Leyla A Garibova, Mikhail V Gorshkov, Mark V Ivanov
{"title":"On the question of correct use of replicates in quantitative label-free proteomics.","authors":"Leyla A Garibova, Mikhail V Gorshkov, Mark V Ivanov","doi":"10.1007/s00216-025-05992-z","DOIUrl":"https://doi.org/10.1007/s00216-025-05992-z","url":null,"abstract":"<p><p>Label-free quantitation is the most popular method in proteomics for assessing changes in protein concentrations. However, practical aspects like the optimal use of technical replicates, the impact of removing low-identified protein runs, and the effect of combining information from technical replicates for subsequent differential expression analysis remain debated. This study utilized five LFQ workflows: MaxQuant + Perseus, FragPipe + MSstats, Proteome Discoverer, DirectMS1Quant, and IdentiPy + IQMMA. Previously published data sets acquired for three-species proteomes using Orbitrap FTMS consisted of spikes of Escherichia coli, yeast, and human lysates with known concentration changes that were used for benchmarking the workflows. All tested workflows gave fairly similar results in terms of the number of differentially expressed proteins (DEPs) and quantitative false discovery rate (FDR). Adding more technical replicates either increased the number of DEPs or decreased the FDR, depending on the workflow. Eliminating runs with the lowest number of protein identifications led to an increase in the number of DEPs, but at the cost of elevated FDR, thus reducing the accuracy and precision of protein fold change estimations. The Match-Between-Runs option provides additional DEPs and does not increase empirical FDR in most methods. We found that the selected set of proteomics workflows turned out to be different in answering the practical questions raised above, even for the simple artificial benchmark data set. Our results should serve as a starting point and encourage researchers to more thoroughly test their own approaches in real-world problems.</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144590152","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}
Louis V Hellequin, Vicent J Borràs, Patrick Romann, Nandita Vishwanathan, Jonathan Souquet, Thomas K Villiger
{"title":"Synthetic spectral libraries for Raman model calibration.","authors":"Louis V Hellequin, Vicent J Borràs, Patrick Romann, Nandita Vishwanathan, Jonathan Souquet, Thomas K Villiger","doi":"10.1007/s00216-025-05985-y","DOIUrl":"https://doi.org/10.1007/s00216-025-05985-y","url":null,"abstract":"<p><p>Raman spectroscopy has become increasingly popular in the process analytical technology (PAT) landscape due to its versatility and predictive capability in bioprocesses. However, model building remains a time-consuming and cost-intensive task. Building upon a fast calibration workflow based on physical pure compounds spiking in water, this work explores the novel use of in silico spiking of pure spectral fingerprints of various analytes. Through data fusion, a synthetic spectral library (SSL) is created that combines base spectra information from mammalian cell culture runs with matrix variability, as well as pure component spectra in water, aiming to greatly reduce the cost and time required for efficient model building. The findings indicate that the in silico addition of pure compounds provides spectral information comparable to physically spiked measurements. Consequently, this approach allows for the generation of an extensive number of information-rich spectra, forming a robust foundation for various regression algorithms and enhancing Raman calibration of existing spectral databases.</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144590155","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}
Tim Åström, Conny Östman, Ioannis Sadiktsis, Maria-Ximena Ruiz-Caldas, Ulrika Nilsson
{"title":"Automated thermal desorption-gas chromatography/mass spectrometry for screening of hazardous chemicals in cotton and cotton blend garments-analytical challenges.","authors":"Tim Åström, Conny Östman, Ioannis Sadiktsis, Maria-Ximena Ruiz-Caldas, Ulrika Nilsson","doi":"10.1007/s00216-025-05993-y","DOIUrl":"https://doi.org/10.1007/s00216-025-05993-y","url":null,"abstract":"<p><p>The global production of textiles involves large amounts of health-hazardous chemicals, constituting possible health risks since residues usually remain in the finished garments. In the present study, a recently published ATD-GC/MS methodology for screening synthetic textiles is further extended to cotton and cotton blend materials. Different textile materials with a high content of cotton were found to exhibit large variations in adsorption strength for a number of chemicals frequently detected in textiles. This was shown to strongly influence the thermal desorption efficiency in ATD-GC/MS. By using absolute response factors from appropriate internal standards spiked directly onto the textile samples, the effects from these differences could be minimized. In this way, accurate quantification was made possible regardless of textile composition, and quantification of native textile chemicals in garments made with the ATD-GC/MS method agreed well with an offline method based on solvent extraction and GC/MS analysis. The ATD-GC/MS method has now been shown to be applicable for quantitative screening of at least 75% of all the clothing textiles on the retail market. The simplified quantification method makes it suitable for screening large numbers of samples. For all fiber materials investigated, the method limit of detection, using only 20 mg of textile, is at least 100 times lower than the current EU regulation for quinoline and a number of toxic arylamines.</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144590150","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}
Paulo Felipe Neves Estrela, Marcio Neres de Souza Júnior, Kézia Gomes de Oliveira, Gabriela Rodrigues Mendes Duarte
{"title":"Stick-and-test: simple tape-based devices for SARS-CoV-2 isothermal molecular detection.","authors":"Paulo Felipe Neves Estrela, Marcio Neres de Souza Júnior, Kézia Gomes de Oliveira, Gabriela Rodrigues Mendes Duarte","doi":"10.1007/s00216-025-05991-0","DOIUrl":"https://doi.org/10.1007/s00216-025-05991-0","url":null,"abstract":"<p><p>Portable analytical devices have been enabling point-of-care molecular diagnostic applications. However, the laborious preparation of conventional microdevices still limits their broader use, especially in resource-limited settings in microinstrumentation. Here, we describe an alternative fabrication process that allows the production of low-cost disposable devices based on double-sided adhesive tape and polyester film (DST-Pe). The applicability of the DST-Pe-based device was demonstrated across molecular diagnostic steps from nucleic acid extraction to detection and result reading for SARS-CoV-2 detection. The device was shown to be able to isolate RNA by dynamic solid-phase extraction (dSPE) from samples of patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection with good repeatability and an efficiency of 56.81%. The reverse transcription loop-mediated isothermal amplification (RT-LAMP) of SARS-CoV-2 RNA was performed in 30 min with a sensitivity of 10 copies μL<sup>-1</sup>. The optical transparency of the DST-Pe devices allowed visual detection with the naked eye by adding the intercalating reagent SYBR Green I DNA at the endpoint. Additionally, we demonstrate the integration of amplification and detection steps, starting from complex samples without extraction, enabling a sample-in-answer-out molecular detection protocol using DST-Pe devices. The overall simplicity of the fabrication process and its biocompatibility with all steps of molecular diagnostics demonstrate its potential for use in isolated steps or even in complete molecular diagnostics for pathogen detection.</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144582760","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}
{"title":"Protein pellet sample preparation for the analysis of N-glycans of therapeutic proteins.","authors":"Ronald L Kowle, Shardrack O Asare","doi":"10.1007/s00216-025-05995-w","DOIUrl":"https://doi.org/10.1007/s00216-025-05995-w","url":null,"abstract":"<p><p>Profiling of N-glycans of therapeutic proteins is a critical component in the control of biopharmaceutical products. N-Glycosylation, a common post-translational modification has been shown to impact the structure, function, stability, pharmacokinetics, and overall therapeutic efficacy of therapeutic proteins. Regulatory agencies around the world require detailed profiling of glycosylation to meet high product quality standards. The standard sample preparation for N-glycan analysis involves the enzymatic release of the glycan from the glycoprotein, fluorescent derivatization, and the time- and resource-consuming solid-phase extraction to remove excess fluorophore and reaction reagents before chromatographic glycan analysis. In this paper, we report a rapid sample preparation workflow that simplifies glycan purification after derivatization. The method uses the \"protein pellet\" approach to purify the fluorescently labeled glycan before analysis. The accuracy of the \"protein pellet\" method was established by comparing the results to the standard solid-phase extraction method that utilizes a polyamide stationary phase. The repeatability and linearity were also demonstrated.</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144590153","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}
{"title":"Development of calcium alginate gel sphere-based SERS substrates for minimally invasive sampling and identification of indigo on the surface of simulated murals and aged imitation cultural relic samples.","authors":"Xuerong Shi, Wanru Wang, Xinyu Xie, Changtian Gong, Wenyuan Zhang, Xinyue Zhu, Xiaoyan Liu, Haixia Zhang","doi":"10.1007/s00216-025-05986-x","DOIUrl":"https://doi.org/10.1007/s00216-025-05986-x","url":null,"abstract":"<p><p>Pigments in painted cultural relics serve as critical historical evidence, offering significant research value for understanding historical contexts and cultural development processes. However, the pigments, especially organic pigments (or dyes), have progressively degraded over time, resulting in severe fading that challenges their sensitive identification. To address this issue, we developed an innovative sampling methodology combined with surface-enhanced Raman spectroscopy (SERS) analysis for identifying indigo pigment in painted cultural relics. The methodology employs calcium alginate gel beads doped with either gold nanobipyramid (Au NBPs/CAGBs) or hybrid Au-Ag nanoprisms (Ag NPrs/Au NBPs/CAGBs), enabling minimally invasive sampling of indigo through controlled interactions with the mural surface. Subsequent SERS analysis of the retrieved substrates demonstrated enhanced molecular identification capabilities compared to conventional in situ non-destructive methods. Furthermore, microscopic examination and color difference quantification (ΔE < 1.5) revealed no observable surface alterations on tested mural samples before and after sampling, which confirmed the method's minimal invasiveness. Finally, the approach was successfully applied to imitation heritage objects, including Tang Tri-color (\"Lady Spring Festival\") replica ceramics and bottle-type simulated ceramic artifacts before and after aging, achieving effective sampling and pigment identification. This study establishes a novel paradigm for sensitive pigment analysis in cultural heritage conservation, with promising implications for future relic restoration and protection strategies.</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144574601","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}
Ariana E Stratton, Hassan Moussa, Yingchan Guo, Justin M Ellenburg, Carl Atkinson, Boone M Prentice
{"title":"A mass spectrometry-based assay for mouse IgG N-glycan screening in biofluids.","authors":"Ariana E Stratton, Hassan Moussa, Yingchan Guo, Justin M Ellenburg, Carl Atkinson, Boone M Prentice","doi":"10.1007/s00216-025-05994-x","DOIUrl":"10.1007/s00216-025-05994-x","url":null,"abstract":"<p><p>N-Glycans represent an important post-translational modification of proteins that can serve as biomarkers of disease, injury, and inflammation. N-Glycosylation of the monoclonal antibody immunoglobulin G (IgG) impacts binding to receptors that initiate an immunological response. Herein, we describe the optimization of a high-throughput method for analyzing IgG glycosylation of multiple murine biofluid samples in a single analysis utilizing matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry. Similar to an enzyme-linked immunosorbent assay (ELISA), our method begins by spotting a capture antibody into a well. However, glycosylation on the capture antibody causes a significant N-glycan background signal that interferes with the signal from IgG-derived glycans in serum samples. To eliminate endogenous capture antibody IgG glycans (i.e., chemical background), the capture antibody was deglycosylated using the enzyme PNGase F, purified using affinity chromatography, and analyzed using ELISAs to confirm there was no loss of binding affinity and selectivity. The performance of the deglycosylated capture antibody was then compared to that of the traditional glycosylated capture antibody using the MALDI IgG N-glycan screening assay. Background subtraction was performed for samples analyzed with both capture antibodies to compare signal intensities before and after background subtraction, which was previously used to correct for the chemical background produced by glycosylated capture antibodies. We show that the use of background subtraction is not necessary with the use of a deglycosylated capture antibody, and that using the deglycosylated capture antibody increases imaging mass spectrometry signal intensity, giving a more sensitive, accurate, and precise analysis of N-glycans present in murine biofluid samples.</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144574600","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}
{"title":"A pseudotargeted metabolomics method for phosphatidyl amino acid analysis in chemotherapy-resistant cells and exosomes.","authors":"Meiyu Gao, Yu Wu, Huihui Yin, Qiang Wang, Yuan Tian, Zunjian Zhang, Fengguo Xu, Pei Zhang","doi":"10.1007/s00216-025-05997-8","DOIUrl":"https://doi.org/10.1007/s00216-025-05997-8","url":null,"abstract":"<p><p>Phosphatidyl amino acids (p-AAs) are metabolites characterized by the phosphorylation of the hydroxyl, amino, carboxyl, and thiol groups of amino acids. Previous research has primarily focused on the phosphorylation sites within macromolecular proteins, with a particular emphasis on typical O-p-AAs. In this study, we established a prediction library of p-AAs based on existing knowledge. To improve detection rates of p-AAs in biological samples, we employed a chemical labeling-based LC-MS/MS method, utilizing p-[3,5-(dimethylamino)-2,4,6-triazine] benzene-1-sulfonyl piperazine (Tmt-PP) and its deuterated form (d12-Tmt-PP) as paired labeling reagents. A preliminary identification was performed by matching characteristic MS fragments with available standards. Additionally, strategies such as in vitro methods were implemented for further identification. The phosphatase treatment aids in identifying phosphate-modified metabolites by dephosphorylating them, while cell extract incubation helps determine if novel phosphorylated amino acids are generated in vivo. Ultimately, we identified 11 p-AAs, 6 of which are novel metabolites reported for the first time. A pseudotargeted metabolomics method covering 11 identified p-AAs was established and applied to investigate the differences between cisplatin-resistant non-small cell lung cancer (NSCLC) cells and their parental cells, as well as their derived exosomes. This approach enhances our understanding of the role of p-AAs in various health and disease conditions and contributes to the discovery of additional novel phosphatidyl metabolites.</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144566922","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}
Yibo Zou, Yuting Li, Feng Zhang, Yan Ge, Wenjuan Wang, Ming Chen
{"title":"Rapid identification of Litopenaeus vannamei pathogenic bacteria: a combined approach using surface-enhanced Raman spectroscopy (SERS) and deep learning.","authors":"Yibo Zou, Yuting Li, Feng Zhang, Yan Ge, Wenjuan Wang, Ming Chen","doi":"10.1007/s00216-025-05974-1","DOIUrl":"https://doi.org/10.1007/s00216-025-05974-1","url":null,"abstract":"<p><p>Pathogenic bacterial infections are one of the leading causes of mortality in Litopenaeus vannamei, seriously affecting the economic efficiency of the shrimp aquaculture industry. However, traditional pathogen detection methods, such as the polymerase chain reaction (PCR), have drawbacks, including complex procedures and long processing times. Raman spectroscopy provides valuable biomolecular feature information and, when combined with deep learning, enables the detection of pathogens. However, the limited availability of spectral data hinders model performance. Therefore, we proposed a novel method that integrated surface-enhanced Raman spectroscopy (SERS), least-squares generative adversarial network (LSGAN), and Transformer to achieve high-precision identification of four common shrimp pathogens. This method employed LSGAN to generate synthetic spectra resembling real spectra for data augmentation and utilized the Transformer for high-precision identification of pathogens. First, the original dataset of 160 spectra was expanded to 2160 using LSGAN. It was shown that the LSGAN-enhanced data could effectively improve the classification performance of the Transformer, and the accuracy of the Transformer in the classification task of shrimp pathogens was 99.69%, which was 2.82% higher than that before the data enhancement. Additionally, Transformer achieved a classification accuracy of 91.04% on a publicly available microbial Raman spectral dataset, demonstrating strong generalization capability. Our research introduces novel insights into the classification of limited Raman spectra and presents a rapid, accurate method for detecting pathogens in shrimp farming, aiding early disease prevention and control.</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144558648","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}
Robert Zimmerleiter, Jovana Kovacevic, Gerhard Leitner, David Wimberger, Daniel Lager, Sebastian Friedl, Eduard Pleschutznig, Tilman Barz, Markus Brandstetter
{"title":"Curing reaction kinetics of paper-based phenolic resin laminates-from laboratory measurements to inline quality control.","authors":"Robert Zimmerleiter, Jovana Kovacevic, Gerhard Leitner, David Wimberger, Daniel Lager, Sebastian Friedl, Eduard Pleschutznig, Tilman Barz, Markus Brandstetter","doi":"10.1007/s00216-025-05983-0","DOIUrl":"https://doi.org/10.1007/s00216-025-05983-0","url":null,"abstract":"<p><p>We describe a comprehensive analysis of the drying and curing kinetics of resol phenol-formaldehyde (PF) resin utilizing multiple different thermophysical and optical measurement techniques and combinations thereof to gain a comprehensive understanding of the physicochemical processes that take place during large-scale production of paper-based PF laminates. This included thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), Fourier-transform infrared evolved gas analysis (FTIR-EGA), and near-infrared (NIR) spectroscopy. In particular, the tailored integration of TGA with simultaneous near-infrared (NIR) spectroscopy in reflection geometry facilitated the evaluation of NIR spectroscopy's suitability for monitoring the ongoing process. This led to the implementation of an NIR-based real-time measurement setup at an industrial production site for a feasibility assessment. NIR spectroscopy in combination with partial least squares (PLS) regression modeling showed highly promising results highlighting the advantages of NIR spectroscopy as a tool for real-time inline quality control for large-scale production of PF resin laminates.</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144551574","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}