An Overview of Different Vitamin D Compounds in the Setting of Adiposity.

A large body of research shows an association between higher body weight and low vitamin D status, as assessed using serum 25-hydroxyvitamin D concentrations. Vitamin D can be metabolised in adipose tissue and has been reported to influence gene expression and modulate inflammation and adipose tissue metabolism in vitro. However, the exact metabolism of vitamin D in adipose tissue is currently unknown. White adipose tissue expresses the vitamin D receptor and hydroxylase enzymes, substantially involved in vitamin D metabolism and efficacy. The distribution and concentrations of the generated vitamin D compounds in adipose tissue, however, are largely unknown. Closing this knowledge gap could help to understand whether the different vitamin D compounds have specific health effects in the setting of adiposity. This review summarises the current evidence for a role of vitamin D in adipose tissue and discusses options to accurately measure vitamin D compounds in adipose tissue using liquid chromatography tandem mass spectrometry (LC/MS-MS).

Characterizing lignins from various sources and treatment processes after optimized sample preparation techniques and analysis via ESI-HRMS and custom mass defect software tools.

Sample preparation of complex, natural mixtures such as lignin prior to mass spectrometry analysis, however minimal, is a critical step in ensuring accurate and interference-free results. Modern shotgun-MS techniques, where samples are directly injected into a high-resolution mass spectrometer (HRMS) with no prior separation, usually still require basic sample pretreatment such as filtration and appropriate solvents for full dissolution and compatibility with atmospheric pressure ionization interfaces. In this study, sample preparation protocols have been established for a unique sample set consisting of a wide variety of degraded lignin samples from numerous sources and treatment processes. The samples were analyzed via electrospray (ESI)-HRMS in negative and positive ionization modes. The resulting information-rich HRMS datasets were then transformed into the mass defect space with custom R scripts as well as the open-source Constellation software as an effective way to visualize changes between the samples due to the sample preparation and ionization conditions as well as a starting point for comprehensive characterization of these varied sample sets. Optimized conditions for the four investigated lignins are proposed for ESI-HRMS analysis for the first time, giving an excellent starting point for future studies seeking to better characterize and understand these complex mixtures.

2-fluoro-1-methylpyridinium p-toluene sulfonate: a new LC-MS/MS derivatization reagent for vitamin D metabolites.

Vitamin D analysis by MS faces several analytical challenges, including inefficient ionization, nonspecific fragmentation, interferences from epimers, isomers, and isobars, as well as very low concentration levels. In this study, we used 2-fluoro-1-methylpyridinium (FMP) p-toluene sulfonate for derivatization of vitamin D3 metabolites to increase detection sensitivity and allow for full chromatographic separation of vitamin D isomers and epimers. UHPLC-MS/MS was used for measurement of five vitamin D3 metabolites in human serum. Compared with Amplifex and 4-phenyl-1,2,4-triazolin-3,5-dion, the FMP p-toluene sulfonate reaction required less time to be performed. The method was optimized and validated to ensure accuracy, precision, and reliability. In-house and commercial quality control samples were used to assure the quality of the results for 25-hydroxyvitamin D3. The method showed very good linearity and intraday and interday accuracy and precision; coefficients of determination (r2) ranged between 0.9977 and 0.9992, relative recovery from 95 to 111%, and coefficient of variation from 0.9 to 11.3. Stability tests showed that the extracted derivatized serum samples were stable for 24 h after storage at -20°C; 24,25-dihydroxyvitamin D3 and 1,25-dihydroxyvitamin D3-FMP derivatives were stable for 1 week at -80°C. The method was applied to samples of healthy individuals for quantitative determination of vitamin D3, the two epimers of 25-hydroxyvitamin D3 and 24,25-dihydroxyvitamin D3.

Comparing derivatization reagents for quantitative LC-MS/MS analysis of a variety of vitamin D metabolites.

The present study systematically compares the sensitivity and selectivity of the analysis of multiple vitamin D metabolites after chemical derivatization using different reagents for liquid chromatography-tandem mass spectrometry (LC-MS/MS). Generally, chemical derivatization is applied to vitamin D metabolites to increase the ionization efficiency, which is particularly important for very low abundant metabolites. Derivatization can also improve the selectivity of the LC separation. A wide variety of derivatization reagents has been reported in recent years, but information on their relative performance and applicability to different vitamin D metabolites is, unfortunately, not available in the literature. To fill this gap, we investigated vitamin D3, 3ß-25-hydroxyvitamin D3 (3ß-25(OH)D3), 3α-25-hydroxyvitamin D3 (3α-25(OH)D3), 1,25-dihydroxyvitamin D3 (1,25(OH)2D3), and 24,25-dihydroxyvitamin D3 (24,25(OH)2D3) and compared response factors and selectivity after derivatizing with several important reagents, including four dienophile reagents (4-phenyl-1,2,4-triazoline-3,5-dione (PTAD), 4-[2-(6,7-dimethoxy-4-methyl-3-oxo-3,4-dihydroquinoxalinyl)ethyl]-1,2,4-triazoline-3,5-dione (DMEQ-TAD), Amplifex, 2-nitrosopyridine (PyrNO)) as well as two reagents targeting hydroxyl groups: isonicotinoyl chloride (INC) and 2-fluoro-1-methylpyridinium-p-toluenesulfonate (FMP-TS). In addition, a combination of dienophiles and hydroxyl group reagents was examined. For LC separations, reversed-phase C-18 and mixed-mode pentafluorophenyl HPLC columns using different compositions of the mobile phase were compared. With respect to detection sensitivity, the optimum derivatization reagent for the profiling of multiple metabolites was Amplifex. Nevertheless, FMP-TS, INC, PTAD, or PTAD combined with an acetylation reaction showed very good performance for selected metabolites. These reagent combinations provided signal enhancements on the order of 3- to 295-fold depending on the compound. Chromatographic separation of the dihydroxylated vitamin D3 species was readily achieved using any of the derivatization reactions, while for 25(OH)D3 epimers, only PyrNO, FMP, INC, and PTAD combined with acetylation enabled complete separation. In conclusion, we believe this study can serve as a useful reference for vitamin D laboratories, to help analytical and clinical scientists decide which derivatization reagent to choose for their application.

Stability of sample extracts of vitamin D3 metabolites after chemical derivatization for LC-MS/MS analysis.

Liquid chromatography/tandem mass spectrometry (LC-MS/MS) is widely used to determine vitamin D3 metabolites in biological samples. The ionization efficiencies of these metabolites, however, are poor under electrospray ionization conditions. Moreover, the chromatographic separation of multiple vitamin D metabolites and their epimers can be challenging. For these reasons, chemical derivatization reagents are often used to improve sensitivity and selectivity of analysis. While the derivatization schemes have been proven to be very effective, one missing aspect is the investigation of the stability of the chemical derivatization products in stored sample extracts. In this study, we investigated the long-term stability of several vitamin D3 metabolites after 1 and 3 months of storage at - 20 °C. Five vitamin D3 metabolites were examined after derivatization with seven different derivatization reagents. Generally, Amplifex products were the most stable in the long term in our study with 11-20% degraded after 1 month of storage and 14-35% after 3 months. The stabilities for some of the metabolites' 4-[2-(6,7-dimethoxy-4-methyl-3-oxo-3,4-dihydroquinoxalyl)ethyl]-1,2,4-triazoline-3,5-dione (DMEQ-TAD), 2-fluoro-1-methylpyridinium p-toluenesulfonate (FMP-TS), isonicotinoyl chloride (INC) and 4-phenyl-1,2,4-triazoline-3,5-dione acetylated (PTAD-Ac) products were also acceptable after 1 month of storage. Other derivatized metabolites, however, degraded extensively already after 1 month of storage, such as 4-phenyl-1,2,4-triazoline-3,5-dione (PTAD) (54-72% degradation) and 2-nitrosopyridine (PyrNO) (32-100% degradation). Importantly, for every metabolite, there was an optimum derivatization reagent that met the criteria of stability proposed by international regulatory bodies after 1 month of storage. Some derivatives were stable for even up to 3 months of storage, with degradation of less than 15%.

Analysis of vitamin D metabolic markers by mass spectrometry: Recent progress regarding the "gold standard" method and integration into clinical practice.

Liquid chromatography/tandem mass spectrometry is firmly established today as the gold standard technique for analysis of vitamin D, both for vitamin D status assessments as well as for measuring complex and intricate vitamin D metabolic fingerprints. While the actual mass spectrometry technology has seen only incremental performance increases in recent years, there have been major, very impactful changes in the front- and back-end of MS-based vitamin D assays; for example, the extension to new types of biological sample matrices analyzed for an increasing number of different vitamin D metabolites, novel sample preparation techniques, new powerful chemical derivatization reagents, as well the continued integration of high resolution mass spectrometers into clinical laboratories, replacing established triple-quadrupole instruments. At the same time, the sustainability of mass spectrometry operation in the vitamin D field is now firmly established through proven analytical harmonization and standardization programs. The present review summarizes the most important of these recent developments.

Sample preparation techniques for extraction of vitamin D metabolites from non-conventional biological sample matrices prior to LC-MS/MS analysis.

The determination of vitamin D metabolites as status marker or for diagnostic purposes is almost entirely conducted from blood serum or plasma. Other biological matrices, however, have also interested researchers, for two main reasons: (1) alternative matrices may allow non-invasive sampling, permit easier sample transfer and require less demanding storage conditions; and (2) the levels of vitamin D metabolites in other body compartments may further aid the understanding of vitamin D metabolism and function. Thus, the development of reliable and efficient sample preparation protocols for sample matrices other than serum/plasma, which will remove potential interferences and selectively extract the targeted metabolites, is of great importance. This review summarizes sample preparation methods for measurement of vitamin D metabolites using liquid chromatography-(tandem)mass spectrometry in more than ten different human tissues, including hair, saliva, adipose tissue, brain and others.

GC-MS analysis of underivatised new psychoactive substances in whole blood and urine.

Herein a method was develop and validated for the detection and quantification of five new psychoactive substances (NPS) belonging to three categories: synthetic cathinones (mephedrone, 3,4-MDPV), opioids (AH-7921) and cannabinoids (JWH-018, AM-2201) by EI GC-MS. Target analytes were quantified in whole blood; in urine the same compounds plus methylone were detected. Liquid-liquid extraction by MTBE - butyl acetate (1:1, v/v) in blood and butyl acetate in urine was applied for the recovery of analytes, while no derivatization was necessary for their sensitive detection and quantification. The method showed good linearity for all analytes within a concentration range from 0.25 to 2 µg/mL for mephedrone, from 0.02 to 0.16 µg/mL for 3,4-MDPV and AH-7921 and from 0.005 to 0.04 µg/mL for JWH-018 and AM-2201. LOD ranged from 0.002 µg/mL (JWH-018 and AM-2201 in blood and urine), to 0.08 µg/mL (mephedrone in urine). LOQ in blood ranged from 0.005 µg/mL for JWH-018 and AM-2201 to 0.25 µg/mL for mephedrone. Accuracy was within acceptable limits with % bias ranging from +20% to -17.98% for intra-assay study and from +18.87% to -11.16% for inter-assay study. Precision was found to be between 2.60% and 17.17% (CV%) for intra-assay study and from 6.03% to 13.72% (CV%) for inter-assay study. An intra laboratory comparison provided proof of the method robustness. The developed method can be used for the reliable and fast quantification of five NPS in blood and the detection of six NPS in urine within the practice of a clinical or forensic toxicology laboratory.

Α Simple Method for the Determination of Lacosamide in Blood by GC-MS.

Lacosamide is a functionalized amino acid with antiepileptic function. Therapeutic drug monitoring (TDM) in patients for lacosamide is critical as it allows clinicians to control epileptic seizures. A single liquid-liquid extraction step was applied for the extraction of lacosamide from whole blood samples which were thereafter analyzed by GC-MS. Optimum extraction conditions were selected on the basis of experiments with various solvents at different pHs, indicating ethyl acetate at pH 12 as the most efficient parameters for the extraction of lacosamide. Method exhibited linearity from 2 to 100 µg/mL with R2  = 0.998. Accuracy and precision were evaluated at three concentrations and found to be within acceptable limits. LOD and LOQ were determined at 0.1 and 0.5 µg/mL, respectively. Lacosamide was found to be stable at storage conditions. The developed method was applied successfully in clinical samples and postmortem blood sample from an overdose case.

C-PAmP: large scale analysis and database construction containing high scoring computationally predicted antimicrobial peptides for all the available plant species.

BACKGROUND: Antimicrobial peptides are a promising alternative to conventional antibiotics. Plants are an important source of such peptides; their pharmacological properties are known since antiquity. Access to relevant information, however, is not straightforward, as there are practically no major repositories of experimentally validated and/or predicted plant antimicrobial peptides. PhytAMP is the only database dedicated to plant peptides with confirmed antimicrobial action, holding 273 entries. Data on such peptides can be otherwise retrieved from generic repositories. DESCRIPTION: We present C-PAmP, a database of computationally predicted plant antimicrobial peptides. C-PAmP contains 15,174,905 peptides, 5-100 amino acids long, derived from 33,877 proteins of 2,112 plant species in UniProtKB/Swiss-Prot. Its web interface allows queries based on peptide/protein sequence, protein accession number and species. Users can view the corresponding predicted peptides along with their probability score, their classification according to the Collection of Anti-Microbial Peptides (CAMP), and their PhytAMP id where applicable. Moreover, users can visualise protein regions with a high concentration of predicted antimicrobial peptides. In order to identify potential antimicrobial peptides we used a classification algorithm, based on a modified version of the pseudo amino acid concept. The classifier tested all subsequences ranging from 5 to 100 amino acids of the plant proteins in UniProtKB/Swiss-Prot and stored those classified as antimicrobial with a high probability score (>90%). Its performance measures across a 10-fold cross-validation are more than satisfactory (accuracy: 0.91, sensitivity: 0.93, specificity: 0.90) and it succeeded in classifying 99.5% of the PhytAMP peptides correctly. CONCLUSIONS: We have compiled a major repository of predicted plant antimicrobial peptides using a highly performing classification algorithm. Our repository is accessible from the web and supports multiple querying options to optimise data retrieval. We hope it will greatly benefit drug design research by significantly limiting the range of plant peptides to be experimentally tested for antimicrobial activity.

PepServe: a web server for peptide analysis, clustering and visualization.

Peptides, either as protein fragments or as naturally occurring entities are characterized by their sequence and function features. Many times the researchers need to massively manage peptide lists concerning protein identification, biomarker discovery, bioactivity, immune response or other functionalities. We present a web server that manages peptide lists in terms of feature analysis as well as interactive clustering and visualization of the given peptides. PepServe is a useful tool in the understanding of the peptide feature distribution among a group of peptides. The PepServe web application is freely available at http://bioserver-1.bioacademy.gr/Bioserver/PepServe/.

A two-dimensional proteomic profile of Tetrahymena thermophila whole cell lysate.

Tetrahymena thermophila is a unicellular eukaryotic model organism used for a variety of biochemical, molecular and biological studies. According to its macronucleus genome sequence, it is expected to contain more than 27,000 protein-coding genes, although only a small proportion of them have information published specifically about them. Here, we present a reference map for whole cell lysate of T. thermophila obtained using two-dimensional gel electrophoresis (2-DE) combined with mass spectrometry. Although (2-DE) is one of the most efficient techniques for resolving complex protein mixtures and revealing the relative high-abundance proteins, it has not yet been applied generally to ciliates. In order to obtain qualitative protein samples for analysis, an appropriate homogenization method is required. Optimization of the homogenization method led to the analysis of nearly 4500 protein spots, the final identification of 375 different proteins using Mascot software and an additional 258 gene products using a newly developed web service, called Peptide Finder, resulting in a total of 631 different gene products that are considered to constitute the proteomic profile of the whole cell lysate of T. thermophila.

UniMaP: finding unique mass and peptide signatures in the human proteome.

UNLABELLED: The uniqueness of a measured molecular mass or peptide sequence plays a very important role in the fields of protein identification and peptide/protein-biomarker investigation. We present a publicly available web application that offers information concerning the uniqueness of one or more molecular masses and one or more peptide sequences in the human proteome. When a sequence is found to be unique in humans, the application is able to search across all species querying whether this sequence is unique, not only in humans but also in other species found in the Swiss-Prot Database. The application is also able to search for unique protein fragments derived computationally from enzymatic digestion driven by certain enzymes. Furthermore, the application can list all the unique masses and peptides of a given protein. Through this application, researchers are able to find unique tags, either on a molecular mass level or on a sequence level. These unique tags are remarkably important in research related to protein identification or biomarker discovery and measurements. AVAILABILITY: UniMaP web-application is available at http://bioserver-1.bioacademy.gr/Bioserver/UniMaP/

Peptide Finder: mapping measured molecular masses to peptides and proteins.

UNLABELLED: The identification of unknown amino acid sequences of peptides as well as protein identification is of great significance in proteomics. Here, we present a publicly available web application that facilitates a high resolution mapping of measured molecular masses to peptides and proteins, irrespectively of the enzyme/digestion method used. Furthermore, multi-filtering may be applied in terms of measured mass tolerance, molecular mass and isoelectric point range as well as pattern matching to refine the results. This approach serves complementary to the existing solutions for protein identification and gives insights in novel peptides discovery and protein identification at the cases where the identification scores from the other approaches may be below significance threshold. Peptide Finder has been proven useful in proteomics procedures with experimental data from MALDI-TOF. AVAILABILITY: Peptide Finder web-application is available at http://bioserver-1.bioacademy.gr/Bioserver/PeptideFinder/.

The role of aging, high fat diet and blue light exposure in an experimental mouse model for basal laminar deposit formation.

We sought to investigate the role of aging as a susceptibility factor for the capacity of dietary fat intake to increase the development of subretinal deposits. Mice of various ages (2, 9 and 16 months) were fed a normal diet or a diet high in saturated and unsaturated fats for a total four and a half months. Some eyes were also exposed to non-phototoxic levels of blue-green light. The outer retina and choroid were examined by light and transmission electron microscopy, and the characteristics, frequency and severity of subRPE deposits was determined. Aged mice fed normal diets developed only very mild subretinal deposits. However, many eyes of mice aged 9 months or older at the time of initiation of diet developed frequent basal laminar deposits of moderate severity, and only 16 month old mice developed more severe deposits after exposure to blue-green light. Some eyes in this older group also developed endothelial invasion into Bruch's membrane. None of the eyes developed classic drusen or linear deposits. These observations demonstrate that age increases the capacity of dietary fat, especially in the presence of environmental light, to induce subRPE deposits.