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This trends article provides an overview of the state of the art in the analysis of intact glycopeptides by proteomics technologies based on LC–MS analysis. A brief description of the main techniques used at the different steps of the analytical workflow is provided, giving special attention to the most recent developments. The topics discussed include the need for dedicated sample preparation for intact glycopeptide purification from complex biological matrices. This section covers the common approaches with a special description of new materials and innovative reversible chemical derivatization strategies, specifically devised for intact glycopeptide analysis or dual enrichment of glycosylation and other post-translational modifications. The approaches are described for the characterization of intact glycopeptide structures by LC–MS and data analysis by bioinformatics for spectra annotation. The last section covers the open challenges in the field of intact glycopeptide analysis. These challenges include the need of a detailed description of the glycopeptide isomerism, the issues with quantitative analysis, and the lack of analytical methods for the large-scale characterization of glycosylation types that remain poorly characterized, such as C-mannosylation and tyrosine O-glycosylation. This bird’s-eye view article provides both a state of the art in the field of intact glycopeptide analysis and open challenges to prompt future research on the topic. Graphical Abstract

Microalgae are unicellular marine organisms that have promoted complex biochemical pathways to survive in greatly competitive marine environments. They could contain significant amounts of high-quality proteins which, because of their structural diversity, contain a range of yet undiscovered novel bioactive peptides. In this work, a peptidomic platform was developed for the separation and identification of bioactive peptides in protein hydrolysates. In this work, a peptidomic platform was developed for the extraction, separation, and identification of bioactive peptides in protein hydrolysates. Indeed, extraction of proteins from recalcitrant tissues is still a challenge due to their strong cell walls and high levels of non-protein interfering compounds. Therefore, seven different protein extraction protocols, based on mechanical and chemical methods, were tested in order to produce high-quality protein extracts. Proteins obtained by means of the best protocol, consisting of milling the recalcitrant tissue with glass beads, were subjected to enzymatic digestion with Alcalase® and subsequently the hydrolysate was purified by two-dimensional semi-preparative reversed phase liquid chromatography. Fractions were assayed for antioxidant and antihypertensive activities and only the most active ones were finally analyzed by RP nanoHPLC-MS/MS. Around 500 peptide sequences were identified in these fractions. The identified peptides were subjected to an in silico analysis by PeptideRanker algorithm in order to assign a score of bioactivity probability. Twenty-five sequenced peptides were found with potential antioxidant and angiotensin-converting-enzyme-inhibitory activities. Four of these peptides, WPRGYFL, GPDRPKFLGPF, WYGPDRPKFL, SDWDRF, were selected for synthesis and in vitro tested for specific bioactivity, exhibiting good values of antioxidant and ACE-inhibitory activity. Graphical abstract Workflow showing the entire peptidomic approach developed for identification of bioactive peptides in microalgae.

The work describes the development of an enrichment method for the analysis of endogenous phosphopeptides in serum. Endogenous peptides can play significant biological roles, and some of them could be exploited as future biomarkers. In this context, blood is one of the most useful biofluids for screening, but a systematic investigation of the endogenous peptides, especially phosphorylated ones, is still lacking, mainly due to the lack of suitable analytical methods. Thus, in this paper, different phosphopeptide enrichment strategies were pursued, based either on metal oxide affinity chromatography (MOAC, in the form of commercial TiO2 spin columns or magnetic graphitized carbon black-TiO2 composite), or on immobilized metal ion affinity chromatography (IMAC, in the form of Ti4+-IMAC magnetic material or commercial Fe3+-IMAC spin columns). While MOAC strategies proved completely unsuccessful, probably due to interfering phospholipids displacing phosphopeptides, the IMAC materials performed very well. Different sample preparation strategies were tested, comprising direct dilution with the loading buffer, organic solvent precipitation, and lipid removal from the matrix, as well as the addition of phosphatase inhibitors during sample handling for maximized endogenous phosphopeptide enrichment. All data were acquired by a shotgun peptidomics approach, in which peptide samples were separated by reversed-phase nanoHPLC hyphenated with high-resolution tandem mass spectrometry. The devised method allowed the identification of 176 endogenous phosphopeptides in fresh serum added with inhibitors by the direct dilution protocol and the Ti4+-IMAC magnetic material enrichment, but good results could also be obtained from the commercial Fe3+-IMAC spin column adapted to the batch enrichment protocol.

Short peptides are important compounds in a variety of fields, including food and nutraceutical applications, but also biomarker discovery, bioactive peptide discovery and peptide drug separation. Despite the importance of short peptides, they are currently less studied than other peptides because of the lack of dedicated methods for their characterization. The method described in this paper comprises a combination of strategies to tackle the main limitations in short peptide analysis. In particular, in this work an untargeted peptidomic approach based on ultrahigh-performance liquid chromatography coupled to high-resolution mass spectrometry was developed for the identification of short peptides in cow milk samples. After milk defatting and precipitation, the sample was purified by cotton-hydrophilic interaction liquid chromatography (HILIC) micro tip in order to avoid suppression phenomena due to contaminants present in milk, such as carbohydrates. The sample was then separated by means of two chromatographic columns, with a complementary selectivity mechanism, namely reversed-phase C18 column and porous graphitic carbon (PGC). By this approach, the method allowed the separation and characterization of di-, tri- and tetrapeptides. A total of 57 and 41 peptides were identified by using a C18 and a PGC column, respectively; in particular, 31 were exclusively identified by using the C18 column, 15 unique peptides were identified by using the PGC column, while 26 were in common between the two data sets, demonstrating that the two columns have a different selectivity mechanism. The results indicated that an integrated approach may be appropriate to improve the separation of different peptides and increase the number of identifications because of the wide range of polarity of short peptides. The method allowed the untargeted identification of short peptides in milk, a complex matrix chosen as a representative real sample for method application, and provides complementary information to that accessible by ordinary peptidomics. [Figure not available: see fulltext.].

Donkey milk is a valuable product for the food industry due to its nutraceutical, nutritional, and functional properties. In this work, the endogenous peptides from donkey milk were investigated for their antioxidant and ACE-inhibitory activities, combining a two-dimensional peptide fractionation strategy with high-resolution mass spectrometry, bioinformatics analysis, and in vitro assays. After extraction, the endogenous peptides were fractionated twice, first by polymeric reversed phase and then by hydrophilic interaction chromatography. Fractions were screened for the investigated bioactivities and only the most active ones were finally analyzed by nanoRP-HPLC-MS/MS; this approach allowed to reduce the total number of possible bioactive sequences. Results were further mined by in silico analysis using PeptideRanker, BioPep, and PepBank, which provided a bioactivity score to the identified peptides and matched sequences to known bioactive peptides, in order to select candidates for chemical synthesis. Thus, five peptides were prepared and then compared to the natural occurring ones, checking their retention times and fragmentation patterns in donkey milk alone and in spiked donkey milk samples. Pure peptide standards were finally in vitro tested for the specific bioactivity. In this way, two novel endogenous antioxidant peptides, namely EWFTFLKEAGQGAKDMWR and GQGAKDMWR, and two ACE-inhibitory peptides, namely REWFTFLK and MPFLKSPIVPF, were successfully validated from donkey milk. Graphical Abstract Analytical workflow for purification and identification of bioactive peptides from donkey milk sample.

Estrogens, phytoestrogens, and mycoestrogens may enter into the surface waters from different sources, such as effluents of municipal wastewater treatment plants, industrial plants, and animal farms and runoff from agricultural areas. In this work, a multiresidue analytical method for the determination of 17 natural estrogenic compounds, including four steroid estrogens, six mycoestrogens, and seven phytoestrogens, in river water samples has been developed. (Fe3O4)-based magnetic nanoparticles coated by polydopamine (Fe3O4@pDA) were used for dispersive solid-phase extraction, and the final extract was analyzed by ultra-high performance liquid chromatography coupled with tandem mass spectrometry. The Fe3O4 magnetic nanoparticles were prepared by a co-precipitation procedure, coated by pDA, and characterized by scanning electron microscopy, infrared spectroscopy, and elemental analysis. The sample preparation method was optimized in terms of extraction recovery, matrix effect, selectivity, trueness, precision, method limits of detection, and method limits of quantification (MLOQs). For all the 17 analytes, recoveries were >70 % and matrix effects were below 30 % when 25 mL of river water sample was treated with 90 mg of Fe3O4@pDA nanoparticles. Selectivity was tested by spiking river water samples with 50 other compounds (mycotoxins, antibacterials, conjugated hormones, UV filters, alkylphenols, etc.), and only aflatoxins and some benzophenones showed recoveries >60 %. This method proved to be simple and robust and allowed the determination of natural estrogenic compounds belonging to different classes in surface waters with MLOQs ranging between 0.003 and 0.1 μg L(-1). Graphical Abstract Determination of natural estrogenic compounds in water by magnetic solid phase extraction followed by liquid chromatography-tandem mass spectrometry analysis.

This trends article describes the analytical approaches for the in-depth characterization of the protein corona on liposome nanoparticles. In particular, examples since 2014 are summarized according to the analytical approach. Traditional protein corona characterizations from in vitro static experiments are provided along with the newly introduced experimental setups for characterization of the protein corona by in vitro dynamic and in vivo studies. Additionally, a special attention is also devoted to the need for introduction of new experimental workflows for characterization of a much wider array of biomolecules. In the most recent years, an extension of the protein corona concept to the biomolecular corona was introduced, and the analytical targets are no longer restricted to proteins, but to other important biomolecules as well, as they can potentially affect the biodistribution and interaction of nanoparticles with the biological systems. The few recent examples in this field are discussed for the characterization of metabolites and lipids in the biomolecular corona with examples, also extending the discussion from liposome to other types of nanoparticles. A final discussion is provided on the potential key role of the most recent omics approaches in the study of the nano-bio interface, with an overview on top-down proteomics, which allows a better elucidation of proteoforms, and on lipidomics and metabolomics, which allow a comprehensive untargeted characterization of lipids and metabolites, respectively. Graphical abstract.

In 1968 Finnigan introduced the first commercial quadrupole mass spectrometer equipped with a computerized dataprocessing unit. Since then, the coupling of gas chromatography to mass spectrometry (GC–MS) for the analysis of contaminants in environmental and biological samples has achieved impressive success, and at the end of the last millennium it was in routine use in many laboratories. Furthermore, GC–MS was used to determine food composition, and thus it was a tool to guarantee food authenticity and safety while also providing information about the nutritional value. The discovery of atmospheric-pressure ion sources during the mid-80s was another important development, because it made the effective coupling of high-performance liquid chromatography (HPLC) to MS possible. With this technique available, the analysis of low-volatility and thermolabile compounds became possible without the need for a long derivatization procedure, which was sometimes difficult to perform and not always successful. However, after the initial excitement, the limitations of the technique soon became evident; these result from the relatively low efficiency of HPLC compared with GC and the large number of compounds present in samples that can interfere with the determination of the analytes of interest. Therefore, the need for higher MS selectivity was soon realized by the research community. The technology to overcome this problem was fortunately already available. Collision-induced dissociation (CID) was introduced by Jennings and McLafferty at end of the 60s; tandem MS (MS–MS) was made possible with the triplestage quadrupole (QqQ) introduced by Yost, Henke, andMorrison at end of the 70s; and finally multi-stage MS was provided by the Paul ion trap, patented in 1953. The addition of one more dimension in separation greatly increased selectivity; furthermore, rapid advances were made toward the design of mass spectrometers with improved sensitivity, in parallel with advances in separation technology and the development of columns with improved efficiency. Currently, HPLC and ultra HPLC (UHPLC) coupled to QqQ working in selectedreaction-monitoring (SRM) mode are the most widespread techniques in both environmental and food analysis because they provide the analyst with a high degree of selectivity and sensitivity. Hence, complex and labor-intensive sample-processing techniques could be substantially simplified. However, the use of SRM mode on QqQ instruments proved to have some limitations, including a limit to the number of compounds monitored per analysis, the inability to screen for unknowns, and the reliance on reference standards. To overcome these limitations, there is a need for an alternative approach using instruments capable of providing full spectral information and high mass resolution and mass accuracy. Classic high-resolution (HR) mass spectrometers, for example double-focus sector or Fourier-transform ion cyclotron resonance (FT-ICR), were too slow, complex to handle, and expensive to buy and to maintain. However, the introduction of modern time-of-flight (TOF) and electrostatic FT trap (Orbitrap) instrumentation totally changed the situation. TOF and Orbitrap have undergone tremendous technological advances giving—in addition to improved mass resolution, accuracy, and sensitivity—fast scan velocity, sufficient dynamic range, and the possibility of MS–MS when part of hybrid instruments. Because of their unrivaled resolution, modern FT-ICR mass spectrometers also have their advocates in the Published in the topical collectionHigh-Resolution Mass Spectrometry in Food and Environmental Analysis with guest editor Aldo Lagana.

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.

A shotgun proteomics approach was used to compare human plasma protein binding capability with cationic liposomes, DNA–cationic lipid complexes (lipoplexes), and lipid–polycation–DNA (LPD) complexes. Nano-high-performance liquid chromatography coupled with a high-resolution LTQ Orbitrap XL mass spectrometer was used to characterize and compare their protein corona. Spectral counting and area under curve methods were used to perform label-free quantification. Substantial qualitative and quantitative differences were found among proteins bound to the three different systems investigated. Protein variety found on lipoplexes and LPD complexes was richer than that found on cationic liposomes. There were also significant differences between the amounts of protein. Such results could help in the design of gene-delivery systems, because some proteins could be more selectively bound rather than others, and their bio-distribution could be driven in vivo for more efficient and effective gene therapy.

Pressurized hot water extraction (PHWE, also known as subcritical water extraction) is commonly considered to be an environmentally friendly extraction technique that could potentially replace traditional methods that use organic solvents. Unfortunately, the applicability of this technique is often limited by the very low water solubility of the target compounds, even at high temperatures. In this paper, the scope for broadening the applicability of PHWE by adjusting the pH of the water used in the extraction is demonstrated in the extraction of curcumin (which exhibits very limited water solubility) from untreated turmeric (Curcuma longa L.) rhizomes. Although poor extraction yields were obtained, even at high temperatures when using degassed water or neutral phosphate buffer as the extraction medium, yields exceeding those obtained by Soxhlet extraction were achieved using highly acidic pH buffers due to curcumin protonation. The influence of the temperature, pH, and buffer concentration on the extraction yield were investigated in detail by means of a series of designed experiments. Optimized conditions for the extraction of curcumin from turmeric by PHWE were estimated at 197 °C using 62 g/L buffer concentration at pH 1.6. The relationships between these variables were subjected to statistical analysis using response surface methodology.

In order to understand the molecular basis of salt stress response, a proteomic approach, employing two-dimensional electrophoresis and matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS), was used to identify proteins affected by salinity in wheat (Triticum durum ‘Ofanto’). Identification of proteins, whose levels were altered, was performed by comparing protein patterns of salt-treated and control plants. A set of control plants was grown without NaCl addition under the same conditions as the salt-treated plants. Proteins were extracted from the leaves of untreated and NaCl-treated plants, and resolved using 24-cm immobilized pH gradient strips with a pH 4–7 linear gradient in the first dimension and a 12.5% sodium dodecyl sulphate polyacrylamide gel electrophoresis in the second dimension; the gels were stained with Coomassie and image analysis was performed. Quantitative evaluation, statistical analyses and MALDI-TOF MS characterization of the resolved spots in treated and untreated samples enabled us to identify 38 proteins whose levels were altered in response to salt stress. In particular, ten proteins were downregulated and 28 were upregulated. A possible role of these proteins in response to salinity is discussed.

A label-free absolute quantitation method based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been developed. This methodology was applied to mouse heart in order to quantify cardiac troponin T (cTnT), which is considered to be a sensitive marker of heart damage. The cTnT was extracted, isolated by reversed-phase high-performance liquid chromatography, digested, and analyzed by MALDI-TOF MS. The MS-based quantitation was performed using matrix-matched calibration curves (due to a matrix effect) of two synthetic peptides, one cTnT-specific peptide and one internal standard peptide, respectively. Recoveries at three spiking levels ranged from 87-96%, with relative standard deviations of below 10%. The method detection limit and the method quantitation limit, expressed as the amount of cTnT for the amount of total sarcomeric protein extract, were 0.03 mg g(-1) and 0.15 mg g(-1), respectively. This method appears to be accurate and generally suitable for improving absolute protein quantitation.