based electrochemical platform.","authors":"Ada Raucci, Giuseppina Sorrentino, Sima Singh, Nicola Borbone, Giorgia Oliviero, Gennaro Piccialli, Monica Terracciano, Stefano Cinti","doi":"10.1007/s00216-025-05764-9","DOIUrl":"10.1007/s00216-025-05764-9","url":null,"abstract":"Thrombin overexpression in serum serves as a critical biomarker and is implicated in several diseases associated with significant morbidity and mortality. Existing techniques for thrombin detection are time-consuming and require sophisticated equipment and extensive sample preparation procedures, which further delay the detection and increase the cost of the procedure. Early and accessible diagnosis at the point of care, especially in limited-resource countries, represents the first step of clinical interventions. To overcome these limitations, we have proposed an innovative, sustainable paper-based electrochemical detection platform for thrombin. In this work, a sustainable paper-based aptasensor was rationally designed, characterized, evaluated against conventional gold standard plastic-based substrates, and applied to human serum, yielding a detection limit of ~ 60 pM. The present method provides an efficient and user-friendly way for the detection of thrombin and potentially leading to better management and treatment outcomes for patients.","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":"1863-1872"},"PeriodicalIF":3.8,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11914299/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143073231","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Oxygen enhanced plasma discharge and its application as carrier gas for high-field asymmetric ion mobility spectroscopy.

IF 3.8 2区化学

Analytical and Bioanalytical Chemistry Pub Date : 2025-04-01 Epub Date: 2025-03-11 DOI: 10.1007/s00216-025-05799-y

Hua Li, Yuqiao Zhang, Xiaoxia Du, Wenxiang Xiao

引用次数: 0

Temporal resolved multi-proteomic analysis enabled the systematic characterization of N-glycosylation pattern changes during Jurkat T cell activation.

IF 3.8 2区化学

Analytical and Bioanalytical Chemistry Pub Date : 2025-04-01 Epub Date: 2025-02-25 DOI: 10.1007/s00216-025-05805-3

Mingming Dong, Xiaoyan Liu, Changrui Zhao, Zheng Fang, Zhongyu Wang, Xin Guo, Yan Wang, Yanan Li, Mingliang Ye, Lingyun Jia

{"title":"Temporal resolved multi-proteomic analysis enabled the systematic characterization of N-glycosylation pattern changes during Jurkat T cell activation.","authors":"Mingming Dong, Xiaoyan Liu, Changrui Zhao, Zheng Fang, Zhongyu Wang, Xin Guo, Yan Wang, Yanan Li, Mingliang Ye, Lingyun Jia","doi":"10.1007/s00216-025-05805-3","DOIUrl":"10.1007/s00216-025-05805-3","url":null,"abstract":"Protein glycosylation plays essential roles in regulating innate and adaptive immune response. Previous studies only focused on individual protein-glycan interactions or specific glycoform changes during T cell activation, yet the systematic characterization of protein glycosylation alterations remains insufficiently elucidated. To address these limitations, we conducted temporally resolved quantitative analysis of glycoforms, site-specific glycans, glycoproteins, and glycosylation enzymes in activated Jurkat T cells, and successfully portrayed the dynamic landscape of protein glycosylation during Jurkat T cell activation. We found the heterogeneity and number of significantly upregulated glycopeptides increased along with activation. For most glycopeptides, their alteration patterns did not correlate with the abundance of their glycoprotein substrates. However, functional molecules including CD69, CD28, and PTPRC demonstrated co-upregulation at both the protein and glycosylation levels. Correlation analysis between glycopeptides and glycotransferases indicated that sialylated or fucosylated peptides were well correlated with enzymes involved in glycan branching and capping. Comparative analysis of global peptides, glycopeptides, and phosphopeptides revealed their distinctive changing patterns along Jurkat T cell activation, and only glycosylation demonstrated a steady increase trend with a large proportion of upregulated glycopeptides. Collectively, this integrated multi-proteomics characterization of activated Jurkat T cells provided insights for the development of novel therapeutic strategy targeting glycosylation.","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":"2169-2183"},"PeriodicalIF":3.8,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143490096","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

Pyrolysis-GC/MS differentiates polyesters and detects additives for improved monitoring of textile labeling accuracy and plastic pollution.

IF 3.8 2区化学

Analytical and Bioanalytical Chemistry Pub Date : 2025-04-01 DOI: 10.1007/s00216-025-05851-x

Josh Forakis, Jennifer Lynch

{"title":"Pyrolysis-GC/MS differentiates polyesters and detects additives for improved monitoring of textile labeling accuracy and plastic pollution.","authors":"Josh Forakis, Jennifer Lynch","doi":"10.1007/s00216-025-05851-x","DOIUrl":"https://doi.org/10.1007/s00216-025-05851-x","url":null,"abstract":"Polyesters comprise the greatest proportion of textile fibers and are found in various everyday goods; hence, polyester fibers are a significant source of microplastic pollution and textile waste. The specific chemical composition of commercial polyester fibers is often proprietary and mostly assumed to be poly(ethylene terephthalate) (PET). Polyester is a class of polymers that include poly(butylene terephthalate) (PBT), poly(cyclohexylenedimethylene terephthalate) (PCT), and poly(ethylene naphthalate) (PEN), as well as biodegradable polymers. Our study aims to clarify whether household polyester products are primarily PET, are labeled accurately, or contain phthalate additives by applying double-shot pyrolysis-gas chromatography/mass spectroscopy (Py-GC/MS). We analyzed four scientific-grade polyester reference standards, 52 manufacturer-grade polyester fibers or pellets, and 229 samples from 193 consumer polyester products. From the pyrograms, samples were predominantly identified as PET (87.4%, 95% CI [93.5-81.3%]), but five samples were identified as a different polyester, nine as non-polyester polymers, and 23 as a blend of PET with another polymer. From the thermal desorption chromatograms, diethyl phthalate was the most frequently detected phthalate, found in 23.3% (95% CI [17.3-29.3%]) of the consumer products, including children's toys. Double-shot py-GC/MS advantageously results in these empirical data that (1) counter the assumption that products labeled polyester are always PET, (2) emphasize the importance of creating spectral libraries with well-characterized materials for accurate polymer identification of unknown plastic particles, and (3) demonstrate that phthalates are common additives in household products.","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750468","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