Development of an Analytical Method for the Metaproteomic Investigation of Bioaerosol from Work Environments.

The metaproteomic analysis of air particulate matter provides valuable information about the properties of bioaerosols in the atmosphere and their influence on climate and public health. In this work, a new method for the extraction and analysis of proteins in airborne particulate matter from quartz microfiber filters is developed. Different protein extraction procedures are tested to select the best extraction protocol based on protein recovery. The optimized method is tested for the extraction of proteins from spores of ubiquitous bacteria species and used for the metaproteomic characterization of filters from three work environments. In particular, ambient aerosol samples are collected in a composting plant, in a wastewater treatment plant, and in an agricultural holding. A total of 179, 15, 205, and 444 proteins are identified in composting plant, wastewater treatment plant, and agricultural holding, (cow stable and blending plant), respectively. In agreement with the major categories of primary biological aerosol particles, all identified proteins originated primarily from fungi, bacteria, and plants. The paper is the first metaproteomic study applied to bioaerosol samples collected in occupationally relevant environmental sites and, even though not aimed at monitoring the risk exposure of workers, it provides information on the possible exposure in the working environmental sites.

A Rapid Magnetic Solid Phase Extraction Method Followed by Liquid Chromatography-Tandem Mass Spectrometry Analysis for the Determination of Mycotoxins in Cereals.

Mycotoxins can contaminate various food commodities, including cereals. Moreover, mycotoxins of different classes can co-contaminate food, increasing human health risk. Several analytical methods have been published in the literature dealing with mycotoxins determination in cereals. Nevertheless, in the present work, the aim was to propose an easy and effective system for the extraction of six of the main mycotoxins from corn meal and durum wheat flour, i.e., the main four aflatoxins, ochratoxin A, and the mycoestrogen zearalenone. The developed method exploited magnetic solid phase extraction (SPE), a technique that is attracting an increasing interest as an alternative to classical SPE. Therefore, the use of magnetic graphitized carbon black as a suitable extracting material was tested. The same magnetic material proved to be effective in the extraction of mycoestrogens from milk, but has never been applied to complex matrices as cereals. Ultra high-performance liquid chromatography tandem mass spectrometry was used for detection. Recoveries were >60% in both cereals, even if the matrix effects were not negligible. The limits of quantification of the method results were comparable to those obtained by other two magnetic SPE-based methods applied to cereals, which were limited to one or two mycotoxins, whereas in this work the investigated mycotoxins belonged to three different chemical classes.

Mycoestrogen determination in cow milk: Magnetic solid-phase extraction followed by liquid chromatography and tandem mass spectrometry analysis.

Recently, magnetic solid-phase extraction has gained interest because it presents various operational advantages over classical solid-phase extraction. Furthermore, magnetic nanoparticles are easy to prepare, and various materials can be used in their synthesis. In the literature, there are only few studies on the determination of mycoestrogens in milk, although their carryover in milk has occurred. In this work, we wanted to develop the first (to the best of our knowledge) magnetic solid-phase extraction protocol for six mycoestrogens from milk, followed by liquid chromatography and tandem mass spectrometry analysis. Magnetic graphitized carbon black was chosen as the adsorbent, as this carbonaceous material, which is very different from the most diffuse graphene and carbon nanotubes, had already shown selectivity towards estrogenic compounds in milk. The graphitized carbon black was decorated with Fe3 O4 , which was confirmed by the characterization analyses. A milk deproteinization step was avoided, using only a suitable dilution in phosphate buffer as sample pretreatment. The overall process efficiency ranged between 52 and 102%, whereas the matrix effect considered as signal suppression was below 33% for all the analytes even at the lowest spiking level. The obtained method limits of quantification were below those of other published methods that employ classical solid-phase extraction protocols.

Multiresidue analysis of endocrine-disrupting compounds and perfluorinated sulfates and carboxylic acids in sediments by ultra-high-performance liquid chromatography-tandem mass spectrometry.

A multiresidue analytical method for the determination of 11 perfluorinated compounds and 22 endocrine-disrupting compounds (ECDs) including 13 natural and synthetic estrogens (free and conjugated forms), 2 alkylphenols, 1 plasticiser, 2 UV-filters, 1 antimicrobial, and 2 organophosphorus compounds in sediments has been developed. Ultrasound-assisted extraction followed by solid phase extraction (SPE) with graphitized carbon black (GCB) cartridge as clean-up step were used. The extraction process yield was optimized in terms of solvent composition. Then, a 3(2) experimental design was used to optimize solvent volume and sonication time by response surface methodology, which simplifies the optimization procedure. The final extract was analyzed by ultra-high performance liquid chromatography coupled with tandem mass spectrometry. The optimized sample preparation method is simple and robust, and allows recovery of ECDs belonging to different classes in a complex matrix such as sediment. The use of GCB for SPE allowed to obtain with a single clean-up procedure excellent recoveries ranging between 75 and 110% (relative standard deviation <16%). The developed methodology has been successfully applied to the analysis of ECDs in sediments from different rivers and lakes of the Lazio Region (Italy). These analyses have shown the ubiquitous presence of chloro-substituted organophosphorus flame retardants and bisphenol A, while other analyzed compounds were occasionally found at concentration between the limit of detection and quantification.

Separation of intact proteins on γ-ray-induced polymethacrylate monolithic columns: A highly permeable stationary phase with high peak capacity for capillary high-performance liquid chromatography with high-resolution mass spectrometry.

Polymethacrylate-based monolithic capillary columns, prepared by γ-radiation-induced polymerization, were used to optimize the experimental conditions (nature of the organic modifiers, the content of trifluoroacetic acid and the column temperature) in the separation of nine standard proteins with different hydrophobicities and a wide range of molecular weights. Because of the excellent permeability of the monolithic columns, an ion-pair reversed-phase capillary liquid chromatography with high-resolution mass spectrometry method has been developed by coupling the column directly to the mass spectrometer without a flow-split and using a standard electrospray interface. Additionally, the high working flow and concomitant high efficiency of these columns allowed us to employ a longer column (up to 50 cm) and achieve a peak capacity value superior to 1000. This work is motivated by the need to develop new materials for high-resolution chromatographic separation that combine chemical stability at elevated temperatures (up to 75°C) and a broad pH range, with a high peak capacity value. The advantage of the γ-ray-induced monolithic column lies in the batch-to-batch reproducibility and long-term high-temperature stability. Their proven high loading capacity, recovery, good selectivity and high permeability, moreover, compared well with that of a commercially available poly(styrene-divinylbenzene) monolithic column, which confirms that such monolithic supports might facilitate analysis in proteomics.

Natural estrogens in dairy products: Determination of free and conjugated forms by ultra high performance liquid chromatography with tandem mass spectrometry.

Natural estrogens are synthesized by mammals in different amounts depending on the developmental stage and pregnancy/lactation period, and they may pass into milk, where they are mostly present as glucuronated and sulfated forms. In modern dairy practices, about 75% of milk is produced from pregnant cows; therefore, the amount of hormones that may pass into milk could be of concern. While estrogen determination in milk has been investigated in depth, the individual determination of estrogens and their conjugated forms in dairy products has not been fully addressed. The aim of this work was to develop and assess a sensitive method, using the peculiar retention properties of graphitized carbon black, to extract natural free estrogens and their major conjugated metabolites, without any enzymatic cleavage, from yogurt, cheese, and butter. The free and conjugated estrogens were eluted in two distinct fractions from the solid-phase extraction cartridge and analyzed separately by ultra high performance liquid chromatography coupled to tandem mass spectrometry. Recoveries were higher than 80% for all the three sample typologies. The highest matrix effects were observed for butter, which was richest in lipid content, but was below 30%. A survey on some commercial dairy products suggests that production processes decreased estrogen content.

Ultra-high-performance liquid chromatography-tandem mass spectrometry for the analysis of free and conjugated natural estrogens in cow milk without deconjugation.

A sensitive liquid chromatography/electrospray ionization-tandem mass spectrometry method for the determination of free and conjugated estrogens in cow milk is described. Milk samples were diluted with water and then extracted and cleaned up by solid-phase extraction using graphitized carbon black as adsorbent material, without any enzymatic cleavage, derivatization, and/or protein precipitation step. Two fractions were collected (free and conjugated estrogens) and analyzed separately. Mass spectrometry analysis was performed in negative ion mode using selected reaction monitoring acquisition mode. For all compounds, the coefficients of determination (R(2)) ranged between 0.9892 and 0.9997. Analytical recoveries were in the range of 86-109% for free estrogens and 85-118% for conjugates, with relative standard deviations below 10%, and the method detection limit ranged between 3 and 80 ng L(-1). Finally, the developed method was used to determine the presence of free and conjugated estrogens in six retail milk samples (five cow milk samples and one goat milk sample) and one goat milk sample provided by a local shepherd. Estrone was found to be the major free estrogen present in commercial milk samples, and estrone 3-sulfate showed the highest concentration among the target conjugated estrogens. Estriol was also observed in some analyzed milk samples, but the concentrations were always below the limit of quantification.

Development of an analytical strategy for the identification of potential bioactive peptides generated by in vitro tryptic digestion of fish muscle proteins.

In the last years, food proteins and peptides are attracting great attention because of the emergence of a new field, that of food-derived bioactive peptides. This paper presents a comparison and evaluation of four different experiments for the identification of sarcoplasmic and myofibrillar fish peptides. This study is aimed at the development of a simple and fast method for the identification of peptides that could arise from fish meat if trypsin was the only digestive enzyme acting on fish meat proteins. In particular, we tested the use of ultrafiltration membranes with a molecular weight cutoff of 3,000 Da. Data analysis has shown that the experiment in which there is neither precipitation nor an ultrafiltration step performed better and allowed the identification of a larger number of peptides and potential antimicrobial peptides (AMPs); this workflow provided 473 and 398 total identified peptides and 44 and 18 AMPs for sarcoplasmic and myofibrillar extracts, respectively. This protocol is found to be faster and more straightforward than the other three tested workflows. The developed strategy could be also useful for other food matrices and could provide information about food quality and safety control.

Multiclass analysis of mycotoxins in biscuits by high performance liquid chromatography-tandem mass spectrometry. Comparison of different extraction procedures.

A sensitive, simple and rapid method for the simultaneous determination of 19 mycotoxins in biscuits (a dry matrix containing cereals and egg) has been developed using high performance liquid chromatography coupled to tandem mass spectrometry with electrospray source working in both positive and negative mode. Due to the matrix complexity and the high amount of contaminants, a solid phase extraction method using graphitized carbon black was optimized for an effective clean-up step. Accuracy was carried out in the selected matrix using blank samples spiked at three analyte concentrations. Recoveries between 63 and 107% and relative standard deviations lower than 12% were obtained. For all considered mycotoxin classes, i.e. thricotecenes A and B, zearalenone and its metabolites, fumonisins, ochratoxin A, enniatins and their structurally related beauvericin, the method was validated in terms of linearity, recovery, matrix effect, precision, limit of detection and limit of quantification. Matrix-matched calibration was used for quantification purposes, in order to compensate for matrix effect. The coefficients of determination obtained were in the range of 0.9927-1. The limits of quantification, ranging from 0.04µgkg(-1) for enniatin B1 to 80.2µgkg(-1) for nivalenol, were always lower than maximum permitted levels for every regulated mycotoxin by the current European legislation.

Comparison of extraction methods for the identification and quantification of polyphenols in virgin olive oil by ultra-HPLC-QToF mass spectrometry.

In this work, liquid-liquid extraction (LLE) and solid phase extraction (SPE), of polyphenols from a VOO sample were optimised by a Plackett-Burman experimental design; then the two extraction techniques capabilities were compared. By using HPLC-DAD, the extraction ability of SPE with the diol phase and LLE were similar. The two methods were further evaluated with ultra HPLC-ESI QToF in negative ion mode by recoveries of standards and matched comparison of the peak area of 40 identified and 27 unidentified compounds. Conclusions indicate that LLE gives better recoveries for highly polar, non-polar, and some polyphenols suspected to contain a nitrogen atom, while for the others the two methods seem to be equally suitable. The presence of nitrogen-containing polyphenols was confirmed in positive ionisation mode in LLE extract, whereas in the SPE extract they were not present. One of them was tentatively identified as a compound containing tyrosine and methyl-decarboxymetyl-eleanoic acid moieties.

High performance liquid chromatography tandem mass spectrometry determination of perfluorinated acids in cow milk.

A new and sensitive liquid chromatography/electrospray-tandem mass spectrometric (LC/ESI-MS/MS) method for the determination of 12 perfluorinated compounds (PFCs) in cow milk is described. Milk samples were extracted with acetone and cleaned-up by a graphitized carbon black solid-phase extraction cartridge, optimizing the entire procedure by using a screening experimental design. LC/ESI-MS/MS was performed in negative ion mode using multiple reaction monitoring mode. The performance of the method was evaluated under the optimized conditions in terms of matrix effects, range of linearity, accuracy, and repeatability. For all compounds, linearity in matrix was observed in the range LOQ-10µgL(-1), and coefficients of determination R(2) ranged from 0.9982 to 0.9999. The analytical recoveries, relative to the isotopic internal standard, measured at 10 and 50ngL(-1) were in the range of 91-105%, with relative standard deviations below 6% and method detection limit, based on the blank value +3 times the standard deviation of the blank, ranged from 0.5 to 3ngL(-1). The final method developed was used to determine the concentration of PFCs in 15 retail milk samples. None of these compounds were detected in cow milk analyzed samples.

Proteomic platform for the identification of proteins in olive (Olea europaea) pulp.

The nutritional and cancer-protective properties of the oil extracted mechanically from the ripe fruits of Olea europaea trees are attracting constantly more attention worldwide. The preparation of high-quality protein samples from plant tissues for proteomic analysis poses many challenging problems. In this study we employed a proteomic platform based on two different extraction methods, SDS and CHAPS based protocols, followed by two precipitation protocols, TCA/acetone and MeOH precipitation, in order to increase the final number of identified proteins. The use of advanced MS techniques in combination with the Swissprot and NCBI Viridiplantae databases and TAIR10 Arabidopsis database allowed us to identify 1265 proteins, of which 22 belong to O. europaea. The application of this proteomic platform for protein extraction and identification will be useful also for other proteomic studies on recalcitrant plant/fruit tissues.

Proteome investigation of the non-model plant pomegranate (Punica granatum L.).

A gel-free, shotgun proteomics approach was used to characterize pomegranate aril proteome by nanoliquid chromatography-high-resolution tandem mass spectrometry. To identify both high-abundance and low-abundance proteins, we applied two distinct sample preparation protocols, i.e., a classical one widely applied in literature and a second one able to reduce the dynamic range of protein concentration of the sample, based on combinatorial hexapeptide ligand library technology. However, the proteins identified with the latter protocol were only a small minority. Because pomegranate is a non-model plant species, i.e., information of its genome sequence are lacking, only a few protein sequences are included in the most widely known protein sequence databases. To improve both the number of identified proteins and data reliability, identification was performed integrating the results obtained with three distinct plant protein databases, since the majority of proteins could only be attributed by homology with other plant species. Nevertheless, many proteins had assigned only one unique peptide, because of the phylogenetic distance of pomegranate from the main model plants. After manual revision of the identified proteins to eliminate the redundant or ambiguous identifications, a list of 1,488 proteins was obtained, only six of which belonging to pomegranate species. To the author's best knowledge, this is the first work aimed at the proteomic characterization of Punica granatum.

Do plasma proteins distinguish between liposomes of varying charge density?

Cationic liposomes (CLs) are one of the most employed nonviral nanovector systems in gene therapy. However, their transfection efficiency is strongly affected by interactions with plasma components, that lead to the formation of a "protein corona" onto CL surface. The interactions between nanoparticles entering the body and biomolecules have an essential role for their biodistribution. Because the knowledge of proteins adsorbed onto vector surface could be useful in the screening of new, more efficient and more biocompatible liposomal formulations, the behavior of three CLs with different membrane charge densities was investigated. The proteins of the three coronas were identified by nano-liquid chromatography-tandem mass spectrometry, and quantified with label-free spectral counting strategy. Fibrinogen displayed higher association with CLs with high membrane charge density, while apolipoproteins and C4b-binding protein with CLs with low membrane charge density. These results are discussed in terms of the different lipid compositions of CLs and may have a deep biological impact for in vivo applications. Surface charge of nanoparticles is emerging as a relevant factor determining the corona composition after interaction with plasma proteins. Remarkably, it is also shown that the charge of the protein corona formed around CLs is strongly related to their membrane charge density.

Polyphenol content in white table grape (Vitis Vinifera) berries of cultivar Italia: interactive effect of irrigation, delayed harvest and storage.

Polyphenol concentrations were quantified by rapid resolution liquid chromatography/mass spectrometry in white table grape. The experimental vineyard was subjected to different kinds of water supply and supply rates. Samples from the same vineyards were also analysed after 6 weeks of storage in a refrigerator and after 6 weeks of delayed harvesting. Berry skins and seeds were analysed separately. A statistical treatment of the screening kind, namely the 2(k) full factorial design, was used for the interpretation of results. Storage, delayed harvesting and the different kinds of water supply appeared to be the variables most affecting grape polyphenol content. In some cases, results showed that polyphenol content diminished by more than 50% after 6 weeks if the grapes were stored in a refrigerator, or if a sprinkler was used for irrigation.

Multiclass mycotoxin analysis in food, environmental and biological matrices with chromatography/mass spectrometry.

Mold metabolites that can elicit deleterious effects on other organisms are classified as mycotoxins. Human exposure to mycotoxins occurs mostly through the intake of contaminated agricultural products or residues due to carry over or metabolite products in foods of animal origin such as milk and eggs, but can also occur by dermal contact and inhalation. Mycotoxins contained in moldy foods, but also in damp interiors, can cause diseases in humans and animals. Nephropathy, various types of cancer, alimentary toxic aleukia, hepatic diseases, various hemorrhagic syndromes, and immune and neurological disorders are the most common diseases that can be related to mycotoxicosis. The absence or presence of mold infestation and its propagation are seldom correlated with mycotoxin presence. Mycotoxins must be determined directly, and suitable analytical methods are necessary. Hundreds of mycotoxins have been recognized, but only for a few of them, and in a restricted number of utilities, a maximum acceptable level has been regulated by law. However, mycotoxins seldom develop alone; more often various types and/or classes form in the same substrate. The co-occurrence might render the individual mycotoxin tolerance dose irrelevant, and therefore the mere presence of multiple mycotoxins should be considered a risk factor. The advantage of chromatography/mass spectrometry (MS) is that many compounds can be determined and confirmed in one analysis. This review illustrates the state-of-the-art of mycotoxin MS-based analytical methods for multiclass, multianalyte determination in all the matrices in which they appear. A chapter is devoted to the history of the long-standing coexistence and interaction among humans, domestic animals and mycotoxicosis, and the history of the discovery of mycotoxins. Quality assurance, although this topic relates to analytical chemistry in general, has been also examined for mycotoxin analysis as a preliminary to the systematic literature excursus. Sample handling is a crucial step to devise a multiclass analytical method; so when possible, it has been treated separately for a better comparison before tackling the instrumental part of the whole analytical method. This structure has resulted sometimes in unavoidable redundancies, because it was also important to underline the interconnection. Most reviews do not deal with all the possible mycotoxin sources, including the environmental ones. The focus of this review is the analytical methods based on MS for multimycotoxin class determination. Because the final purpose to devise multimycotoxin analysis should be the assessment of the danger to health of exposition to multitoxicants of natural origin (and possibly also the interaction with anthropogenic contaminants), therefore also the analytical methods for environmental relevant mycotoxins have been thoroughly reviewed. Finally, because the best way to shed light on actual risk assessment could be the individuation of exposure biomarkers, the review covers also the scarce literature on biological fluids.

Evolution of the protein corona of lipid gene vectors as a function of plasma concentration.

The concept that the effective unit of interest in the cell-nanomaterial interaction is the particle and its corona of associated proteins is emerging. Here we investigate the compositional evolution of the protein corona of 1,2-dioleoyl-3-trimethylammonium propane (DOTAP) cationic liposomes (CLs) and DOTAP/DNA lipoplexes over a wide range of plasma concentrations (2.5-80%). The composition of the hard corona of lipoplexes is quite stable, but that of CLs does evolve considerably. We show that the protein corona of CLs is made of both low-affinity and competitive-binding proteins whose relative abundance changes with the plasma concentration. This result may have deep biological implications for the application of lipid-based gene vectors both in vitro and in vivo.

Differential analysis of "protein corona" profile adsorbed onto different nonviral gene delivery systems.

A shotgun proteomics approach was used to characterize and compare the proteins that lead to the formation of a rich "protein corona" adsorbed onto the surfaces of cationic liposomes (CLs), lipoplexes, and lipid/polycation/DNA (LPD) complexes, when they come into contact with plasma. After separation of the nanoparticle-protein complex from plasma, the protein mixture was digested, and peptides were analyzed by nanoliquid chromatography-Orbitrap LTQ-XL mass spectrometry. The number of proteins bound to lipoplexes was double that of those identified in the corona of CLs (208 vs 105), while 77 proteins were common to both coronas. The number of proteins bound to the surface of the LPD complexes (158, 133 of which are common to lipoplexes) is intermediate between those found in the protein corona of both CLs and lipoplexes. About half of them were found in the protein corona of CLs. By overlapping the three formulations, it can be seen that only 12 proteins are peculiar to LPD complexes. These results may help in designing gene delivery systems capable of binding the minimum possible quantity of proteins that influence transfection negatively, binding selectively proteins capable of helping in steering in vivo the vector toward the target, and obtaining more efficient and effective gene therapy.

DNA affects the composition of lipoplex protein corona: a proteomics approach.

The distribution of drug delivery systems into the body is affected by plasma proteins adsorbed onto their surface. Furthermore, an exact understanding of the structure and morphology of drug carriers is fundamental to understand their role as gene delivery systems. In this work, the adsorption of human plasma proteins bound to cationic liposomes and to their relative DNA lipoplexes was compared. A shotgun proteomics approach based on HPLC coupled to high resolution MS was used for an efficient identification of proteins adsorbed onto liposome and lipoplex surfaces. The distinct pattern of proteins adsorbed helps to better understand the DNA compaction process. The experimental evidence leads us to hypothesize that polyanionic DNA is associated to the lipoplex surface and can interact with basic plasma proteins. Such a finding is in agreement with recent results showing that lipoplexes are multilamellar DNA/lipid domains partially decorated with DNA at their surface. Proteomics experiments showed that the lipoplex corona is rich of biologically relevant proteins such as fibronectin, histones and complement proteins. Our results provide novel insights to understand how lipoplexes activate the immune system and why they are rapidly cleared from the blood stream. The differences in the protein adsorption data detected in the presented experiments could be the basis for the establishment of a correlation between protein adsorption pattern and in vivo fate of intravenously administered nanoparticles and will require some consideration in the future.

Intact protein separation by chromatographic and/or electrophoretic techniques for top-down proteomics.

Mass spectrometry used in combination with a wide variety of separation methods is the principal methodology for proteomics. In bottom-up approach, proteins are cleaved with a specific proteolytic enzyme, followed by peptide separation and MS identification. In top-down approach intact proteins are introduced into the mass spectrometer. The ions generated by electrospray ionization are then subjected to gas-phase separation, fragmentation, fragment separation, and automated interpretation of mass spectrometric and chromatographic data yielding both the molecular weight of the intact protein and the protein fragmentation pattern. This approach requires high accuracy mass measurement analysers capable of separating the multi-charged isotopic cluster of proteins, such as hybrid ion trap-Fourier transform instruments (LTQ-FTICR, LTQ-Orbitrap). Front-end separation technologies tailored for proteins are of primary importance to implement top-down proteomics. This review intends to provide the state of art of protein chromatographic and electrophoretic separation methods suitable for MS coupling, and to illustrate both monodimensional and multidimensional approaches used for LC-MS top-down proteomics. In addition, some recent progresses in protein chromatography that may provide an alternative to those currently employed are also discussed.