High-Throughput Phospholipidic Fingerprinting by Online Desorption of Dried Spots and Quadrupole-Linear Ion Trap Mass Spectrometry: Evaluation of Atherosclerosis Biomarkers in Mouse Plasma

Use of information dependent acquisition mass spectra and sequential window acquisition of all theoretical fragment-ion mass spectra for fruit juices metabolomics and authentication

INTRODUCTION

LC-MS based untargeted metabolomics are the main untargeted methods used for juice metabolomics to solve the authentication problem faced in fruit juice industry.

OBJECTIVES

To evaluate the performances of different untargeted metabolomics methods on fruit juices metabolomics and authentication, orange and apple fruit juices were selected for this study.

METHODS

IDA-MS and SWATH-MS based on UHPLC-QTOF were used for the metabolomics and authenticity determination of apple and orange juices, including the lab-made samples of oranges (Citrus sinensis Osb.) from Jiangxi Province, apples (Malus domestica Borkh) from Shandong Province, and different brands of commercial orange and apple juice samples from markets.

RESULTS

IDA-MS and SWATH-MS could both acquire numerous MS1 features and MS2 information of juice components, while SWATH-MS excels at the acquisition rate of MS2. Distinctive separation between authentic orange juice and not authentic orange juice could be seen from principal component analysis and hierarchical clustering analysis based on both IDA-MS and SWATH-MS. After analysis of variance, fold change analysis and orthogonal projection to latent structures discriminant mode, 53 and 46 potential markers were defined by IDA-MS and SWATH-MS (with 77.4% and 100% MS2 acquisition rate) separately. Subsequently, these potential markers were putatively annotated using general chemical databases with 6 more annotated by SWATH-MS. Furthermore, 7 of the potential markers, l-asparagine, umbelliferone, glucosamine, phlorin, epicatechin, phytosphingosine and chlorogenic acid, were identified with standards. For the consideration of model simplicity, two determined makers (umbelliferone and chlorogenic acid) were selected to construct the DD-SIMCA model in commercial samples because of their good correlation with apple adulteration proportion, and the sensitivity and specificity of the model were 100% and 95%.

CONCLUSION

SWATH-MS excels at the MS2 acquisition of juice components and potential markers. This study provides an overall performance comparison between IDA-MS and SWATH-MS, and guidance for the method selection on fruit juice metabolomics and juice authenticity determination. Two of the potential markers determined, umbelliferone and chlorogenic acid, could be used as apple juice indicators in orange juice.

Toward the Rational Design of Universal Dual Polarity Matrix for MALDI Mass Spectrometry

A series of novel anthranilic acid derivatives I-IV, of which COOH-NH₂ (I) and COOH-NHMe (IV) are endowed with acid and base bifunctionality, were designed and synthesized for matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry applications in dual polarity molecular imaging of biological samples, particularly for lipids. The heat of protonation, deprotonation, and proton transfer reaction as well as the capability of analyzing biomolecules in both positive and negative ion modes for I-IV were systematically investigated under standard 355 nm laser excitation. The results indicate correlation between dual polarity and acid-base property. Further, COOH-NHMe (IV) showed a unique performance and was successfully applied as the matrix for MALDI-TOF mass spectrometry imaging (MSI) for studying the mouse brain. Our results demonstrate the superiority of COOH-NHMe (IV) in detecting more lipid and protein species compared to commercially available matrices. Moreover, MALDI-TOF MSI results were obtained for lipid distributions, making COOH-NHMe (IV) a potential next generation universal matrix.

Relative quantitation of phosphatidylcholines with interfered masses of protonated and sodiated molecules by tandem and Fourier-transform ion cyclotron resonance mass spectrometry

The present work deals with deconvolution of interfered peaks of protonated and sodiated phosphatidylcholines to solve the problem of relative quantitation of these compounds. The method was developed based on the fact that adducts of phosphatidylcholines with proton and sodium ion give unique characteristic peaks in tandem mass spectrometry. Ultra-high-resolution Fourier-transform ion cyclotron resonance mass spectrometry was used to resolve interfered peaks and thus validate the results of tandem mass spectrometry-based deconvolution. Applicability of the method was tested with synthesized phosphatidylcholines and applied for tissue-spray analysis of the clinical samples and demonstrated good correlation (0.996) between MS/MS and Fourier-transform ion cyclotron resonance mass spectrometry results.

Phospholipids as cancer biomarkers: Mass spectrometry-based analysis

Lipids, particularly phospholipids (PLs), are key components of cellular membrane. PLs play important and diverse roles in cells such as chemical-energy storage, cellular signaling, cell membranes, and cell-cell interactions in tissues. All these cellular processes are pertinent to cells that undergo transformation, cancer progression, and metastasis. Thus, there is a strong possibility that some classes of PLs are expected to present in cancer cells and tissues in cellular physiology. The mass spectrometric soft-ionization techniques, electrospray ionization (ESI), and matrix-assisted laser desorption/ionization (MALDI) are well-established in the proteomics field, have been used for lipidomic analysis in cancer research. This review focused on the applications of mass spectrometry (MS) mainly on ESI-MS and MALDI-MS in the structural characterization, molecular composition and key roles of various PLs present in cancer cells, tissues, blood, and urine, and on their importance for cancer-related problems as well as challenges for development of novel PL-based biomarkers. The profiling of PLs helps to rationalize their functions in biological systems, and will also provide diagnostic information to elucidate mechanisms behind the control of cancer, diabetes, and neurodegenerative diseases. The investigation of cellular PLs with MS methods suggests new insights on various cancer diseases and clinical applications in the drug discovery and development of biomarkers for various PL-related different cancer diseases. PL profiling in tissues, cells and body fluids also reflect the general condition of the whole organism and can indicate the existence of cancer and other diseases. PL profiling with MS opens new prospects to assess alterations of PLs in cancer, screening specific biomarkers and provide a basis for the development of novel therapeutic strategies. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 37:107-138, 2018.

Proteome and Metabolome of Subretinal Fluid in Central Serous Chorioretinopathy and Rhegmatogenous Retinal Detachment: A Pilot Case Study

PURPOSE

To investigate the molecular composition of subretinal fluid (SRF) in central serous chorioretinopathy (CSCR) and rhegmatogenous retinal detachment (RRD) using proteomics and metabolomics.

METHODS

SRF was obtained from one patient with severe nonresolving bullous CSCR requiring surgical subretinal fibrin removal, and two patients with long-standing RRD. Proteins were trypsin-digested, labeled with Tandem-Mass-Tag and fractionated according to their isoelectric point for identification and quantification by tandem mass spectrometry. Independently, metabolites were extracted on cold methanol/ethanol, and identified by untargeted ultra-high performance liquid chromatography and high-resolution mass spectrometry. Bioinformatics analyses were conducted.

RESULTS

In total, 291 proteins and 651 metabolites were identified in SRF samples. Compared with RRD, 128 proteins (77 downregulated; 51 upregulated) and 76 metabolites (43 downregulated; 33 upregulated) differed in the SRF from CSCR. Protein and metabolites notably deregulated in CSCR were related to glycolysis/gluconeogenesis, inflammation (including serum amyloid P component, versican), alternative complement pathway (complement factor H and complement factor H-related protein), cellular adhesion, biliary acid metabolism (farnesoid X receptor/retinoid X receptor), and gluco- and mineralocorticoid systems (aldosterone, angiotensin, and corticosteroid-binding globulin).

CONCLUSIONS

Proteomics and metabolomics can be performed on SRF. A unique SRF sample from CSCR exhibited a distinct molecular profile compared with RRD.

TRANSLATIONAL RELEVANCE

This first comparative multiomics analysis of SRF improved the understanding of CSCR and RRD pathophysiology. It identified pathways potentially involved in the better photoreceptor preservation in CSCR, suggesting neuroprotective targets that will require additional confirmation.

Mass spectrometry for the evaluation of cardiovascular diseases based on proteomics and lipidomics

The identification and quantification of proteins and lipids is of major importance for the diagnosis, prognosis and understanding of the molecular mechanisms involved in disease development. Owing to its selectivity and sensitivity, mass spectrometry has become a key technique in analytical platforms for proteomic and lipidomic investigations. Using this technique, many strategies have been developed based on unbiased or targeted approaches to highlight or monitor molecules of interest from biomatrices. Although these approaches have largely been employed in cancer research, this type of investigation has been met by a growing interest in the field of cardiovascular disorders, potentially leading to the discovery of novel biomarkers and the development of new therapies. In this paper, we will review the different mass spectrometry- based proteomic and lipidomic strategies applied in cardiovascular diseases, especially atherosclerosis. Particular attention will be given to recent developments and the role of bioinformatics in data treatment. This review will be of broad interest to the medical community by providing a tutorial of how mass spectrometric strategies can support clinical trials.

Myoglobinemia markers with potential applications in forensic sample analysis: lipid markers in myoglobinemia for postmortem blood

The crush syndrome, in which rhabdomyolysis and trauma occur as a result of heat stroke and drug intoxication, can lead to myoglobinemia. This condition can be diagnosed by measuring myoglobin (Mb) levels in blood and urine. However, postmortem Mb levels are unreliable indicators, since blood Mb concentration drastically increases within a very short time after death and urine cannot always be obtained at dissection; this makes it difficult to diagnose myoglobinemia in a corpse. To address this issue, in this study, we used a lipidomics approach to identify markers that can be used to detect myoglobinemia in postmortem blood samples. We found that increases in levels of fatty acid oxides such as stearic, oleic, linoleic, and arachidonic acid and decreases in levels of plasmalogens and phosphatidylethanolamine in the blood were associated with high Mb level. These results demonstrate that postmortem samples are amenable to lipidomics analysis and provide a set of markers other than Mb that can be used for postmortem diagnosis of myoglobinemia.

Dynamic and temporal assessment of human dried blood spot MS/MSALL shotgun lipidomics analysis

BACKGROUND

Real-time and dynamic assessment of an individual's lipid homeostatic state in blood is complicated due to the need to collect samples in a clinical environment. In the context of precision medicine and population health, tools that facilitate sample collection and empower the individual to participate in the process are necessary to complement advanced bioanalytical analysis. The dried blood spot (DBS) methodology via finger prick or heel prick is a minimally invasive sample collection method that allows the relative ease and low cost of sample collection as well as transport. However, it has yet to be integrated into broad scale personalized lipidomic analysis. Therefore, in this study we report the development of a novel DBS high resolution MS/MSALL lipidomics workflow.

METHODS

In this report we compared lipidomic analysis of four types of blood sample collection methods (DBS, venous whole blood, serum, and plasma) across several parameters, which include lipidomics coverage of each matrix and the effects of temperature and time on the coverage and stability of different lipid classes and molecular species. The novel DBS-MS/MSALL lipidomics platform developed in this report was then applied to examine postprandial effects on the blood lipidome and further to explore the temporal fluctuation of the lipidome across hours and days.

RESULTS

More than 1,200 lipid molecular species from a single DBS sample were identified and quantified. The lipidomics profile of the DBS samples is comparable to whole blood matrix. DBS-MS/MSALL lipidomic analysis in postprandial experiments revealed significant alterations in triacylglyceride species. Temporal analysis of the lipidome at various times in the day and across days identified several lipid species that fluctuate as a function of time, and a subset of lipid species were identified to be significantly altered across hours within a day and within successive days of the week.

CONCLUSIONS

A novel DBS-MS/MSALL lipidomics method has been established for human blood. The feasibility and application of this method demonstrate the potential utility for lipidomics analysis in both healthy and diverse diseases states. This DBS MS-based lipidomics analysis represents a formidable approach for empowering patients and individuals in the era of precision medicine to uncover novel biomarkers and to monitor lipid homeostasis.

Effects of fatty acyl chain length, double-bond number and matrix on phosphatidylcholine responses in matrix-assisted laser desorption/ionization on an Orbitrap mass spectrometer

RATIONALE

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is used for the fast qualitative and quantitative analysis of phosphatidylcholines (PC). Fatty acyl chain lengths and the number of double bonds (DB) affect relative responses of PC; hence the determination of correction factors of individual PC is important for the accurate quantitation. The signal intensity in MALDI-MS strongly depends on the matrix; therefore, the following matrices typically used in lipidomics are studied in the present work: 2,5-dihydroxybenzoic acid (DHB), 1,5-diaminonaphthalene (DAN) and 9-aminoacridine (9AA).

METHODS

Series of PC with various fatty acyl chain lengths are synthesized for this study. PC concentrations over two orders of magnitude are studied with MALDI-MS. These experiments provide sets of calibration curves for each of the synthesized PC and the further analysis of parameters of calibration curves is performed.

RESULTS

Correction factors for PC decrease with increasing fatty acyl chain length for all matrices. These dependences are steeper for unsaturated PC than for saturated ones. MALDI matrices also have a significant effect on this dependence. The weakest dependence on fatty acyl chain length is found for saturated PC in 9AA. In the case of the other matrices, the effect of fatty acyl chain length on the response is essential for both saturated and unsaturated PC. Calibration curves and parameters of calibration curves for both saturated and monounsaturated PC are fitted by a linear function with regression coefficients decreasing in the order 9AA > DAN > DHB.

CONCLUSIONS

Differences in relative responses for PC in MALDI-MS measurements must be taken into account for accurate quantitation. Parameters of calibration curves can be used for the determination of PC concentrations using a single internal standard (IS). This method gives good results for the 9AA matrix, but the reproducibility of measurements for the DHB and DAN matrices is lower and the method can be used for a rough estimation only. These matrices are less convenient for the quantitation of PC.

Potential missing steps for a wide use of dried matrix spots in biomedical analysis

Microsampling, mainly as DBS, has been significantly expanded in the biomedical and pharmaceutical communities in the last 10 years. In parallel, technology and methodology have evolved to overcome some of the issues associated with this sampling procedure. Despite the continuous developments and interest, only a few validated and routinely implemented clinical applications have arisen beyond the initial inborn screening. Based on the latest developments in this field, this perspective aims to discuss some of the missing steps (i.e., the habits to change, the Health Authorities acceptance and the shift for dried plasma generation), which may turn the current use of microsampling into an established and standard procedure in clinical and pharmaceutical analysis.

Mass spectrometry analysis of blood plasma lipidome as method of disease diagnostics, evuation of effectiveness and optimization of drug therapy

A new method for the analysis of blood lipid based on direct mass spectrometry of lipophilic low molecular weight fraction of blood plasma has been considered. Such technique allows quantification of hundreds of various types of lipids and this changes existing concepts on diagnostics of lipid disorders and related diseases. The versatility and quickness of the method significantly simplify its wide use. This method is applicable for diagnostics of atherosclerosis, diabetes, cancer and other diseases. Detalization of plasma lipid composition at the molecular level by means of mass spectrometry allows to assess the effectiveness of therapy and to optimize the drug treatment of cardiovascular diseases by phospholipid preparations.

Application of direct-infusion ESI–MS/MS for toxicological screening

Background: Direct-infusion ESI–MS/MS is a powerful approach for the identification of substances in complex mixtures. The aim of this work was to investigate its applicability to the toxicological screening of blood samples. A simple protein precipitation was used, followed by a 15 min infusion of the extract in the mass spectrometer. Results: The application of the procedure to commercial quality controls and authentic post-mortem blood samples demonstrated that the direct-infusion ESI–MS/MS approach enables the simultaneous identification of substances that require different chromatographic conditions. However, poor sensitivity was observed for benzodiazepine, amphetamines and opiate compounds. Conclusion: Considering the facile implementation and positive performance of direct-infusion ESI–MS/MS, this approach may to be a valuable complementary technique for systematic toxicological analysis procedures.

Variation of the detergent-binding capacity and phospholipid content of membrane proteins when purified in different detergents

Purified membrane proteins are ternary complexes consisting of protein, lipid, and detergent. Information about the amounts of detergent and endogenous phospholipid molecules bound to purified membrane proteins is largely lacking. In this systematic study, three model membrane proteins of different oligomeric states were purified in nine different detergents at commonly used concentrations and characterized biochemically and biophysically. Detergent-binding capacities and phospholipid contents of the model proteins were determined and compared. The insights on ternary complexes obtained from the experimental results, when put into a general context, are summarized as follows. 1), The amount of detergent and 2) the amount of endogenous phospholipids bound to purified membrane proteins are dependent on the size of the hydrophobic lipid-accessible protein surface areas and the physicochemical properties of the detergents used. 3), The size of the detergent and lipid belt surrounding the hydrophobic lipid-accessible surface of purified membrane proteins can be tuned by the appropriate choice of detergent. 4), The detergents n-nonyl-β-D-glucopyranoside and Cymal-5 have exceptional delipidating effects on ternary complexes. 5), The types of endogenous phospholipids bound to membrane proteins can vary depending on the detergent used for solubilization and purification. 6), Furthermore, we demonstrate that size-exclusion chromatography can be a suitable method for estimating the molecular mass of ternary complexes. The findings presented suggest a strategy to control and tune the numbers of detergent and endogenous phospholipid molecules bound to membrane proteins. These two parameters are potentially important for the successul crystallization of membrane proteins for structure determination by crystallographic approaches.

State-of-the-art dried blood spot analysis: an overview of recent advances and future trends

Dried blood spots have become a popular method in a variety of micro blood-sampling techniques in the life sciences sector, consequently competing with the field of conventional, invasive blood sampling by venepuncture. Dried blood spots are widely applied in numerous bioanalytical assays and have gained a significant role in the screening of inherited metabolic diseases, in PK and PD modeling; in the treatment and diagnosis of infectious diseases; and in therapeutic drug monitoring. Recent technological developments such as automation, online extraction, mass spectrometric direct analysis and also conventional dried blood spot bioanalysis, as well as future developments in dried blood spot bioanalysis are highlighted and presented in this article.

Histology-driven data mining of lipid signatures from multiple imaging mass spectrometry analyses: application to human colorectal cancer liver metastasis biopsies

Imaging mass spectrometry (IMS) represents an innovative tool in the cancer research pipeline, which is increasingly being used in clinical and pharmaceutical applications. The unique properties of the technique, especially the amount of data generated, make the handling of data from multiple IMS acquisitions challenging. This work presents a histology-driven IMS approach aiming to identify discriminant lipid signatures from the simultaneous mining of IMS data sets from multiple samples. The feasibility of the developed workflow is evaluated on a set of three human colorectal cancer liver metastasis (CRCLM) tissue sections. Lipid IMS on tissue sections was performed using MALDI-TOF/TOF MS in both negative and positive ionization modes after 1,5-diaminonaphthalene matrix deposition by sublimation. The combination of both positive and negative acquisition results was performed during data mining to simplify the process and interrogate a larger lipidome into a single analysis. To reduce the complexity of the IMS data sets, a sub data set was generated by randomly selecting a fixed number of spectra from a histologically defined region of interest, resulting in a 10-fold data reduction. Principal component analysis confirmed that the molecular selectivity of the regions of interest is maintained after data reduction. Partial least-squares and heat map analyses demonstrated a selective signature of the CRCLM, revealing lipids that are significantly up- and down-regulated in the tumor region. This comprehensive approach is thus of interest for defining disease signatures directly from IMS data sets by the use of combinatory data mining, opening novel routes of investigation for addressing the demands of the clinical setting.

Storage of oral fluid as dried spots on alginate and chitosan foam – a new concept for oral fluid collection

Background: In recent years, there has been a major focus on analyzing drug substances from dried µl volumes of biological fluids, commonly known as dried matrix spotting. Results: 10 µl oral fluid, spiked with five basic drugs, was collected and stored as dried spots on alginate and chitosan foam, and subsequently dissolved; the drugs were thereafter isolated with electromembrane extraction and analyzed by LC–MS. The correlation coefficients were above 0.9885 for all drugs in the range 25–1000 ng/ml. The reported RSD values were below 15%. Conclusion: Storage of oral fluid as dried spots on alginate and chitosan foam have been investigated for the first time. The extract obtained after electromembrane extraction was directly compatible with LC–MS, and apparently free from coextracted matrix components.

Simultaneous profiling of polar lipids by supercritical fluid chromatography/tandem mass spectrometry with methylation

Supercritical fluid chromatography/tandem mass spectrometry (SFC/MS/MS) with methylation was used for the simultaneous profiling of diverse polar lipids in a mixture. A high throughput, high resolution analysis of nineteen classes of polar lipids including phospholipids, lysophospholipids, and sphingolipids was performed in 6 min. Methylation by trimethylsilyl-diazomethane suppressed peak tailing and improved detection sensitivity of phosphatidylserine (PS), phosphatidic acid (PA), lysophosphatidylserine (LPS), lysophosphatidylinositol (LPI), lysophosphatidic acid (LPA), ceramide-1-phosphate (Cer1P), sphingosine-1-phosphate (So1P), and sphinganine-1-phosphate (Sa1P). The limits of detection for PS, PA, LPS, LPI, LPA, Cer1P, So1P, and Sa1P were enhanced 7.5-, 26.7-, 600-, 116.7-, 500-, 75-, 3000-, and 4500-fold, respectively. Global qualitative and quantitative analysis of not only the high-abundance species but also the low-abundance species in the polar lipids was achieved. When the method was applied to mouse liver, 4 PSs, 24 PAs, 3 lysophosphatidylethanolamines, 11 LPSs, 6 lysophosphatidylglycerols, 4 LPIs, 13 LPAs, 7 sphingomyelins, 11 Cer1Ps, So1P, and Sa1P were additionally analyzed. Furthermore, the quantification of various molecular species in each polar lipid was carried out.

A reversed-phase capillary ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) method for comprehensive top-down/bottom-up lipid profiling

Lipidomics is a critical part of metabolomics and aims to study all the lipids within a living system. We present here the development and evaluation of a sensitive capillary UPLC-MS method for comprehensive top-down/bottom-up lipid profiling. Three different stationary phases were evaluated in terms of peak capacity, linearity, reproducibility, and limit of quantification (LOQ) using a mixture of lipid standards representative of the lipidome. The relative standard deviations of the retention times and peak abundances of the lipid standards were 0.29% and 7.7%, respectively, when using the optimized method. The linearity was acceptable at >0.99 over 3 orders of magnitude, and the LOQs were sub-fmol. To demonstrate the performance of the method in the analysis of complex samples, we analyzed lipids extracted from a human cell line, rat plasma, and a model human skin tissue, identifying 446, 444, and 370 unique lipids, respectively. Overall, the method provided either higher coverage of the lipidome, greater measurement sensitivity, or both, when compared to other approaches of global, untargeted lipid profiling based on chromatography coupled with MS.

Oral flurbiprofen metabolic ratio assessment using a single-point dried blood spot

We investigated whether a single blood measurement using the minimally invasive technique of a finger prick to draw a blood sample of 5 µl (to yield a dried blood spot (DBS)) is suitable for the assessment of flurbiprofen (FLB) metabolic ratio (MR). Ten healthy volunteers who had been genotyped for CYP2C9 were recruited as subjects. They received FLB alone in session 1 and FLB with fluconazole in session 2. In session 3, the subjects were pretreated for 4 days with rifampicin and received FLB with the last dose of rifampicin on day 5. Plasma and DBS samples were obtained between 0 and 8 h after FLB administration, and urine was collected during the 8 h after administration. The pharmacokinetic profiles of the drugs were comparable in DBS and plasma. FLB's apparent clearance values decreased by 35% in plasma and DBS during session 2 and increased by 75% in plasma and by 30% in DBS during session 3. Good correlations were observed between MRs calculated from urine, plasma, and DBS samples.

Tracking phospholipid profiling of muscle from Ctennopharyngodon idellus during storage by shotgun lipidomics

This paper aims to study phospholipid (PL) profiling of muscle from Ctenopharyngodon idellus during room-temperature storage for 72 h by direct-infusion electrospray ionization tandem mass spectrometry (ESI-MS/MS). Five classes of PLs, including phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylinositol (PI), phosphatidylserine (PS), and sphingomyelin (SM), were analyzed. At least 110 molecular species of PLs were identified, including 32 species of PC, 34 species of PE, 24 species of PS, 18 species of PI, and 2 species of SM. The result showed that oxidation and hydrolysis are the two main causes for the deterioration of PLs in fish muscle during storage. Most content of PL molecular species increased and then decreased gradually. However, some special PE molecular species with former low abundance, such as PE 32:1, PE 34:2, and PE 34:1, emerged during the storage in quantity. It indicated that those PE molecular species may come from the microbe bred in the muscle. This phenomenon was found and discussed for the first time. The possible relevance between the emergence of these special PE molecular species and the freshness of the fish muscle during storage will be investigated in further studies.