The lipid droplet lipidome.

Lipid droplets (LDs) are intracellular organelles with a hydrophobic core formed by neutral lipids surrounded by a phospholipid monolayer harboring a variety of regulatory and enzymatically active proteins. Over the last few decades, our understanding of LD biology has evolved significantly. Nowadays, LDs are appreciated not just as passive energy storage units, but rather as active players in the regulation of lipid metabolism and quality control machineries. To fulfill their functions in controlling cellular metabolic states, LDs need to be highly dynamic and responsive organelles. A large body of evidence supports a dynamic nature of the LD proteome and its contact sites with other organelles. However, much less is known about the lipidome of LDs. Numerous examples clearly indicate the intrinsic link between LD lipids and proteins, calling for a deeper characterization of the LD lipidome in various physiological and pathological settings. Here, we reviewed the current state of knowledge in the field of the LD lipidome, providing a brief overview of the lipid classes and their molecular species present within the neutral core and phospholipid monolayer.

Investigating the Potential of Drift Tube Ion Mobility for the Analysis of Oxidized Lipids.

Epilipids, a subset of the lipidome that comprises oxidized, nitrated, and halogenated lipid species, show important biochemical activity in the regulation of redox lipid metabolism by influencing cell fate decisions, including death, health, and aging. Due to the large chemical diversity, reversed-phase liquid chromatography-high-resolution mass spectrometry (RPLC-HRMS) methods have only a limited ability to separate numerous isobaric and isomeric epilipids. Ion mobility spectrometry (IMS) is a gas-phase separation technique that can be combined with LC-HRMS to improve the overall peak capacity of the analytical platform. Here, we illustrate the advantages and discuss the current limitations of implementing IMS in LC-HRMS workflows for the analysis of oxylipins and oxidized complex lipids. Using isomeric mixtures of oxylipins, we demonstrated that while deprotonated ions of eicosanoids were poorly resolved by IMS, sodium acetate and metal adducts (e.g., Li, Na, Ag, Ba, K) of structural isomers often showed ΔCCS% above 1.4% and base peak separation with high-resolution demultiplexing (HRDm). The knowledge of the IM migration order was also used as a proof of concept to help in the annotation of oxidized complex lipids using HRDm and all-ion fragmentation spectra. Additionally, we used a mixture of deuterium-labeled lipids for a routine system suitability test with the purpose of improving harmonization and interoperability of IMS data sets in (epi)lipidomics.

An overview of food lipids toward food lipidomics.

Increasing evidence regarding lipids' beneficial effects on human health has changed the common perception of consumers and dietary officials about the role(s) of food lipids in a healthy diet. However, lipids are a wide group of molecules with specific nutritional and bioactive properties. To understand their true nutritional and functional value, robust methods are needed for accurate identification and quantification. Specific analytical strategies are crucial to target specific classes, especially the ones present in trace amounts. Finding a unique and comprehensive methodology to cover the full lipidome of each foodstuff is still a challenge. This review presents an overview of the lipids nutritionally relevant in foods and new trends in food lipid analysis for each type/class of lipids. Food lipid classes are described following the LipidMaps classification, fatty acids, endocannabinoids, waxes, C8 compounds, glycerophospholipids, glycerolipids (i.e., glycolipids, betaine lipids, and triglycerides), sphingolipids, sterols, sercosterols (vitamin D), isoprenoids (i.e., carotenoids and retinoids (vitamin A)), quinones (i.e., coenzyme Q, vitamin K, and vitamin E), terpenes, oxidized lipids, and oxylipin are highlighted. The uniqueness of each food group: oil-, protein-, and starch-rich, as well as marine foods, fruits, and vegetables (water-rich) regarding its lipid composition, is included. The effect of cooking, food processing, and storage, in addition to the importance of lipidomics in food quality and authenticity, are also discussed. A critical review of challenges and future trends of the analytical approaches and computational methods in global food lipidomics as the basis to increase consumer awareness of the significant role of lipids in food quality and food security worldwide is presented.

Fatty acid desaturase 2 determines the lipidomic landscape and steroidogenic function of the adrenal gland.

Corticosteroids regulate vital processes, including stress responses, systemic metabolism, and blood pressure. Here, we show that corticosteroid synthesis is related to the polyunsaturated fatty acid (PUFA) content of mitochondrial phospholipids in adrenocortical cells. Inhibition of the rate-limiting enzyme of PUFA synthesis, fatty acid desaturase 2 (FADS2), leads to perturbations in the mitochondrial lipidome and diminishes steroidogenesis. Consistently, the adrenocortical mitochondria of Fads2-/- mice fed a diet with low PUFA concentration are structurally impaired and corticoid levels are decreased. On the contrary, FADS2 expression is elevated in the adrenal cortex of obese mice, and plasma corticosterone is increased, which can be counteracted by dietary supplementation with the FADS2 inhibitor SC-26192 or icosapent ethyl, an eicosapentaenoic acid ethyl ester. In humans, FADS2 expression is elevated in aldosterone-producing adenomas compared to non-active adenomas or nontumorous adrenocortical tissue and correlates with expression of steroidogenic genes. Our data demonstrate that FADS2-mediated PUFA synthesis determines adrenocortical steroidogenesis in health and disease.

Analytical Toolbox to Unlock the Diversity of Oxidized Lipids.

Lipids are diverse class of small biomolecules represented by a large variety of chemical structures. In addition to the classical biosynthetic routes, lipids can undergo numerous modifications via introduction of small chemical moieties forming hydroxyl, phospho, and nitro derivatives, among others. Such modifications change the physicochemical properties of a parent lipid and usually result in new functionalities either by mediating signaling events or by changing the biophysical properties of lipid membranes. Over the last decades, a large body of evidence indicated the involvement of lipid modifications in a variety of physiological and pathological events. For instance, lipid (per)oxidation for a long time was considered as a hallmark of oxidative stress and related proinflammatory signaling. Recently, however, with the burst in the development of the redox biology field, oxidative modifications of lipids are also recognized as a part of regulatory and adaptive events that are highly specific for particular cell types, tissues, and conditions.The initial diversity of lipid species and the variety of possible lipid modifications result in an extremely large chemical space of the epilipidome, the subset of the natural lipidome formed by enzymatic and non-enzymatic lipid modifications occurring in biological systems. Together with their low natural abundance, structural annotation of modified lipids represents a major analytical challenge limiting the discovery of their natural variety and functions. Furthermore, the number of available chemically characterized standards representing various modified lipid species remains limited, making analytical and functional studies very challenging. Over the past decade we have developed and implemented numerous analytical methods to study lipid modifications and applied them in the context of different biological conditions. In this Account, we outline the development and evolution of modern mass-spectrometry-based techniques for the structural elucidation of modified/oxidized lipids and corresponding applications. Research of our group is mostly focused on redox biology, and thus, our primary interest was always the analysis of lipid modifications introduced by redox disbalance, including lipid peroxidation (LPO), oxygenation, nitration, and glycation. To this end, we developed an array of analytical solutions to measure carbonyls derived from LPO, oxidized and nitrated fatty acid derivatives, and oxidized and glycated complex lipids. We will briefly describe the main analytical challenges along with corresponding solutions developed by our group toward deciphering the complexity of natural epilipdomes, starting from in vitro-oxidized lipid mixtures, artificial membranes, and lipid droplets, to illustrate the diversity of lipid modifications in the context of metabolic diseases and ferroptotic cell death.

Guiding the choice of informatics software and tools for lipidomics research applications.

Progress in mass spectrometry lipidomics has led to a rapid proliferation of studies across biology and biomedicine. These generate extremely large raw datasets requiring sophisticated solutions to support automated data processing. To address this, numerous software tools have been developed and tailored for specific tasks. However, for researchers, deciding which approach best suits their application relies on ad hoc testing, which is inefficient and time consuming. Here we first review the data processing pipeline, summarizing the scope of available tools. Next, to support researchers, LIPID MAPS provides an interactive online portal listing open-access tools with a graphical user interface. This guides users towards appropriate solutions within major areas in data processing, including (1) lipid-oriented databases, (2) mass spectrometry data repositories, (3) analysis of targeted lipidomics datasets, (4) lipid identification and (5) quantification from untargeted lipidomics datasets, (6) statistical analysis and visualization, and (7) data integration solutions. Detailed descriptions of functions and requirements are provided to guide customized data analysis workflows.

Variations in the milk lipidomes of two dairy cow herds fed hay- or silage-based diets over a full year.

Bovine milk plays an important role in human nutrition and is one of the main products of dairy industry. Its composition changes in response to various factors including forage, which are rapidly reflected by the milk lipidome. Most cows receive a silage-based diet despite a recent trend towards more traditional husbandry relying on hay-feeding. Here, changes in the lipidome upon different animal diets were addressed by studying milk of cows from two different feeding regimes and associated seasonal variations over one year. Extracted lipids were analyzed by reversed-phase liquid chromatography coupled on-line to high resolution mass spectrometry. Overall, 1302 lipid molecular species were identified including 1038 triacylglycerides (∼80%), whereas the remaining 20% were represented by a variety of species from twelve lipid classes. A semi-absolute quantitation of 264 lipid species showed diet- and season-induced variations in the milk lipidome with many odd chain triacylglycerides upregulated in hay milk.

Differentiation and Quantitation of Coeluting Isomeric Amadori and Heyns Peptides Using Sugar-Specific Fragment Ion Ratios.

d-glucose and d-fructose present in blood, tissues, and organs of all mammals can react with amino groups, leading to glucated (Amadori) and fructated (Heyns) products, i.e., proteins glycated at lysine residues. While typically present at low concentration in humans, metabolic diseases including diabetes elevate sugar levels, favoring glycation and consecutive reactions leading to advanced glycation end products (AGEs) linked to diabetic complications and cardiovascular diseases. Analytical methods able to differentiate and to individually quantify Amadori- and Heyns-modified proteins in complex sample mixtures, e.g., serum, are still very limited. Here, we show that the reported and supposedly specific neutral losses displayed in tandem mass spectra of Heyns peptides cannot be used for a reliable differentiation as they were also observed for Amadori peptides. However, the combination of several neutral loss signals in fragment ion ratios at both precursor and fragment ion signals allowed the differentiation and relative quantitation of coeluting isomeric Amadori and Heyns peptides at different concentrations and peptide ratios. This was also true for digested human plasma. Thus, the presented strategy allows the quantitation of Amadori and Heyns peptides in complex samples, especially by spiking isotope-labeled peptides. This will allow searching for glucated and fructated biomarkers in clinical samples.

Evaluation of Sample Preparation Strategies for Human Milk and Plasma Proteomics.

Sample preparation is the most critical step in proteomics as it directly affects the subset of proteins and peptides that can be reliably identified and quantified. Although a variety of efficient and reproducible sample preparation strategies have been developed, their applicability and efficacy depends much on the biological sample. Here, three approaches were evaluated for the human milk and plasma proteomes. Protein extracts were digested either in an ultrafiltration unit (filter-aided sample preparation, FASP) or in-solution (ISD). ISD samples were desalted by solid-phase extraction prior to nRPC-ESI-MS/MS. Additionally, milk and plasma samples were directly digested by FASP without prior protein precipitation. Each strategy provided inherent advantages and disadvantages for milk and plasma. FASP appeared to be the most time efficient procedure with a low miscleavage rate when used for a biological sample aliquot, but quantitation was less reproducible. A prior protein precipitation step improved the quantitation by FASP due to significantly higher peak areas for plasma and a much better reproducibility for milk. Moreover, the miscleavage rate for milk, the identification rate for plasma, and the carbamidomethylation efficiency were improved. In contrast, ISD of both milk and plasma resulted in higher miscleavage rates and is therefore less suitable for targeted proteomics.

Analysis of the Endogenous Peptidomes of Different Infant Formula Types and Human Milk.

Infant formula (IF) is a commonly used replacement whenever mother's own milk is not available. Most IFs are based on cow milk (powders, liquids). Alternatives, based on other sources such as goat milk or plants, exist. Independent of the source, IF production and composition are strictly regulated. Besides proteins, minerals, and lipids, milk contains a variety of endogenous peptides. Whereas the human milk peptidome has been studied intensively, the peptidomes of IFs have been mostly neglected. This study investigated the peptidomes of different types of first stage IF, including cow milk-based powders and liquids, and powdered goat milk-based IF, highlighting major similarities and differences to human milk. Extracted native peptidomes were analyzed by nanoRPC-ESI-MS/MS using two different fragmentation techniques allowing the confident identification of 1587 peptides. ß-Casein peptides dominated in all samples. Interestingly, powdered and liquid cow milk-based IFs differed in the numbers of ß- and αS1-casein peptides, indicating processing-derived variations. However, the peptidomes of cow and goat milk-based IF appeared to be more comparable to each other than to human milk. Despite an overlap in the major source proteins, many peptide sequences were different, i.e., species-specific. Remarkably, the data indicate that the human milk peptidome might be donor-specific as well.

Influence of seasonal variation and processing on protein glycation and oxidation in regular and hay milk.

Climate and feeding influence the composition of bovine milk, which is further affected by thermal treatment inducing oxidation and Maillard reactions. This study aimed to evaluate season- and processing-related changes in the modified proteome of milk from two different feeding systems. Therefore, tryptic digests of regular and hay milk were analyzed by targeting 26 non-enzymatic modifications using LC-MS. Forty-five glycated, 48 advanced glycation endproduct (AGE-) modified, and 20 oxidized/carbonylated peptides representing 44 proteins were identified with lactosylation, formyllysine, and carboxymethyllysine being most common. The numbers and quantities of glycation- and oxidation-related modifications were similar between regular and hay milk and among seasons. The effects of pasteurization and ultra-high temperature (UHT) treatment were comparable for both milk types. In particular UHT treatment increased the numbers of identified modifications and the relative quantities of lactosylated peptides. The number of identified AGE-modified and oxidized residues increased slightly after UHT-treatment, but the contents were stable.

Comprehensive Profiling of the Native and Modified Peptidomes of Raw Bovine Milk and Processed Milk Products.

Bovine milk contains a variety of endogenous peptides, partially formed by milk proteases that may exert diverse bioactive functions. Milk storage allows further protease activities altering the milk peptidome, while processing, e.g., heat treatment can trigger diverse chemical reactions, such as Maillard reactions and oxidations, leading to different posttranslational modifications (PTMs). The influence of processing on the native and modified peptidome was studied by analyzing peptides extracted from raw milk (RM), ultra-high temperature (UHT) milk, and powdered infant formula (IF) by nano reversed-phase liquid chromatography coupled online to electrospray ionization (ESI) tandem mass spectrometry. Only unmodified peptides proposed by two independent software tools were considered as identified. Thus, 801 identified peptides mainly originated from αS- and ß-caseins, but also from milk fat globular membrane proteins, such as glycosylation-dependent cell adhesion molecule 1. RM and UHT milk showed comparable unmodified peptide profiles, whereas IF differed mainly due to a higher number of ß-casein peptides. When 26 non-enzymatic posttranslational modifications (PTMs) were targeted in the milk peptidomes, 175 modified peptides were identified, i.e., mostly lactosylated and a few hexosylated or oxidized peptides. Most modified peptides originated from αS-caseins. The numbers of lactosylated peptides increased with harsher processing.

Profiling of Low-Molecular-Weight Carbonyls and Protein Modifications in Flavored Milk.

Thermal treatments of dairy products favor oxidations, Maillard reactions, and the formation of sugar or lipid oxidation products. Additives including flavorings might enhance these reactions or even induce further reactions. Here we aimed to characterize protein modifications in four flavored milk drinks using samples along the production chain-raw milk, pasteurization, mixing with flavorings, heat treatment, and the commercial product. Therefore, milk samples were analyzed using a bottom up proteomics approach and a combination of data-independent (MSE) and data-dependent acquisition methods (DDA). Twenty-one small carbonylated lipids were identified by shotgun lipidomics triggering 13 protein modifications. Additionally, two Amadori products, 12 advanced glycation end products (AGEs), and 12 oxidation-related modifications were targeted at the protein level. The most common modifications were lactosylation, formylation, and carboxymethylation. The numbers and distribution of modification sites present in raw milk remained stable after pasteurization and mixing with flavorings, while the final heat treatment significantly increased lactosylation and hexosylation in qualitative and quantitative terms. The processing steps did not significantly affect the numbers of AGE-modified, oxidized/carbonylated, and lipid-carbonylated sites in proteins.

Smart functional polymer coatings for paper with anti-fouling properties.

Cellulose, as the main component of paper, is becoming more and more important for several high tech applications because of its beneficial properties, such as abundance, low cost, renewability, mechanical robustness and biocompatibility. To make cellulose accessable for new applications it is necessary to introduce new properties, which can be done by surface modification e.g. grafting of polymers onto surfaces. In this work, two comb copolymers, poly[(2-methyl-2-oxazoline methacrylate)-co-glycidyl methacrylate] and poly[(2-methacryloyloxyethyl phosphorylcholine)-co-glycidyl methacrylate], were synthesized by free radical polymerization of glycidyl methacrylate and oligo(2-methyl-2-oxazoline) as well as 2-methacryloyloxyethyl phosphorylcholine. After extensive characterization the polymers were covalently attached to thin cellulose model layers and filter paper using a one-step grafting-to approach. For the comprehensive analysis of these layers, thin cellulose films were fabricated on silicon wafers by spin coating of trimethylsilyl cellulose followed by acid hydrolysis which resulted in homogeneous layers as substrates for the grafting process of the functional polymers. The layers were characterized by X-ray photoelectron spectroscopy (XPS), attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR), atomic force microscopy (AFM) and energy-dispersive X-ray spectroscopy (EDX). To demonstrate the high potential of such polymer-modified cellulose materials, protein repellance of the cellulose films, containing peptidomimetic 2-methyl-2-oxazoline and zwitterionic phosphorylcholine groups after successful functionalization, is shown. Cell adhesion experiments using Bacillus subtilis, Escherichia coli and Saccharomyces cerevisiae indicate the considerable anti-fouling capacity against both Gram-positive and Gram-negatve bacteria as well as the yeast fungus.