Comparative evaluation of the extraction and analysis of urinary phospholipids and lysophospholipids using MALDI-TOF/MS

Addressing the untargeted lipidomics challenge in urine samples: Comparative study of extraction methods by UHPLC-ESI-QTOF-MS

Urine analysis has remained a fundamental and widely used method in clinical diagnostics for over a century. With its minimal invasive nature and comprehensive range of analytes, urine has established itself as a clinical diagnostic tool for various disorders, including renal, urological, metabolic, and endocrine diseases. Furthermore, urine's unique attributes make it an attractive matrix for biomarker discovery, as well as in assessing the metabolic and physiological states of patients and healthy individuals alike. However, limitations in our knowledge of average values and sources of urinary lipids decrease the wider clinical application of urinary lipidomics. In this context, untargeted lipidomics analysis relies heavily on the extraction and analysis of lipids in biological samples. Nevertheless, this type of analysis presents challenges in lipid identification due to the diverse nature of lipids. Therefore, proper sample treatment before analysis is crucial to obtain robust and reproducible lipidomic profiles. To address this gap, we conducted a comparative study of a urine pool sample collected from twenty healthy volunteers using four different lipid extraction methods: one biphasic and three monophasic protocols. The extracted lipids were then analyzed using UHPLC-MS and MS/MS, and the semi-quantification of all the accurately annotated lipid species was performed for each extraction method.

A Five-Year Update on Matrix Compounds for MALDI-MS Analysis of Lipids

Matrix-assisted laser desorption and ionization (MALDI) is a widely used soft-ionization technique of modern mass spectrometry (MS). MALDI enables the analysis of nearly all chemical compounds—including polar and apolar (phospho)lipids—with a minimum extent of fragmentation. MALDI has some particular advantages (such as the possibility to acquire spatially-resolved spectra) and is competitive with the simultaneously developed ESI (electrospray ionization) MS. Although there are still some methodological aspects that need to be elucidated in more detail, it is obvious that the careful selection of an appropriate matrix plays the most important role in (lipid) analysis. Some lipid classes can be detected exclusively if the optimum matrix is used, and the matrix determines the sensitivity by which a particular lipid is detected within a mixture. Since the matrix is, thus, crucial for optimum results, we provide here an update on the progress in the field since our original review in this journal in 2018. Thus, only the development during the last five years is considered, and lipids are sorted according to increasing complexity, starting with free fatty acids and ending with cardiolipins and phosphoinositides.

Comparison of Small Biomolecule Ionization and Fragmentation in Pseudomonas aeruginosa Using Common MALDI Matrices

Different bacterial cell surface associated biomolecules can be analyzed by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry and coupled with collision induced dissociation (CID) for identification. Pseudomonas aeruginosa is an opportunistic, Gram-negative bacterium that causes acute or chronic biofilm infections. Cells of P. aeruginosa communicate through a system of signaling biomolecules known as quorum sensing (QS). The QS system can result in the production of biosurfactant rhamnolipids known to associate and alter the cellular membrane. MALDI-TOF utilizes a variety of matrices that can interact differently with biomolecules for selective ionization. We examined six common matrices to determine the optimal matrix specific to different molecule classes in P. aeruginosa associated with cell surfaces. Three major molecule classes (quinolones, rhamnolipids, and phospholipids) were observed to ionize selectively with the different matrices tested. Sodiated and protonated adducts differed between matrices utilized in our study. Isobaric ions were identified as different molecule classes depending on the matrix used. We highlight the role of matrix selection in MALDI-TOF identification of molecules within a complex biological mixture.

qShot MALDI analysis: A rapid, simple, convenient, and reliable quantitative phospholipidomics approach using MALDI-TOF/MS

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI/MS) has potential applications in the qualitative analysis of phospholipids (PLs). However, its capability for quantitative analysis is limited by the unavailability and/or high cost of isotope-labeled internal standards (interSTDs, e.g., 1-oleoyl (d7)-2-hydroxy-sn-glycero-3-phosphocholine, 1-pentadecanoyl-2-oleoyl (d7)-sn-glycero-3-phosphocholine). This study investigated and validated whether only two PL interSTDs could be used to normalize the entire PL species in a complex bio-lipid background (i.e., urinary lipid extracts). The normalized intensities of PL ionization standards (ionSTDs) were found to have better linear regressions (R² > 0.984 for all PL subcategories) than those of traditional methods, such as total ion current and matrix-peak normalization methods. Furthermore, the intra-day precision of all the analyte concentrations after normalizing using our ionSTD method was superior to those of traditional methods. The inter-day precision of all the negatively charged analytes also differed statistically between our ionSTD and the two traditional methods. Meanwhile, a comparison of the three normalization methods revealed that the precision of all the positive analytes using the ionSTD method was comparable. Consequently, a cost-effective, fast, simple, convenient, and reliable quantitative method, defined as "qShot MALDI analysis," was developed to analyze PLs that could potentially be applied in clinical biomarker screening, especially in a negative mode.

MALDI-TOF/MS Analysis of Non-Invasive Human Urine and Saliva Samples for the Identification of New Cancer Biomarkers

Cancer represents a group of heterogeneous diseases that are a leading global cause of death. Even though mortality has decreased in the past thirty years for different reasons, most patients are still diagnosed at the advanced stage, with limited therapeutic choices and poor outcomes. Moreover, the majority of cancers are detected using invasive painful methods, such as endoscopic biopsy, making the development of non-invasive or minimally invasive methods for the discovery and fast detection of specific biomarkers a crucial need. Among body fluids, a valuable non-invasive alternative to tissue biopsy, the most accessible and least invasive are undoubtedly urine and saliva. They are easily retrievable complex fluids containing a large variety of endogenous compounds that may provide information on the physiological condition of the body. The combined analysis of these fluids with matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF/MS), a reliable and easy-to-use instrumentation that provides information with relatively simple sample pretreatments, could represent the ideal option to rapidly achieve fast early stage diagnosis of tumors and their real-time monitoring. On this basis, the present review summarizes the recently reported applications relevant to the MALDI analysis of human urine and saliva samples.

Multigeneration toxicity of Geunsami® (a glyphosate-based herbicide) to Allonychiurus kimi (Lee) (Collembola) from sub-individual to population levels

Glyphosate-based herbicide (GBH) is the most widely used herbicide worldwide and has long been considered to have significantly low toxicity to non-target soil invertebrates based on short-term toxicity tests (<56 d). However, long-term GBH toxicity assessment is necessary as GBH is repeatedly applied in the same field annually because of the advent of glyphosate-resistant crops. In this study, a multigeneration test was conducted where Allonychiurus kimi (Collembola) was exposed to GBH for three generations (referred to as F0, F1, and F2) to evaluate the long-term toxic effect. The endpoints used were adult survival and juvenile production for the individual level toxicity assessment. Phospholipid profile and population age structure were the endpoints used for sub-individual and population levels, respectively. GBH was observed to have no negative effects on adult survivals of all generations, but juvenile production was found to decrease in a concentration-dependent manner, with EC50s being estimated as 572.5, 274.8, and 59.8 mg a.i. kg-1 in the F0, F1, and F2 generations, respectively. The age structure of A. kimi population produced in the test of all generations was altered by GBH exposure, mainly because of the decrease in the number of young juveniles. Further, differences between the phospholipid profiles of the control and GBH treatments became apparent over generations, with PA 16:0, PA 12:0, and PS 42:0 lipids not being detected at the highest concentration of 741 mg kg-1 in F2. Considering all our findings from sub-individual to population levels, repeated and long-term use of GBH could have significantly higher negative impacts on non-target soil organisms than expected.

Molecular tissue profiling by MALDI imaging: recent progress and applications in cancer research

Matrix-assisted laser desorption/ionization (MALDI) imaging is an emergent technology that has been increasingly adopted in cancer research. MALDI imaging is capable of providing global molecular mapping of the abundance and spatial information of biomolecules directly in the tissues without labeling. It enables the characterization of a wide spectrum of analytes, including proteins, peptides, glycans, lipids, drugs, and metabolites and is well suited for both discovery and targeted analysis. An advantage of MALDI imaging is that it maintains tissue integrity, which allows correlation with histological features. It has proven to be a valuable tool for probing tumor heterogeneity and has been increasingly applied to interrogate molecular events associated with cancer. It provides unique insights into both the molecular content and spatial details that are not accessible by other techniques, and it has allowed considerable progress in the field of cancer research. In this review, we first provide an overview of the MALDI imaging workflow and approach. We then highlight some useful applications in various niches of cancer research, followed by a discussion of the challenges, recent developments and future prospect of this technique in the field.

High level of phosphatidylcholines/lysophosphatidylcholine ratio in urine is associated with prostate cancer

The altered levels of phospholipids (PLs) and lysophospholipids (LPLs) in prostate cancer (CaP) and benign tissues in our previous findings prompted us to explore PLs and LPLs as potential biomarkers for CaP. Urinary lipidomics has attracted increasing attention in clinical diagnostics and prognostics for CaP. In this study, 31 prostate tissues obtained from radical prostatectomy were assessed using high‐resolution matrix‐assisted laser desorption/ionization imaging mass spectrometry (HR‐MALDI‐IMS). Urine samples were collected after digital rectal examination (DRE), and urinary lipids were extracted using the acidified Bligh‐Dyer method. The discovery set comprised 75 patients with CaP and 44 with benign prostatic hyperplasia (BPH) at Kyoto University Hospital; the validation set comprised 74 patients with CaP and 59 with BPH at Osaka University Hospital. Urinary lipidomic screening was performed using MALDI time‐of‐flight MS (MALDI‐TOF/MS). The levels of urinary lysophosphatidylcholine (LPC) and phosphatidylcholines (PCs) were compared between the CaP and BPH groups. The (PC [34:2] + PC [34:1])/LPC (16:0) ratio was significantly higher (P < .001) in CaP tissues than in benign epithelial tissues. The urinary PCs/LPC ratio was significantly higher (P < .001) in the CaP group than in the BPH group in the discovery and validation sets.

Experimental and Computational Study of Aminoacridines as MALDI(-)-MS Matrix Materials for the Analysis of Complex Samples

Monoaminoacridines (1-, 2-, 3-, 4-, and 9-aminoacridine) were studied for suitability as matrices in the negative ion mode matrix-assisted laser desorption/ionization mass spectrometry (MALDI(-)-MS) analysis of various samples. This is the first study to examine 1-, 2-, and 4-aminoacridine as potential matrix material candidates for MALDI(-)-MS. In addition, spectral (UV-Vis absorption and fluorescence), proton transfer-related (basicity and autoprotolysis), and crystallization properties of these compounds were characterized experimentally and/or computationally. For testing the capabilities of these aminoacridines as matrix materials, four samples related to cultural heritage materials-stearic acid, colophony resin, dyer's madder dye, and a resinous case-study sample from a shipwreck-were analyzed with MALDI(-)-MS. A novel algorithm (implemented as an executable Python script) for MS data analysis was developed to compare the five matrix materials and to help mass spectrometrists rapidly identify peaks originating from the sample and matrix material. It was determined that all five of the studied aminoacridines can successfully be used as matrix materials in MALDI(-)-MS analysis. As an interesting finding, in several cases, the best mass spectra were obtained by using a relatively small amount of matrix material mixed with an excess amount of sample. 3- and 4-aminoacridine outperformed the other aminoacridines in the ease of obtaining acceptable spectra, average number of ions identified in the mass spectra, and low dependence of the sample-to-matrix mass ratio on experimental results.

A narrative review of urinary phospholipids: from biochemical aspect towards clinical application

As a newly emerged discipline, lipidomic studies have focused on the comprehensive characterization and quantification of lipids in a given biological system, which has remarkably advanced in recent years owing to the rapid development of analytical techniques, especially mass spectrometry. Among diverse lipid classes, phospholipids, which have fundamental roles in the formation of cellular membranes, signaling processes, and bioenergetics have gained momentum in several fields of research. The altered composition, concentration, spatial distribution, and metabolism of phospholipids in cells, tissues, and body fluids have been elucidated in various human diseases such as cancer, inflammation, as well as cardiovascular and metabolic disorders. Among the different kinds of phospholipid sources in the human body, urine has not been extensively investigated in recent years owing to the extremely low concentrations of phospholipids and high levels of salts and other contaminants, which can interfere with precise detection. However, with profound advances and rapid expansion in analytical methods, urinary phospholipids have attracted increasing attention in current biomedical research as urine is an easily available source for the discovery of noninvasive biomarkers. In this review, we provide an overview of urinary phospholipids, including their biochemical aspects and clinical applications, aimed at promoting this field of research.

Designing Nanoparticle-based Drug Delivery Systems for Precision Medicine

Traditional drugs are facing bottlenecks of lower solubility, absorption, and especially the inefficient organs or cells targeting during the precision medicine era. It is urgently needed to discover and establish new methods or strategies to modify old drugs or create new ones against the above defects. With the support of nanotechnology, the solubility, absorption and targeting of traditional drugs were greatly improved by modifying and fabricating with various types of nanoparticles to some extent, though many shortages remain. In this mini-review we will focus on advances in several most commonly used nanoparticles, from their nature and design, to drug delivery system and clinical application, that they overcome heterogeneous barriers in precision medicine, thereby ultimately improve patient outcome overall.

Fatty Acid Composition of the Lipids from Atlantic Salmon-Comparison of Two Extraction Methods without Halogenated Solvents

The scope of this paper was to apply two recently developed methods for lipid extraction: the methyl tert-butyl ether (MTBE) method and the BUME method. These two methods do not include halogenated solvents, which makes them less hazardous to the environment, less toxic, and needed in less volume compared to the standard methods for lipid extraction. Fatty acid composition of the lipids from Atlantic salmon (Salmo salar Linnæus, 1758) was obtained by both procedures. The methods were effective and thirty-three fatty acids were identified. The amounts of the omega-3 polyunsaturated fatty acids obtained by the MTBE method were found to be similar to the overall mean values observed in farmed salmon. The yield of the total lipids obtained by the BUME method was 13% lower. Although the methods involved different solvents, they showed similar fatty acids profile of the lipids from Atlantic salmon. Both methods were validated and some practical challenges were discussed.

De novo synthesis of phospholipids and sphingomyelin in multipotent stromal cells - Monitoring studies by mass spectrometry

Musculoskeletal diseases are extremely widespread and a significant burden on the health systems of the industrialized countries. The use of mesenchymal stromal cells is a promising approach to cure cartilage and tendon injuries, which often also occur in younger people as consequences of sport accidents. Although particular interest is on the collagen and the glycosaminoglycan composition of the tendon and potential alterations compared to healthy tissue, there is nowadays also increasing evidence that some selected phospholipids (PL) are potential mediators of tissue regeneration. Therefore, PL (and potential changes thereof) attract increasing interest in this field. We have used positive and negative ion matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) to elucidate the lipid compositions of human mesenchymal stromal cells in dependence on the composition of the cell culture medium and the cultivation time. The de novo biosynthesis of PL was monitored by adding ¹³C labeled glucose or deuterated palmitic acid (d₃₁-PA) to the cells and the incorporation of ¹³C or ²H into the different PL classes was investigated by electrospray ionization (ESI) mass spectrometry (MS). It is remarkable that all PL classes (for instance, phosphatidylcholine and -inositol) exhibited ¹³C incorporation - but not the sphingomyelin (SM) which is the most abundant sphingolipid in the majority of human tissues and body fluids. Using suitable internal standards it could be shown, that only ¹²C-containing SM is de novo generated while no ¹³C-labeled SM could be monitored - independent of the cultivation time, which was varied between 7 and 28 days. SM impurities stemming from the cell culture medium and the used MALDI matrix compounds (2,5-dihydroxybenzoic acid (DHB) or 9-aminoacridine (9-AA)) could be ruled out. However, incorporation of deuterated palmitic acid (d₃₁-PA) could be observed for multiple PL, including SM. Therefore, it is suggested that there must exist another, so far unknown SM biosynthesis pathway. This pathway does not make use of glucose but relies on the use of other molecules as energy sources. Potential pathways to explain the experimental observations are discussed.

Characterization of glycerophospholipid molecular species in muscles from three species of cephalopods by direct infusion-tandem mass spectrometry

More than 200 molecular species of glycerophospholipids (GP) including glycerophosphocholine (GPC), glycerophosphoethanolamine (GPE), glycerophosphoserine (GPS), lysoglycerophosphocholine (LGPC), lysoglycerophosphoethanolamine (LGPE) and lysoglycerophosphoserine (LGPS), as well as 18 kinds of sphingomyelin (SM) were characterized by using a direct infusion-tandem mass (MS/MS) spectrometry method for lipids from the muscles of cephalopods Sepiella maindroni, Octopus ocellatus and Loligo chinensis for the first time. The majority of the GP molecular species contained long-chain omega-3 polyunsaturated fatty acids (n-3 LC-PUFA), especially eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). Therefore, cephalopods can be a good possible source of dietary GP carrying n-3 LC-PUFA. The total lipids were composed of phospholipid (PL, 72.29-83.32 wt% of total lipids), cholesterol (12.70-23.60 wt% of total lipids), triacylglycerol (1.86-2.93 wt% of total lipids), diacylglycerol (0.15-1.09 wt% of total lipids), monoacylglycerol (0.06-0.18 wt% of total lipids) and free fatty acid (0.72-1.86 wt% of total lipids). For PL, phosphatidylcholine (44.47-62.30 mol%), phosphatidylethanolamine (22.57-39.08 mol%), phosphatidylserine (6.15-10.18 mol%), phosphatidylglycerol (0.68-3.11 mol%), phosphatidylinositol (2.41-7.15 mol%) and lysophosphatidylcholine (1.84-5.24 mol%) were detected. Furthermore, the total lipids from the muscles of cephalopods Sepiella maindroni, Octopus ocellatus and Loligo chinensis contained 41.80-50.02 mol% of saturated fatty acids, 11.53-21.54 mol% of monounsaturated fatty acids and 36.67-40.82 mol% of PUFA, whilst DHA (15.25-26.71 mol%) and EPA (6.29-16.57 mol%) were found to account for the majority of the PUFA. With these data presented, cephalopod muscle can be considered as a healthy food for humans.

Data processing on a comparative evaluation of the extraction and analysis procedures for urinary phospholipid and lysophospholipid using MALDI-TOF/MS

In this dataset we provide MALDI-TOF/MS spectra for the testing and application of a quantitative method using external ionization standards (ionization STDs) for peak-intensity normalization. The presented data is related to our recent article entitled “a comparative evaluation of the extraction and analysis procedures for urinary phospholipid and lysophospholipid using MALDI-TOF/MS”. Gradient dilutions of mixture containing thirteen phospho- and lysophospho-lipid species (internal STDs) were mixed with constant concentration of the ionization STDs and analyzed together. Peak intensities of the internal and ionization STDs were picked by a homemade workflow based on OpenMS (steps including noise filtration, baseline subtraction and peak-picking). The peak-intensity ratios between the internal and ionization STDs were linearly correlated with their concentration ratios. Using this method, the evaluation of efficiencies of six different lipid extraction methods was performed in urine samples. In summary, a free and easy-to-use method for phospholipid and lysophospholipid quantitative analysis based on MALDI-TOF/MS is provided in this article.