Accurate mass and retention time library of serum lipids for type 1 diabetes research

Challenges in Lipidomics Biomarker Identification: Avoiding the Pitfalls and Improving Reproducibility

Identification of features with high levels of confidence in liquid chromatography-mass spectrometry (LC-MS) lipidomics research is an essential part of biomarker discovery, but existing software platforms can give inconsistent results, even from identical spectral data. This poses a clear challenge for reproducibility in biomarker identification. In this work, we illustrate the reproducibility gap for two open-access lipidomics platforms, MS DIAL and Lipostar, finding just 14.0% identification agreement when analyzing identical LC-MS spectra using default settings. Whilst the software platforms performed more consistently using fragmentation data, agreement was still only 36.1% for MS2 spectra. This highlights the critical importance of validation across positive and negative LC-MS modes, as well as the manual curation of spectra and lipidomics software outputs, in order to reduce identification errors caused by closely related lipids and co-elution issues. This curation process can be supplemented by data-driven outlier detection in assessing spectral outputs, which is demonstrated here using a novel machine learning approach based on support vector machine regression combined with leave-one-out cross-validation. These steps are essential to reduce the frequency of false positive identifications and close the reproducibility gap, including between software platforms, which, for downstream users such as bioinformaticians and clinicians, can be an underappreciated source of biomarker identification errors.

Multi-omics Analyses Reveal Function of Apolipoprotein E in Alternative Splicing and Tumor Immune Microenvironment in Kidney Renal Clear Cell Carcinoma via Pan-cancer Analysis

Apolipoprotein E (APOE) regulates lipid metabolism, associated with the development of various cancers. However, its precise prognostic significance and functions in alternative splicing and the tumor immune microenvironment remain unclear. In this study, we extracted APOE expression in pan-cancer from TCGA and analyzed mRNA transcriptome, cell lines, and protein levels. Furthermore, we analyzed the alternative splicing expression of the APOE gene transcript with prognostic profiles using the OncoSplicing database. We obtained 73 common APOE genes to perform functional enrichment analysis, assess the correlation between genes and immune cells using TIMER, EPIC, and ssGSEA methods, and examine the prognostic significance using the UALCAN database. Finally, single-cell data was employed to assess the correlation between APOE genes and cell functions. Our findings revealed that APOE expression varies across different tumor types and cancer cell lines. The alternative splicing analysis demonstrated that APOE transcript expression levels have prognostic value in cancers such as LGG, KIRC, and KIRP. Functional enrichment analysis indicated significant associations between APOE and various immune cells, such as macrophages, CD8 T cells, and NK cells, with significant implications for prognosis. Moreover, single-cell data indicated that APOE was primarily expressed in renal epithelial cells among stromal cells and in macrophages among immune cells, significantly negatively correlated with five functional states. Our study represents the first comprehensive exploration of APOE's function in pan-cancers and identifies APOE as a potential biomarker in cancer pathogenesis, prognosis, and immune therapeutic target.

Recent Analytical Methodologies in Lipid Analysis

Lipids represent a large group of biomolecules that are responsible for various functions in organisms. Diseases such as diabetes, chronic inflammation, neurological disorders, or neurodegenerative and cardiovascular diseases can be caused by lipid imbalance. Due to the different stereochemical properties and composition of fatty acyl groups of molecules in most lipid classes, quantification of lipids and development of lipidomic analytical techniques are problematic. Identification of different lipid species from complex matrices is difficult, and therefore individual analytical steps, which include extraction, separation, and detection of lipids, must be chosen properly. This review critically documents recent strategies for lipid analysis from sample pretreatment to instrumental analysis and data interpretation published in the last five years (2019 to 2023). The advantages and disadvantages of various extraction methods are covered. The instrumental analysis step comprises methods for lipid identification and quantification. Mass spectrometry (MS) is the most used technique in lipid analysis, which can be performed by direct infusion MS approach or in combination with suitable separation techniques such as liquid chromatography or gas chromatography. Special attention is also given to the correct evaluation and interpretation of the data obtained from the lipid analyses. Only accurate, precise, robust and reliable analytical strategies are able to bring complex and useful lipidomic information, which may contribute to clarification of some diseases at the molecular level, and may be used as putative biomarkers and/or therapeutic targets.

Rapid quantification of 50 fatty acids in small amounts of biological samples for population molecular phenotyping

Efficient quantification of fatty-acid (FA) composition (fatty-acidome) in biological samples is crucial for understanding physiology and pathophysiology in large population cohorts. Here, we report a rapid GC-FID/MS method for simultaneous quantification of all FAs in numerous biological matrices. Within eight minutes, this method enabled simultaneous quantification of 50 FAs as fatty-acid methyl esters (FAMEs) in femtomole levels following the efficient transformation of FAs in all lipids including FFAs, cholesterol-esters, glycerides, phospholipids and sphingolipids. The method showed satisfactory inter-day and intra-day precision, stability and linearity (R2 > 0.994) within a concentration range of 2-3 orders of magnitude. FAs were then quantified in typical multiple biological matrices including human biofluids (urine, plasma) and cells, animal intestinal content and tissue samples. We also established a quantitative structure-retention relationship (QSRR) for analytes to accurately predict their retention time and aid their reliable identification. We further developed a novel no-additive retention index (NARI) with endogenous FAMEs reducing inter-batch variations to 15 seconds; such NARI performed better than the alkanes-based classical RI, making meta-analysis possible for data obtained from different batches and platforms. Collectively, this provides an inexpensive high-throughput analytical system for quantitative phenotyping of all FAs in 8-minutes multiple biological matrices in large cohort studies of pathophysiological effects.

Hepatoviruses promote very-long-chain fatty acid and sphingolipid synthesis for viral RNA replication and quasi-enveloped virus release

Virus-induced changes in host lipid metabolism are an important but poorly understood aspect of viral pathogenesis. By combining nontargeted lipidomics analyses of infected cells and purified extracellular quasi-enveloped virions with high-throughput RNA sequencing and genetic depletion studies, we show that hepatitis A virus, an hepatotropic picornavirus, broadly manipulates the host cell lipid environment, enhancing synthesis of ceramides and other sphingolipids and transcriptionally activating acyl-coenzyme A synthetases and fatty acid elongases to import and activate long-chain fatty acids for entry into the fatty acid elongation cycle. Phospholipids with very-long-chain acyl tails (>C22) are essential for genome replication, whereas increases in sphingolipids support assembly and release of quasi-enveloped virions wrapped in membranes highly enriched for sphingomyelin and very-long-chain ceramides. Our data provide insight into how a pathogenic virus alters lipid flux in infected hepatocytes and demonstrate a distinction between lipid species required for viral RNA synthesis versus nonlytic quasi-enveloped virus release.

Metabolic remission precedes possible weight regain after gastric bypass surgery

OBJECTIVE

Some patients regain weight to a variable extent from 1 year after Roux-en-Y gastric bypass surgery (RYGB), though rarely reaching preoperative values. The aim of the present study was to investigate whether, when, and to what extent metabolic remission occurs.

METHODS

Fasting metabolite and lipid profiles were determined in blood plasma collected from a nonrandomized intervention study involving 148 patients before RYGB and at 2, 12, and 60 months post RYGB. Both short-term and long-term alterations in metabolism were assessed. Anthropometric and clinical variables were assessed at all study visits.

RESULTS

This study found that the vast majority of changes in metabolite levels occurred during the first 2 months post RYGB. Notably, thereafter the metabolome started to return toward the presurgical state. Consequently, a close-to-presurgical metabolome was observed at the time when patients reached their lowest weight and glucose level. Lipids with longer acyl chains and a higher degree of unsaturation were altered more dramatically compared with shorter and more saturated lipids, suggesting a systematic and reversible lipid remodeling.

CONCLUSIONS

Remission of the metabolic state was observed prior to notable weight regain. Further and more long-term studies are required to assess whether the extent of metabolic remission predicts future weight regain and glycemic deterioration.

Intensity-dependent mass search for improving metabolite database matches in chemical isotope labeling LC-QTOF-MS-based metabolomics

Liquid chromatography mass spectrometry (LC-MS) has been increasingly used for metabolome analysis. One of the critical steps in the LC-MS metabolome analysis workflow is related to metabolite identification. Among the measured parameters, peak mass is commonly used to search against a database for potential metabolite matches. Higher accuracy mass measurement allows the use of a narrower mass tolerance window for mass search. While various types of mass analyzers can routinely measure a peak mass with an error of less than a few ppm, mass measurement accuracy is not uniform for peaks with different intensities, particularly for quadrupole time-of-flight (QTOF) MS. Herein we present a simple and convenient method to determine the relation between peak intensity and mass error in LC-QTOF-MS-based metabolome analysis, followed by intensity-dependent mass search (IDMS) of a database for metabolite matches. This method is based on running a series of sodium formate mass calibrants, as part of the standard operating procedure (SOP) in LC-MS data acquisition, and then curve-fitting the measured mass errors and peak intensities. We show that, in two different quadrupole time-of-flight (QTOF) mass analyzers, mass accuracy is generally reduced as peak intensity decreases, which is independent of m/z values in the range commonly used for metabolite detection (e.g., m/z < 1000). We demonstrate the improvement in metabolite matches using IDMS in the analyses of dansyl labeled standards and human urine samples. We have implemented the IDMS method in the freely available MCID database at www.mycompoundid.org, which is composed of 8021 known human endogenous metabolites and their predicted metabolic products (375,809 compounds from one metabolic reaction and 10,583,901 compounds from two reactions).

Nanocapillary sampling coupled to liquid chromatography mass spectrometry delivers single cell drug measurement and lipid fingerprints

This work describes the development of a new approach to measure drug levels and lipid fingerprints in single living mammalian cells. Nanocapillary sampling is an approach that enables the selection and isolation of single living cells under microscope observation. Here, live single cell nanocapillary sampling is coupled to liquid chromatography for the first time. This allows molecular species to be separated prior to ionisation and improves measurement precision of drug analytes. The efficiency of transferring analytes from the sampling capillary into a vial was optimised in this work. The analysis was carried out using standard flow liquid chromatography coupled to widely available mass spectrometry instrumentation, highlighting opportunities for widespread adoption. The method was applied to 30 living cells, revealing cell-to-cell heterogeneity in the uptake of different drug molecules. Using this system, we detected 14-158 lipid features per single cell, revealing the association between bedaquiline uptake and lipid fingerprints.

Lysophosphatidic acid shifts metabolic and transcriptional landscapes to induce a distinct cellular state in human pluripotent stem cells

Pluripotent stem cells (PSCs) can be maintained in a continuum of cellular states with distinct features. Exogenous lipid supplements can relieve the dependence on de novo lipogenesis and shift global metabolism. However, it is largely unexplored how specific lipid components regulate metabolism and subsequently the pluripotency state. In this study, we report that the metabolic landscape of human PSCs (hPSCs) is shifted by signaling lipid lysophosphatidic acid (LPA), which naturally exists. LPA leads to a distinctive transcriptome profile that is not associated with de novo lipogenesis. Although exogenous lipids such as cholesterol, common free fatty acids, and LPA can affect cellular metabolism, they are not necessary for maintaining primed pluripotency. Instead, LPA induces distinct and reversible phenotypes in cell cycle, morphology, and mitochondria. This study reveals a distinct primed state that could be used to alter cell physiology in hPSCs for basic research and stem cell applications.

Untargeted UHPLC-ESI-QTOF-MS/MS analysis with targeted feature extraction at precursor and fragment level for profiling of the platelet lipidome with ex vivo thrombin-activation

Lipids play a major role in platelet signaling and activation. In this study, we analyzed the platelet lipidome in an untargeted manner by reversed-phase UHPLC for lipid species separation coupled to high-resolution QTOF-MS/MS in data-independent acquisition (DIA) mode with sequential window acquisition of all theoretical fragment ion mass spectra (SWATH) for compound detection. Lipid identification and peak picking was supported by the characteristic regular elution pattern of lipids differing in carbon and double bond numbers. It was primarily based on post-acquisition targeted feature extraction from the SWATH data. Multiple extracted ion chromatograms (EICs) from SWATH data of diagnostic ions on MS1 and MS2 level from both positive and negative ion mode allowed to distinguish between poorly resolved isomeric lipids based on their distinct fragment ions, which were used for relative quantification at a molecular lipid species level. It supports assay specificity for relative lipid quantitation via multiple quantifiably ions unlike to data-dependent acquisition methods which rely on precursor ions only. This approach was used to analyze human platelet samples. 457 lipids were annotated. Concentrations of lipids were estimated by stable isotope-labelled lipid class-specific internal standards as surrogate calibrants. Heatmaps of lipid concentrations in dependence on carbon and double bond numbers for the distinct lipid classes revealed a snapshot of the platelet lipidome in the resting state with lipid species distributions within classes supporting some functional interpretations. As expected, activation of the platelets by thrombin has led to significant alterations in the platelet lipidome as proven by univariate (volcano plot) and multivariate (PLS-DA) statistics. Several lipids were significantly up-regulated (lysophosphatidylinositols, oxylipins such as thromboxane B2 (TXB2), hydroxyheptadecatrienoic acid (HHT), hydroxyeicosatetraenoic acid (HETE), hydroxyoctadecadienoic acid (HODE), sphingoid-bases, (very) long chain saturated fatty acids) or down-regulated (lysophosphatidylethanolamines, polyunsaturated fatty acids, phosphatidylinositols). Several of them are well known as biomarkers of platelet activation while others may provide some further insights into pathways of platelet activation and platelet metabolism.

Identification, mapping and relative quantitation of SARS-CoV-2 Spike glycopeptides by Mass-Retention Time Fingerprinting

We describe an analytical method for the identification, mapping and relative quantitation of glycopeptides from SARS-CoV-2 Spike protein. The method may be executed using a LC-TOF mass spectrometer, requires no specialized knowledge of glycan analysis and exploits the differential resolving power of reverse phase HPLC. While this separation technique resolves peptides with high efficiency, glycans are resolved poorly, if at all. Consequently, glycopeptides consisting of the same peptide bearing different glycan structures will all possess very similar retention times and co-elute. Rather than a disadvantage, we show that shared retention time can be used to map multiple glycan species to the same peptide and location. In combination with MSMS and pseudo MS3, we have constructed a detailed mass-retention time database for Spike glycopeptides. This database allows any accurate mass LC-MS laboratory to reliably identify and quantify Spike glycopeptides from a single overnight elastase digest in less than 90 minutes.

Ganglioside isomer analysis using ion polarity switching liquid chromatography-tandem mass spectrometry

Gangliosides are ubiquitously present on cell surface. They are more abundantly expressed in nerve cells and tissues and involved in pathology of various diseases. Diversity of molecular structures in the carbohydrate head group, fatty acyl, and long chain base increases the complexity of analyzing gangliosides. In this study, an ultrahigh-performance liquid chromatography-tandem mass spectrometry method is developed for analysis of the co-eluting ganglioside isomers, which uses ion polarity switching to integrate glycan head isomer identification, ceramide isomer differentiation, and quantification of ganglioside into one analysis. The method is facilitated with an extensive ganglioside target list by combining the various glycan head groups, long chain bases, and the experimentally determined fatty acyls. Correlation between the retention time of ganglioside and its ceramide total carbon number is experimentally validated and used to predict retention time of ganglioside target list for scheduling the final multiple reaction monitoring method. This method was validated according to the FDA guidelines: 96.5% of gangliosides with good accuracy (80-120%), precision (< 15%), and linearity R² > 0.99. The authenticated gangliosides were quantified from mouse brain by isotope dilution. Overall, 165 gangliosides were quantified using 10 mg mouse brain tissue, including 100 isomers of GM1, GM2, GM3, GD1a, GD1b, GD2, GD3, and GT1b.

Developing an integrated microfluidic and miniaturized electrochemical biosensor for point of care determination of glucose in human plasma samples

A cost-effective, point of care (POC) device based on highly oriented CNT arrays was developed as an electrochemical assay for real-time and sensitive detection of glucose in complex samples. A low-cost, microcontroller-based potentiostat consisting of Arduino Due and LMP9100-EVM was developed to perform electrochemical measurements such as cyclic voltammetry (CV) and amperometry. A syringe pump based on open-source electronics was designed to direct the flow through a microfluidic chip. Vertically aligned carbon nanotube (VACNT) sensor arrays, in combination with the miniature potentiostat and the syringe pumps, were utilized as a POC device for the rapid and accurate detection of glucose. The structure and morphology of samples were characterized by field emission scanning electron microscopy (FESEM) and attenuated total reflectance Fourier transform infrared spectrometry (ATR-FTIR). CV as well as electrochemical impedance spectroscopy (EIS) was performed to investigate the electrochemical behavior of the electrode with respect to different diffusion regimes. The mediator-less biosensor had a limit of detection of 23 μM and sensitivity of 1462 μA mM^-1 cm^-2 and 1050 μA mM^-1 cm^-2 at the linear range of 1.2-7.8 mM and 7.8-11.2 mM, respectively. The presence of other biological compounds such as uric acid (UA) and ascorbic acid (AA) did not interfere with the detection of glucose. Finally, the designed POC device was successfully applied for the determination of glucose in human blood plasma samples.

Enhancing Coverage of Phosphatidylinositol Species in Canola Through Specialised Liquid Chromatography-Mass Spectrometry Buffer Conditions

Phosphatidylinositols (PIs) constitute a minor class of phospholipid with wide-spread influence throughout various cellular functions. Monitoring the distribution of these lipids can therefore provide insight as to the state of cellular processes or reveal the development of various pathologies. The speciation of these compounds is often performed either as part of a comprehensive characterisation of lipids, or specifically targeted using the same methods, however, such methods were intended to maximise coverage of lipid classes rather than provide an in-depth analysis of any single class. In the particular case of PIs, the majority of reported molecular diversity is limited to a small proportion of the already minor class, as such the cursory glance enabled by such methods is insufficient. Therefore, this work compared the suitability of both established and novel LC-MS buffers with the aim of maximising the ionisation efficiency of PIs, in an attempt to enhance coverage of the class. Through experimentation, it was determined that a 0.25 mM ammonium fluoride buffer provided up to a 6-fold increase in signal intensity, and on average a 38-fold increase in the signal-to-noise ratio. Using these new conditions, 14 PI species, and 12 PI candidates were identified within a dilute lipid extract sourced from canola seed, compared to 0 species identified using the generalised method. As a result, it is suggested that this procedure has yielded the highest number of PI species identifications for a sample of this concentration. Methods which therefore intend to characterise PI species in dilute quantities, such as those extracted from mammalian cells, are henceforth provided with the means to conduct more comprehensive characterisations.

A UPLC-MRM-MS method for comprehensive profiling of Amadori compound-modified phosphatidylethanolamines in human plasma

Phosphatidylethanolamines (PEs) are targets of non-enzymatic glycation, a chemical process that occurs between glucose and primary amine-containing biomolecules. As the early-stage non-enzymatic glycation products of PE, Amadori-PEs are implicated in the pathogenesis of various diseases. However, only a few Amadori-PE molecular species have been identified so far; a comprehensive profiling of these glycated PE species is needed to establish their roles in disease pathology. Herein, based on our previous work using liquid chromatography-coupled neutral loss scanning and product ion scanning tandem mass spectrometry (LC-NLS-MS and LC-PIS-MS) in tandem, we extend identification of Amadori-PE to the low-abundance species, which is facilitated by using plasma lipids glycated in vitro. The confidence of identification is improved by high-resolution tandem mass spectrometry and chromatographic retention time regression. A LC-coupled multiple reaction monitoring mass spectrometry (LC-MRM-MS) assay is further developed for more sensitive quantitation of the Amadori compound-modified lipids. Using synthesized stable isotope-labeled Amadori lipids as internal standards, levels of 142 Amadori-PEs and 33 Amadori-LysoPEs are determined in the NIST human plasma standard reference material. These values may serve as an important reference for future investigations of Amadori-modified lipids in human diseases.

[Blood lipid metabolic profile of overweight/obese boys aged 9-12 years]

OBJECTIVE

To study the features of blood lipid metabolic profile in overweight/obese boys aged 9-12 years and the possible mechanism of overweight/obesity in children.

METHODS

According to body mass index (BMI), 72 boys, aged 9-12 years, were divided into a control group with 42 boys and an overweight/obesity group with 30 boys. Fasting venous blood samples were collected early in the morning. BMI, waist-hip ratio, body composition, and blood lipids were measured. Ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry technique was used to analyze the serum lipid compounds. A statistical analysis and visualization of the data were performed.

RESULTS

Compared with the control group, the overweight/obesity group had significantly higher waist-hip ratio, body fat percentage, and triglyceride level (P<0.05) and a significantly lower level of high-density lipoprotein cholesterol (P<0.05). The metabolomic analysis identified 150 differentially expressed lipid compounds between the two groups, mainly glycerolipids (40.7%), glycerophospholipids (24.7%), fatty acyls (10.7%), and sphingolipids (7.3%). The levels of most of glycerolipids were significantly upregulated in the overweight/obesity group, while those of most of glycerophospholipids and sphingolipids were downregulated in this group. Key lipids with differential expression were enriched into two KEGG metabolic pathways, i.e., ether lipid metabolism pathway and terpenoid backbone biosynthesis pathway (P<0.05), and might further affected the biosynthesis and metabolism of downstream coenzyme Q and other terpenoids (P=0.06).

CONCLUSIONS

Disordered lipid metabolic profile is observed in overweight/obese boys aged 9-12 years, with increases in most glycerolipids and reductions in glycerophospholipids and sphingolipids. Overweight/obese boys may have disorders in ether lipid metabolism and biosynthesis of terpenoid and even coenzyme Q.

[Blood lipid metabolic profile of overweight/obese boys aged 9-12 years]

OBJECTIVE

To study the features of blood lipid metabolic profile in overweight/obese boys aged 9-12 years and the possible mechanism of overweight/obesity in children.

METHODS

According to body mass index (BMI), 72 boys, aged 9-12 years, were divided into a control group with 42 boys and an overweight/obesity group with 30 boys. Fasting venous blood samples were collected early in the morning. BMI, waist-hip ratio, body composition, and blood lipids were measured. Ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry technique was used to analyze the serum lipid compounds. A statistical analysis and visualization of the data were performed.

RESULTS

Compared with the control group, the overweight/obesity group had significantly higher waist-hip ratio, body fat percentage, and triglyceride level (P<0.05) and a significantly lower level of high-density lipoprotein cholesterol (P<0.05). The metabolomic analysis identified 150 differentially expressed lipid compounds between the two groups, mainly glycerolipids (40.7%), glycerophospholipids (24.7%), fatty acyls (10.7%), and sphingolipids (7.3%). The levels of most of glycerolipids were significantly upregulated in the overweight/obesity group, while those of most of glycerophospholipids and sphingolipids were downregulated in this group. Key lipids with differential expression were enriched into two KEGG metabolic pathways, i.e., ether lipid metabolism pathway and terpenoid backbone biosynthesis pathway (P<0.05), and might further affected the biosynthesis and metabolism of downstream coenzyme Q and other terpenoids (P=0.06).

CONCLUSIONS

Disordered lipid metabolic profile is observed in overweight/obese boys aged 9-12 years, with increases in most glycerolipids and reductions in glycerophospholipids and sphingolipids. Overweight/obese boys may have disorders in ether lipid metabolism and biosynthesis of terpenoid and even coenzyme Q.

Advances in lipidomics

The present article examines recently published literature on lipids, mainly focusing on research involving glycero-, glycerophospho- and sphingo-lipids. The primary aim is identification of distinct profiles in biologic lipidomic systems by ultra-high-performance liquid chromatography (UHPLC) coupled with mass spectrometry (MS, tandem MS) with multivariate data analysis. This review specifically targets lipid biomarkers and disease pathway mechanisms in humans and artificial targets. Different specimen matrices such as primary blood derivatives (plasma, serum, erythrocytes, and blood platelets), faecal matter, urine, as well as biologic tissues (liver, lung and kidney) are highlighted.

Polydopamine-capped AgNPs as a novel matrix overcoming the ion suppression of phosphatidylcholine for MALDI MS comprehensive imaging of glycerophospholipids and sphingolipids in impact-induced injured brain

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) is a powerful tool for the characterization and localization of analytes without the need for extraction, purification, separation or labeling of samples. However, in tissue sections the most abundant lipids, phosphatidylcholines (PCs), could suppress the signals of other classes of coexisting lipids. In this work, polydopamine (PDA)-capped AgNPs (AgNPs@PDA) were synthesized as a matrix of MALDI MSI to analyze lipids in both positive and negative ion modes. By adjusting the thickness of the PDA layer, the signal of silver cluster ions of AgNPs@PDA was effectively controlled, and the ability of AgNPs@PDA serving as a matrix was optimized. More interestingly, using AgNPs@PDA as a matrix, the sensitivity of PCs was dramatically decreased, and the PC signals were greatly suppressed, while for other lipids (including PE, HexCer, PS, PI, PIP, and ST), they were just the opposite. The reason, we believe, is related to the positively charged surface of AgNPs@PDA, and the polyhydroxy and amino groups of PDA. Benefitting from the suppression of the signals of PCs and the improvement of detection sensitivity of other lipids, 58 glycerophospholipids and 25 sphingolipids in brain tissue sections could be imaged in one run with AgNPs@PDA as a matrix by MALDI MSI, much better than when using traditional organic matrices 2,5-dihydroxybenzoic acid and 9-aminoacridine.