Fast Photochemical Oxidation of Proteins (FPOP) is a promising technique for studying protein structure and dynamics. The quality of insight provided by FPOP depends on the reliability of the determination of the modification site. This study investigates the performance of two search engines, Mascot and PEAKS, for the data processing of FPOP analyses. Comparison of Mascot and PEAKS of the hemoglobin--haptoglobin Bruker timsTOF data set (PXD021621) revealed greater consistency in the Mascot identification of modified peptides, with around 26% of the IDs being mutual for all three replicates, compared to approximately 22% for PEAKS. The intersection between Mascot and PEAKS results revealed a limited number (31%) of shared modified peptides. Principal Component Analysis (PCA) using the peptide-spectrum match (PSM) score, site probability, and peptide intensity was applied to evaluate the results, and the analyses revealed distinct clusters of modified peptides. Mascot showed the ability to assess confident site determination, even with lower PSM scores. However, high PSM scores from PEAKS did not guarantee a reliable determination of the modification site. Fragmentation coverage of the modification position played a crucial role in Mascot assignments, while the AScore localizations from PEAKS often become ambiguous because the software employs MS/MS merging.
Candida haemulonii complex (Candida haemulonii [I], Candida duobushaemulonii [II], and Candida haemulonii var. vulnera [III]) has become relevant in recent times, not so much because of a high incidence in human clinical sample cultures but because of its remarkable antifungal resistance. The objective of this study was to evaluate several methods for the identification of this uncommon species of Candida. Ten isolates of C. haemulonii were identified by biochemical and proteomic methods, and their antifungal susceptibility testing was performed by both commercial and reference methods. MALDI-TOF MS (Vitek MS and Vitek MS PRIME) and Vitek2 correctly identified these genera but API method did not. There was a good correlation between the commercial methods and the reference methods for the AST. In conclusion Vitek MS, Vitek MS PRIME, and Vitek2 systems, but not API32C, are reliable for identification of C. haemulonii complex. Furthermore, MALDI-TOF MS systems could identify to the subspecies level. Commercial methods for antifungal susceptibility testing are valid for the study of this species and confirm amphotericin B and to azole resistance.
Microflow liquid chromatography interfaced with mass spectrometry (μLC-MS/MS) is increasingly applied for high-throughput profiling of biological samples and has been proven to have an acceptable trade-off between sensitivity and reproducibility. However, lipidomics applications are scarce. We optimized a μLC-MS/MS system utilizing a 1 mm inner diameter × 100 mm column coupled to a triple quadrupole mass spectrometer to establish a sensitive, high-throughput, and robust single-shot lipidomics workflow. Compared to conventional lipidomics methods, we achieve a ∼4-fold increase in response, facilitating quantification of 351 lipid species from a single iPSC-derived cerebral organoid during a 15 min LC-MS analysis. Consecutively, we injected 303 samples over ∼75 h to prove the robustness and reproducibility of the microflow separation. As a proof of concept, μLC-MS/MS analysis of Alzheimer's disease patient-derived iPSC cerebral organoid reveals differential lipid metabolism depending on APOE phenotype (E3/3 vs E4/4). Microflow separation proves to be an environmentally friendly and cost-effective method as it reduces the consumption of harmful solvents. Also, the data demonstrate robust, in-depth, high-throughput performance to enable routine clinical or biomedical applications.
- MeSH
- apolipoproteiny E MeSH
- chromatografie kapalinová metody MeSH
- fenotyp MeSH
- kapalinová chromatografie-hmotnostní spektrometrie * MeSH
- lidé MeSH
- lipidomika MeSH
- reprodukovatelnost výsledků MeSH
- tandemová hmotnostní spektrometrie * metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Thermophilic bacteria of four genera in contrast to the commonly used production strains such as Bacillus subtilis, produce homologs other than menaquinone (MK) with seven isoprene units. The number of isoprene units and the configuration of double bonds are essential factors for their biological activity. The goal was to obtain a strain of bacteria that produces a wide range of MK homologs and only all-trans geometrical isomers, which was the strain G. kaustophilus. Using off-line two-dimensional LC-tandem MS in columns with the RP18 phase and the COSMOSIL cholester phase (separation according to the geometric configuration of double bonds) it was shown that thermophilic bacteria grown at different temperatures produce only all-trans isomers of menaquinones from MK-5 (menaquinone with five isoprenyl units) to MK-15 (fifteen isoprenyl units). Therefore, G. kaustophilus appears to be a biotechnologically important strain produces only trans isomers and additionally homologs from 5 to 15 isoprene units.
- MeSH
- Bacteria * MeSH
- butadieny * MeSH
- hmotnostní spektrometrie MeSH
- vitamin K 2 chemie MeSH
- Publikační typ
- časopisecké články MeSH
Among different substance classes, New Psychoactive Substances (NPS) comprise chiral amphetamines for stimulant and empathic effects. There is little knowledge in terms of clinical studies about possibly different effects of the two enantiomers of novel amphetamine derivatives. For this reason, there is a big demand for enantioseparation method development of this new substance class. Regarding gas chromatography, cyclodextrins proved to be effective for enantioseparation of NPS. In our attempt, an Astec® ChiraldexTM G-PN column containing 2,6-di-O-pentyl-3-propionyl-γ-cyclodextrin and a LipodexTM D column containing heptakis-(2,6-di-O-pentyl-O-acetyl)-β-cyclodextrin as chiral selector served as stationary phases in a Shimadzu GCMS-QP2010 SE system. Because of the special coating, maximum temperature is limited to 200 °C isothermal or 220 °C in programmed mode. To ensure detection, trifluoroacetic anhydride (TFAA) was used to increase sample volatility.1 As a result, 35 amphetamines were tested as their TFAA-derivatives. A screening method with a temperature gradient from 140 °C to 200 °C at a heating ramp of 1 °C per minute and final time of 5 min, showed baseline separation for seven and partial separations for 16 trifluoro acetylated amphetamines using the ChiraldexTM G-PN column. Six baseline and nine partial separations were observed with the LipodexTM D column, respectively.
Identifikace etiologického agens v krvi je jedno z nejdůležitějších, ale zároveň nejdelších vyšetření v diagnostice bakteriálních infekcí. Klasický postup hemokultivace za použití automatizovaných přístrojů, identifikace z 24hodinové bakteriální kultury a stanovení kvantitativní citlivosti k antibiotikům trvá zhruba 3–5 dní. V posledních letech byly implementovány do praxe nové metody umožňující identifikaci bakteriálního původce a stanovení citlivosti/rezistence k antibiotikům, včetně detekce genů rezistence pomocí amplifikačních technik, přímo z pozitivních hemokultivačních lahviček. Tyto metody umožňují výrazně zkrátit čas od odběru krve do hlášení výsledku a současně aplikaci cílené antibiotické terapie. Předložený přehledový článek má za cíl seznámit klinické lékaře s novinkami v oblasti bakteriologického vyšetření krve používanými v rutinní mikrobiologické praxi.
Identifying the etiological agent in blood is one of the most crucial yet time-consuming investigations in diagnosing bacterial infections. The conventional approach of blood culture utilizing automated systems, followed by identification from a 24-hour bacterial culture and determination of quantitative antibiotic susceptibility, typically takes about 3-5 days. However, in recent years, new methods have been implemented in practice, enabling the identification of bacterial pathogens and the determination of sensitivity/resistance to antibiotics, including the detection of resistance genes through amplification techniques directly from positive blood culture bottles. These methods significantly reduce the turnaround time from blood collection to result reporting, while also facilitating the application of targeted antibiotic therapy. The presented review article aims to acquaint clinical physicians with the latest advancements in the field of blood bacteriological testing.
BACKGROUND: Atherosclerosis is a major cause of ischemic stroke, and early detection of advanced atherosclerosis in the carotid artery is important for reducing morbidity and mortality. What is even more important is not only detection of atherosclerosis but early determination whether the patients are at high risk of an event with adverse effects as the size of the plaque does not necessarily reflect its potential to trigger such events. AIM: We studied whether plasma lipidomics profile can be used as a diagnostic tool for stratification of stable or unstable plaques without the need of removing the carotid plaque. METHODS: This study used liquid chromatography high-resolution tandem mass spectrometry lipidomics to characterize lipid profiles in patients' plasma and found that patients with significant and complicated (vulnerable) atherosclerotic plaque had distinct lipid profiles compared to those with insignificant plaques. RESULTS: The lipid classes that were most predictive of vulnerable plaque were lysophosphoethanolamines, fatty acyl esters of hydroxy fatty acids, free fatty acids, plasmalogens, and triacylglycerols. Most of these compounds were found decreased in plasma of patients with unstable plaques which enabled sufficient performance of a statistical model used for patient stratification. CONCLUSIONS: Plasma lipidomes measured by liquid chromatography-mass spectrometry show differences in patients with stable and unstable carotid plaques, therefore these compounds could potentially be used as biomarkers for unstable plaque in future clinical diagnosis.
- MeSH
- aterosklerotický plát * krev MeSH
- biologické markery * krev MeSH
- chromatografie kapalinová MeSH
- lidé středního věku MeSH
- lidé MeSH
- lipidomika * MeSH
- lipidy * krev MeSH
- nemoci arterie carotis * krev diagnóza MeSH
- prediktivní hodnota testů MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- spontánní ruptura MeSH
- studie případů a kontrol MeSH
- tandemová hmotnostní spektrometrie * MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři nad 80 let MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- srovnávací studie MeSH
Arthrospira (Limnospira) maxima (A. maxima) and Chlorella vulgaris (Ch. vulgaris) are among the approved microalgae and cyanobacteria (MaC) in the food industry that are known to be safe for consumption. However, both organisms are controversial regarding their vitamin B12 content, due to the possible occurrence of pseudo-cobalamin. Concurrently, their nutrition profiles remain understudied. The main purpose of the present study was to identify their nutrition profiles, focusing mainly on vitamin B12, amino acids, and micronutrients under iron-induced hormesis (10 mg/L Fe in treated samples). Our findings indicate a higher B12 content in A. maxima compared to Ch. vulgaris (both control and treated samples). Using liquid chromatography with tandem mass spectrometry (LC-MS/MS), the cyanocobalamin content was determined as 0.42 ± 0.09 μg/g dried weight (DW) in the A. maxima control and 0.55 ± 0.02 μg/g DW in treated A. maxima, resulting in an insignificant difference. In addition, the iron-enriched medium increased the amount of iron in both tested biomasses (p < 0.01). However, a more pronounced (approximately 100×) boost was observed in Ch. vulgaris, indicating a better absorption capacity (control Ch. vulgaris 0.16 ± 0.01 mg/g Fe, treated Ch. vulgaris 15.40 ± 0.34 mg/g Fe). Additionally, Ch. vulgaris also showed a higher micronutrient content. Using both tested microalgae, meeting the sufficient recommended daily mineral allowance for an adult is possible. By combining biomass from A. maxima and Ch. vulgaris in a ratio of 6:1, we can fulfill the recommended daily allowance of vitamin B12 and iron by consuming 6 tablets/6 g. Importantly, iron hormesis stimulated amino acid composition in both organisms. The profile of amino acids may suggest these biomasses as promising potential nutrition sources.
- MeSH
- aminokyseliny * metabolismus analýza MeSH
- Chlorella vulgaris * chemie metabolismus růst a vývoj MeSH
- mikrořasy chemie metabolismus růst a vývoj MeSH
- mikroživiny * analýza metabolismus MeSH
- nutriční hodnota MeSH
- Spirulina * chemie metabolismus MeSH
- tandemová hmotnostní spektrometrie MeSH
- vitamin B 12 * metabolismus analýza MeSH
- železo metabolismus analýza MeSH
- Publikační typ
- časopisecké články MeSH
Neuroactive steroids are a group of steroid molecules that are involved in the regulation of functions of the nervous system. The nervous system is not only the site of their action, but their biosynthesis can also occur there. Neuroactive steroid levels depend not only on the physiological state of an individual (person's sex, age, diurnal variation, etc.), but they are also affected by various pathological processes in the nervous system (some neurological and psychiatric diseases or injuries), and new knowledge can be gained by monitoring these processes. The aim of our research was to develop and validate a comprehensive method for the simultaneous determination of selected steroids with neuroactive effects in human serum. The developed method enables high throughput and a sensitive quantitative analysis of nine neuroactive steroid substances (pregnenolone, progesterone, 5α-dihydroprogesterone, allopregnanolone, testosterone, 5α-dihydrotestosterone, androstenedione, dehydroepiandrosterone, and epiandrosterone) in 150 μL of human serum by ultrahigh-performance liquid chromatography with tandem mass spectrometry. The correlation coefficients above 0.999 indicated that the developed analytical procedure was linear in the range of 0.90 nmol/L to 28.46 μmol/L in human serum. The accuracy and precision of the method for all analytes ranged from 83 to 118% and from 0.9 to 14.1%, respectively. This described method could contribute to a deeper understanding of the pathophysiology of various diseases. Similarly, it can also be helpful in the search for new biomarkers and diagnostic options or therapeutic approaches.
- MeSH
- lidé MeSH
- neurosteroidy krev MeSH
- reprodukovatelnost výsledků MeSH
- steroidy krev analýza MeSH
- tandemová hmotnostní spektrometrie * metody MeSH
- vysokoúčinná kapalinová chromatografie metody MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Surface and treated wastewater are contaminated with highly complex mixtures of micropollutants, which may cause numerous adverse effects, often mediated by endocrine disruption. However, there is limited knowledge regarding some important modes of action, such as interference with thyroid hormone (TH) regulation, and the compounds driving these effects. This study describes an effective approach for the identification of compounds with the potential to bind to transthyretin (TTR; protein distributing TH to target tissues), based on their specific separation in a pull-down assay followed by non-target analysis (NTA). The method was optimized with known TTR ligands and applied to complex water samples. The specific separation of TTR ligands provided a substantial reduction of chromatographic features from the original samples. The applied NTA workflow resulted in the identification of 34 structures. Twelve compounds with available standards were quantified in the original extracts and their TH-displacement potency was confirmed. Eleven compounds were discovered as TTR binders for the first time and linear alkylbenzene sulfonates (LAS) were highlighted as contaminants of concern. Pull-down assay combined with NTA proved to be a well-functioning approach for the identification of unknown bioactive compounds in complex mixtures with great application potential across various biological targets and environmental compartments.
