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Percolator is a widely used software tool that increases yield in shotgun proteomics experiments and assigns reliable statistical confidence measures, such as q values and posterior error probabilities, to peptides and peptide-spectrum matches (PSMs) from such experiments. Percolator’s processing speed has been sufficient for typical data sets consisting of hundreds of thousands of PSMs. With our new scalable approach, we can now also analyze millions of PSMs in a matter of minutes on a commodity computer. Furthermore, with the increasing awareness for the need for reliable statistics on the protein level, we compared several easy-to-understand protein inference methods and implemented the best-performing method—grouping proteins by their corresponding sets of theoretical peptides and then considering only the best-scoring peptide for each protein—in the Percolator package. We used Percolator 3.0 to analyze the data from a recent study of the draft human proteome containing 25 million spectra (PM:24870542). The source code and Ubuntu, Windows, MacOS, and Fedora binary packages are available from http://percolator.ms/ under an Apache 2.0 license. Graphical Abstract ᅟ

In recent years, the consumption of polyphenols has been increasing, largely due to its beneficial effects on health. They are present in a wide variety of foods, but their extraction and characterization are complicated since they are mostly in complex matrices. For this reason, the use of selective, sensitive, and versatile analytical techniques such as liquid chromatography coupled to tandem mass spectrometry (LC–MS/MS) is necessary. In this review, the most relevant studies of the last years regarding the analysis of polyphenols in different matrices by comprehensive LC–MS/MS are discussed. Relevant steps such as extraction, sample purification, and chromatographic analysis methods are emphasized. In particular, the following methodological aspects are discussed: (a) the proper selection of the extraction technique, (b) the extraction and elution solvents, (c) the purification step, (d) the selection of both stationary and mobile phases for the chromatographic separation of compounds, and (e) the different conditions for mass spectrometry. Overall, this review presents the data from the most recent studies, in a comprehensive way, thus providing and simplifying the information of the great variety of works that exist in the literature on this wide topic.

The physiological functions of lysophosphatidylethanolamine (lysoPE) have not been fully elucidated. In this study, the effects of lysoPE on lipogenesis and lipolysis were investigated in a cultured human liver-derived cell line. The intracellular lipid profile was investigated in detail using liquid chromatography–tandem mass spectrometry (LC-MS/MS) to better understand the underlying mechanism. The expression of genes related to lipid metabolism and catabolism was analyzed using real-time PCR. LysoPE supplementation induced cellular lipid droplet formation and altered triacylglycerol (TAG) profiles. Furthermore, lysoPE downregulated expression of the TAG hydrolyzation regulation factor ATGL, and reduced the expression of fatty acid biosynthesis-related genes SREBP1 and SCD1. LC-MS/MS-based lipidomic profiling revealed that the addition of lysoPE 18:2 increased the PE species containing linoleic acyl, as well as the CE 18:2 species, likely due to the incorporation of linoleic acyl from lysoPE 18:2. Collectively, these findings suggest that lysoPE 18:2 is involved in lipid droplet formation by suppressing lipolysis and fatty acid biosynthesis. Thus, lysoPE might play a pathological role in the induction of fatty liver disease.

Cortisol is the main glucocorticoid released during stress responses in most fish and has been employed to investigate different stressors, including organic pollutants. This review discusses shifts in cortisol concentrations and examines different matrix sampling methods (invasive vs. minimally or non-invasive) and the main analytical cortisol determination techniques (immunoassays and liquid chromatography-tandem mass spectrometry). Assessments on organic pollutant exposure in fish and associated adverse effects are also discussed. Studies in this regard may aid in identifying organic pollutant toxicological modes of action, mechanistic response, toxicokinetics, and toxicodynamics, as well as pollution sources and associated health risks in fish, ultimately aiding in the development of effective management strategies to mitigate the impacts of organic pollutants on fish populations and their associated ecosystems.

Mycotoxins are the most widely studied biological toxins, which contaminate foods at very low concentrations. This review describes the emerging extraction techniques and the current and alternatives analytical techniques and methods that have been used to successfully detect and identify important mycotoxins. Some of them have proven to be particularly effective in not only the detection of mycotoxins, but also in detecting mycotoxin-producing fungi. Chromatographic techniques such as high-performance liquid chromatography coupled with various detectors like fluorescence, diode array, UV, liquid chromatography coupled with mass spectrometry, and liquid chromatography-tandem mass spectrometry, have been powerful tools for analyzing and detecting major mycotoxins. Recent progress of the development of rapid immunoaffinity-based detection techniques such as immunoassays and biosensors, as well as emerging technologies like proteomic and genomic methods, molecular techniques, electronic nose, aggregation-induced emission dye, quantitative NMR and hyperspectral imaging for the detection of mycotoxins in foods, have also been presented.

This study investigated the occurrence of 5 unregulated mycotoxins in a total of 250 traditional dry-cured meat products sampled in 2020 and 2021 in five Croatian regions (eastern, northern, central, western, and southern). Aflatoxin B1 (AFB1), ochratoxin A (OTA), sterigmatocystin (STC), citrinin (CIT), and cyclopiazonic acid (CPA) concentrations were related to the geographical region of the product’s origin and to local weather. The results revealed the contamination of 27% of samples, namely, STC in 4% of samples in concentrations of up to 3.93 µg/kg, OTA in 10% of samples in concentrations of up to 4.81 µg/kg, and CPA in 13% of samples in concentrations of up to 335.5 µg/kg. No AFB1 or CIT contamination was seen. Although no statistically significant differences in concentrations of individual mycotoxins across the production regions were found, differences in mycotoxin occurrence were revealed. The eastern and western regions, with moderate climate, delivered the largest number of contaminated samples, while the southern region, often compared with subtropics, delivered the smallest, so that the determined mycotoxins were probably mainly produced by the Penicillium rather than the Aspergillus species. Due to the interaction of various factors that may affect mycotoxin biosynthesis during production, the detected concentrations cannot be related solely to the weather.

Phenolic compounds present in coffee beans could generate flavor and bring benefits to health. This study aimed to evaluate the impacts of commercial roasting levels (light, medium, and dark) on phenolic content and antioxidant potential of Arabica coffee beans (Coffea arabica) comprehensively via antioxidant assays. The phenolic compounds in roasted samples were characterized via liquid chromatography–electrospray ionization quadrupole time‐of‐flight mass spectrometry (LC‐ESI‐QTOF‐MS/MS). Furthermore, the coffee volatile compounds were identified and semi‐quantified by headspace/gas chromatography–mass spectrometry (HS‐SPME‐GC‐MS). Generally, for phenolic and antioxidant potential estimation, light roasted samples exhibited the highest TPC (free: 23.97 ± 0.60 mg GAE/g; bound: 19.32 ± 1.29 mg GAE/g), DPPH, and FRAP. The medium roasted beans performed the second high in all assays but the highest ABTS+ radicals scavenging capacity (free: 102.37 ± 8.10 mg TE/g; bound: 69.51 ± 4.20 mg TE/g). Totally, 23 phenolic compounds were tentatively characterized through LC‐ESI‐QTOF‐MS/MS, which is mainly adopted by 15 phenolic acid and 5 other polyphenols. The majority of phenolic compounds were detected in the medium roasted samples, followed by the light. Regarding GC‐MS, a total of 20 volatile compounds were identified and semi‐quantified which exhibited the highest in the dark followed by the medium. Overall, this study confirmed that phenolic compounds in coffee beans would be reduced with intensive roasting, whereas their antioxidant capacity could be maintained or improved. Commercial medium roasted coffee beans exhibit relatively better nutritional value and organoleptic properties. Our results could narrow down previous conflicts and be practical evidence for coffee manufacturing in food industries. Therefore, this research aimed to assess the impact of commercial roasting degrees (light, medium, and dark) on the content and the composition of phenolic and volatile compounds of coffee beans as well as their antioxidant potential. Total phenolic (TPC), flavonoids (TFC), and condensed tannins (TCT) content, reducing powder (RPA), ferric reducing antioxidant potential (FRAP), and ferrous ion chelating activity (FICA), 2,2′‐diphenyl‐1‐picrylhydrazyl (DPPH), 2,2′‐azinobis‐(3‐ethylbenzothiazoline‐6‐sulfonic acid) (ABTS), and hydroxyl radical scavenging activity (·OH‐RSA) were applied to estimate the antioxidant potential of phenolic compounds with the combination of ultraviolet‐visible spectroscopy. Liquid chromatography–electrospray ionization quadrupole time‐of‐flight mass spectrometry (LC‐ESI‐QTOF‐MS/MS) was used for the characterization and identification of phenolic compounds. Furthermore, headspace/gas chromatography–mass spectrometry (HS‐SPME‐GC‐MS) was applied for the identification and quantification of volatile compounds in the roasted coffee beans.

Background: Upon ingestion, nanoparticles can interact with the intestinal epithelial barrier potentially resulting in systemic uptake of nanoparticles. Nanoparticle properties have been described to influence the protein corona formation and subsequent cellular adhesion, uptake and transport. Here, we aimed to study the effects of nanoparticle size and surface chemistry on the protein corona formation and subsequent cellular adhesion, uptake and transport. Caco-2 intestinal cells, were exposed to negatively charged polystyrene nanoparticles (PSNPs) (50 and 200 nm), functionalized with sulfone or carboxyl groups, at nine nominal concentrations (15-250 μg/ml) for 10 up to 120 min. The protein coronas were analysed by LC-MS/MS. Results: Subtle differences in the protein composition of the two PSNPs with different surface chemistry were noted. High-content imaging analysis demonstrated that sulfone PSNPs were associated with the cells to a significantly higher extent than the other PSNPs. The apparent cellular adhesion and uptake of 200 nm PSNPs was not significantly increased compared to 50 nm PSNPs with the same surface charge and chemistry. Surface chemistry outweighs the impact of size on the observed PSNP cellular associations. Also transport of the sulfone PSNPs through the monolayer of cells was significantly higher than that of carboxyl PSNPs. Conclusions: The results suggest that the composition of the protein corona and the PSNP surface chemistry influences cellular adhesion, uptake and monolayer transport, which might be predictive of the intestinal transport potency of NPs.

Yanfei Lu,1,2 Fang Cai1,2 1Center for Rehabilitation Medicine, Department of Anesthesiology, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital, Hangzhou Medical College), Hangzhou, Zhejiang, People’s Republic of China; 2Research Institute of Anesthesiology and Perioperative Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of ChinaCorrespondence: Fang Cai, Email gumpy@126.com

Polyethylene glycolylation (PEGylation) technology is a long-acting delivery platform used to increase the half-life of protein therapeutics. Quantitation of PEGylated anti-Factor D Fab (PEG-aFD) poses bioanalytical challenges. An ELISA was developed to determine total Fab concentration in cynomolgus monkey serum following intravitreal administration of PEG-aFD. However, assay characterization showed a low recovery of about 25% for free unconjugated Fab whereas recovery for PEG-conjugated Fab was within 80–120%. To overcome this challenge, an immunoaffinity liquid chromatography tandem mass spectrometry (IA LC–MS/MS) assay was developed, achieving recovery within 80–120% for both free and conjugated Fab. Immunoaffinity LC–MS/MS is more suitable than ELISA to accurately quantify the total protein concentration of PEG-aFD in cynomolgus monkey serum.