Simultaneous Relative Quantification of Various Polyglycerophospholipids with Isotope-Labeled Methylation by Nanoflow Ultrahigh Performance Liquid Chromatography-Tandem Mass Spectrometry.

Herein, we introduce a comprehensive analytical method for the separation and relative quantification of polyglycerophospholipids (PGPLs), including phosphatidylglycerol (PG), bis(monoacylglycero)phosphate (BMP), bis(diacylglycero)phosphate (BDP), Hemi BDP, cardiolipin (CL), monolysocardiolipin (MLCL), and dilysocardiolipin (DLCL), using isotope-labeled methylation (ILM) with nanoflow ultrahigh performance liquid chromatography-electrospray ionization-tandem mass spectrometry (nUHPLC-ESI-MS/MS). Abnormal levels of BMP and CL have been associated with the pathology of lysosomal storage and neurodegenerative diseases. Thus, simultaneous analysis of all PGPLs is important to understand the mechanisms and pathologies of such diseases. In this study, improved separation and MS detection of PGPLs, including their regioisomers, was achieved by the methylation of PGPL. ILM-based relative quantification was applied to lipid extracts from a dopaminergic cell line (SH-SY5Y) treated with drugs commonly used for Parkinson's disease (PD), resulting in the identification of 229 unique PGPLs, including 121 CLs, 71 MLCLs, and 16 Hemi BDP species. The drug treatment induced significant increases in the amount of CLs containing polyunsaturated fatty acyl chains, including 20:4 and 22:6, as well as decreased levels of BMP, Hemi BDP, and BDP species, demonstrating the feasibility of using ILM for the comprehensive and high-speed relative quantification of PGPLs.

Online Proteolysis and Glycopeptide Enrichment with Thermoresponsive Porous Polymer Membrane Reactors for Nanoflow Liquid Chromatography-Tandem Mass Spectrometry.

In this Article, we have reported a fully automated online method to carry out proteolysis and glycopeptide enrichment in sequence for nanoflow liquid chromatography-tandem mass spectrometry (nLC-ESI-MS/MS) analysis. By implementing two serial thermoresponsive porous polymer membrane reactors (TPPMRs), in which the TPPM could be immobilized either with trypsin for proteolysis or with lectins for glycopeptide enrichment, the entire pretreatment procedure can be performed online in about an hour. The TPPM was fabricated by coating polystyrene-maleic anhydride- N-isopropylacrylamide (PS-MAn-PNIPAm), which was synthesized by reversible addition-fragmentation chain transfer polymerization, on a Nylon sheet. Because of the thermoresponsive nature of PNIPAm, it formed micelle cavities and changed its morphology at elevated temperatures, resulting in enhanced interactions between the enzyme or lectins and the proteins/peptides flowing through the membrane. The performances of the TPPMs were evaluated by varying the temperature conditions and the amount of standard proteins, showing that both proteolysis and glycopeptide enrichment with online deglycosylation were highly efficient at 37 °C. The developed online serial TPPMRs-nLC-ESI-MS/MS method was applied to the human plasma sample (1.5 µL) and a total of 262 N-glycopeptides could be identified from 155 glycoproteins. Thus, the present work demonstrates a fully automated high speed analytical protocol for online proteolysis and glycopeptide enrichment, which is extremely useful for analyzing small amounts of the proteome samples.

Size Dependent Lipidomic Analysis of Urinary Exosomes from Patients with Prostate Cancer by Flow Field-Flow Fractionation and Nanoflow Liquid Chromatography-Tandem Mass Spectrometry.

Exosomes are membrane-bound extracellular vesicles involved in intercellular communication and tumor cell metastasis. In this study, flow field-flow fractionation (FlFFF) was utilized to separate urinary exosomes by size, demonstrating a significant difference in exosome sizes between healthy controls and patients with prostate cancer (PCa). Exosome fractions of different sizes were collected for microscopic analysis during an FlFFF run and evaluated with exosome marker proteins using Western blot analysis. The results indicated that exosomes of different sizes originated from different types of cells. Collected exosome fractions were further examined using nanoflow ultrahigh performance liquid chromatography-electrospray ionization-tandem mass spectrometry (nUPLC-ESI-MS/MS) for lipidomic analysis. A total of 162 lipids (from 286 identified) were quantified using a selected reaction monitoring (SRM) method. The overall amount of lipids increased by 1.5- to 2-fold in patients with PCa and degree of increase was more significant in the smaller fractions (diameter <150 nm) than in the larger ones (diameter >150 nm) some classes of lipids. In addition, neutral lipids like diacylglycerol (DAG) and triacylglycerol (TAG) decreased in all exosomes without size dependency. Moreover, a dramatic increase in 22:6/22:6-phosphatidylglycerol (PG) was observed and significant decrease in (16:0,16:0)- and (16:1, 18:1)-DAG species (nearly 5-fold) and high abundant TAG species (>2.5-fold) was observed in patients with PCa. The results of this study indicate that FlFFF can be employed for the high-speed screening of urinary exosome sizes in patients with PCa and lipidomic analysis of the fractionated exosomes has potential for developing and distinguishing biomarkers of PCa.

High Speed Size Sorting of Subcellular Organelles by Flow Field-Flow Fractionation.

Separation/isolation of subcellular species, such as mitochondria, lysosomes, peroxisomes, Golgi apparatus, and others, from cells is important for gaining an understanding of the cellular functions performed by specific organelles. This study introduces a high speed, semipreparative scale, biocompatible size sorting method for the isolation of subcellular organelle species from homogenate mixtures of HEK 293T cells using flow field-flow fractionation (FlFFF). Separation of organelles was achieved using asymmetrical FlFFF (AF4) channel system at the steric/hyperlayer mode in which nuclei, lysosomes, mitochondria, and peroxisomes were separated in a decreasing order of hydrodynamic diameter without complicated preprocessing steps. Fractions in which organelles were not clearly separated were reinjected to AF4 for a finer separation using the normal mode, in which smaller sized species can be well fractionated by an increasing order of diameter. The subcellular species contained in collected AF4 fractions were examined with scanning electron microscopy to evaluate their size and morphology, Western blot analysis using organelle specific markers was used for organelle confirmation, and proteomic analysis was performed with nanoflow liquid chromatography-tandem mass spectrometry (nLC-ESI-MS/MS). Since FlFFF operates with biocompatible buffer solutions, it offers great flexibility in handling subcellular components without relying on a high concentration sucrose solution for centrifugation or affinity- or fluorescence tag-based sorting methods. Consequently, the current study provides an alternative, competitive method for the isolation/purification of subcellular organelle species in their intact states.

Wide-Range Size Fractionation of Graphene Oxide by Flow Field-Flow Fractionation.

Many interesting properties of 2D materials and their assembled structures are strongly dependent on the lateral size and size distribution of 2D materials. Accordingly, effective size separation of polydisperse 2D sheets is critical for desirable applications. Here, we introduce flow field-flow fractionation (FlFFF) for a wide-range size fractionation of graphene oxide (GO) up to 100 µm. Two different separation mechanisms are identified for FlFFF, including normal mode and steric/hyperlayer mode, to size fractionate wide size-distributed GOs while employing a crossflow field for either diffusion or size-controlled migration of GO. Obviously, the 2D GO sheet reveals size separation behavior distinctive from typical spherical particles arising from its innate planar geometry. We also investigate 2D sheet size-dependent mechanical and electrical properties of three different graphene fibers produced from size-fractionated GOs. This FlFFF-based size selection methodology can be used as a generic approach for effective wide-range size separation for 2D materials, including rGO, TMDs, and MXene.

Evaluation of exosome separation from human serum by frit-inlet asymmetrical flow field-flow fractionation and multiangle light scattering.

Exosomes are extracellular vesicles that mediate intercellular communication, immune response, and tumour metastasis. However, exosome isolation from the blood is complicated because their size and density are similar to those of blood lipoproteins. Here, we employed field programming frit-inlet asymmetrical flow field-flow fractionation (FIAF4) coupled with multiangle light scattering (MALS) for the effective separation of exosomes from free unbound proteins and lipoproteins present in serum samples using different pre-treatment methods, namely, a commercial exosome isolation kit, ultracentrifugation (UC), and a simple centrifugation followed by ultrafiltration (UF). Sizes of the eluted exosomes, as calculated by MALS signals, approximated well with the results of batch dynamic light scattering of the collected fractions and with the sizes of polystyrene particles. Exosome separation from lipoproteins was validated by western blotting with several markers of exosomes and lipoproteins, followed by proteomic analysis using nanoflow ultrahigh-performance liquid chromatography-electrospray ionisation-tandem mass spectrometry. UC requires relatively large amounts of serum samples (at least 2 mL) but is more efficient at removing lipoproteins. The UF method with a centrifugal concentrator (300 kDa) was found to be more effective in retrieving exosomes with low serum volumes (50 µL). Altogether, this study demonstrates the application of field programming FIAF4 for the isolation/purification of exosomes from proteins and lipoproteins in the serum.

Perturbations of Lipids and Oxidized Phospholipids in Lipoproteins of Patients with Postmenopausal Osteoporosis Evaluated by Asymmetrical Flow Field-Flow Fractionation and Nanoflow UHPLC-ESI-MS/MS.

Osteoporosis, a degenerative bone disease characterized by reduced bone mass and high risk of fragility, is associated with the alteration of circulating lipids, especially oxidized phospholipids (Ox-PLs). This study evaluated the lipidomic changes in lipoproteins of patients with postmenopausal osteoporosis (PMOp) vs. postmenopausal healthy controls. High-density lipoproteins (HDL) and low-density lipoproteins (LDL) from plasma samples were size-sorted by asymmetrical flow field-flow fractionation (AF4). Lipids from each lipoprotein were analyzed by nanoflow ultrahigh performance liquid chromatography-electrospray ionization-tandem mass spectrometry (nUHPLC-ESI-MS/MS). A significant difference was observed in a subset of lipids, most of which were increased in patients with PMOp, when compared to control. Phosphatidylethanolamine plasmalogen, which plays an antioxidative role, was increased in both lipoproteins (P-16:0/20:4, P-18:0/20:4, and P-18:1/20:4) lysophosphatidic acid 16:0, and six phosphatidylcholines were largely increased in HDL, but triacylglycerols (50:4 and 54:6) and overall ceramide levels were significantly increased only in LDL of patients with PMOp. Further investigation of 33 Ox-PLs showed significant lipid oxidation in PLs with highly unsaturated acyl chains, which were decreased in LDL of patients with PMOp. The present study demonstrated that AF4 with nUHPLC-ESI-MS/MS can be utilized to systematically profile Ox-PLs in the LDL of patients with PMOp.

Investigation of lipidomic perturbations in oxidatively stressed subcellular organelles and exosomes by asymmetrical flow field-flow fractionation and nanoflow ultrahigh performance liquid chromatography-tandem mass spectrometry.

We investigated the effect of oxidative stress (OS) on lipidomic perturbations in the subcellular fractions and exosomes of human embryonic kidney (HEK) 293 cells using asymmetrical flow field-flow fractionation (AF4) and nanoflow ultrahigh performance liquid chromatography-electrospray ionization-tandem mass spectrometry (nUHPLC-ESI-MS/MS). We treated HEK 293 cells with hydrogen peroxide (H2O2) and fractionated the cell lysates using AF4 to determine the change in size and population of the subcellular fractions and exosomes, and to obtain narrow size fractions for lipid analysis. A total of 438 lipids from 642 identified species-including oxidized lipids-were quantified. The relative amount of secreted exosomes increased by 28% during OS, whereas the amount of subcellular species decreased by 35%. There was a significant increase in the level of oxidized phospholipids in the mitochondrion-enriched subcellular fractions, but not in the exosomes. Most high-abundance triacylglycerol (TG) species increased in the stressed cells, whereas they decreased in the exosomes. During OS, ceramides involved in the apoptotic mitochondrial pathway were accumulated in the subcellular fractions, whereas their levels were unaffected in the exosomes. The present study demonstrated that AF4 and nUHPLC-ESI-MS/MS can be used to investigate lipid alterations in subcellular and extracellular species during OS, and the pathological relationships in diseases caused by reactive oxygen species.

Flow optimisations with increased channel thickness in asymmetrical flow field-flow fractionation.

Retention in flow field-flow fractionation (flow FFF) is generally governed by the combination of crossflow and migration flowrates. Especially for an asymmetrical flow FFF (AF4) channel in which the channel-inlet flow is divided into crossflow and outflow, the separation of low-molecular-weight proteins or macromolecules requires a relatively high crossflow rate along with a very low outflow rate for a reasonable level of resolution, which often leads to a limitation in channel pressure. In this study, the performances of AF4 with increased channel thicknesses have been investigated by adjusting the effective channel flowrates in the asymmetrical channels according to the variation of channel thickness. Four AF4 channels of different channel thicknesses (350, 490, 600, and 740 µm) were employed to examine the potential usefulness of employing a thick channel in the high-resolution separation of low-molecular-weight proteins (< 100 kDa) and to determine the relationship between higher channel thickness and the recovery of elution. Experiments showed that the ratio of crossflow rate to the effective channel flowrate should be considered in the selection of a run condition at an increased channel thickness. The study also demonstrated that a thick AF4 channel can be useful for the high-resolution separation of low-molecular-weight species such as protein aggregates without using extremely high crossflow rates.

Investigation of steric transition with field programming in frit inlet asymmetrical flow field-flow fractionation.

Steric transition in flow field-flow fractionation (FlFFF) was investigated under field programming by varying the channel thickness of a frit inlet asymmetrical FlFFF (FI-AF4). Steric transition is a typical inversion in sample elution mode from the increasing order of diameter (normal mode) to the opposite order (steric mode). Owing to the co-elution of two different-sized particles in the steric transition region where particles elute by the combination of the two elution modes, a loss of information in determining the accurate size of sample components in field-flow fractionation occurs. In this study, the effect of field programming on the steric transition in FI-AF4 was examined with the increase in channel thickness in order to increase the diffusional contribution of particle retention with the simultaneous reduction of steric contribution. This study demonstrated that the steric inversion diameter can be increased to >1 µm by programming the crossflow rate and by increasing the channel thickness to 350 and 490 µm. The present study also investigated the effects of outflow rate and initial field strength on the particle separation in field-programmed FI-AF4.

Analysis of lipoprotein-specific lipids in patients with acute coronary syndrome by asymmetrical flow field-flow fractionation and nanoflow liquid chromatography-tandem mass spectrometry.

A comprehensive lipid analysis was performed at the plasma lipoprotein level in patients with acute coronary syndrome (ACS) and stable coronary artery disease (CAD). Because the lipids in lipoproteins are related to the pathology of the cardiovascular system, lipoprotein-specific lipid analysis can be useful for understanding the mechanism of lipid-associated cardiovascular diseases. Lipoproteins were size-sorted into high density lipoproteins (HDL) and low density lipoproteins (LDL) using asymmetrical flow field-flow fractionation, then lipids of each lipoprotein were analysed using nanoflow ultrahigh performance liquid chromatography-electrospray ionization-tandem mass spectrometry. A total of 365 lipids were structurally identified and quantified by selected reaction monitoring method. Two high abundance lysophosphatidylcholines (16:0 and 18:0) were significantly increased only in the HDL of the ACS group (vs. the stable CAD group). Phosphatidylethanolamines (38:5 and 40:5) significantly increased in ACS by >2-fold in both lipoproteins. (18:0, 22:6)-diacylglycerol increased in ACS by 3.5-fold only in LDL; however, most high abundance triacylglycerols decreased 2-fold in both lipoproteins. The present study revealed the usefulness of lipoprotein-specific analysis of lipids in distinguishing ACS from stable CAD, and the selected lipids analysed in this study may be useful in the development of lipid markers for the early detection of ACS.

Lipidomic alterations in lipoproteins of patients with mild cognitive impairment and Alzheimer's disease by asymmetrical flow field-flow fractionation and nanoflow ultrahigh performance liquid chromatography-tandem mass spectrometry.

Alzheimer's disease (AD) is an irreversible neurodegenerative disorder with the clinical symptom of the progressive loss of cognitive function and mild cognitive impairment (MCI) is a translational state between cognitive changes of normal aging and AD. Lipid metabolism and pathogenesis of Alzheimer's disease (AD) are closely linked. Despite obviously discrete lipidome constitutions across lipoproteins, lipidomic approaches of AD has been mostly conducted without considering lipoprotein-dependent alterations. This study introduces a combination of asymmetrical flow field-flow fractionation (AF4) and nanoflow ultrahigh performance liquid chromatography-tandem mass spectrometry (nUHPLC-ESI-MS/MS) for a comprehensive lipid profiling in different lipoprotein level of patients plasma with AD and amnestic MCI in comparison to age-matched healthy controls. Lipoproteins in plasma samples were size-sorted by a semi-preparative scale AF4, followed by non-targeted lipid identification and high speed targeted quantitation with nUHPLC-ESI-MS/MS. It shows 14 significantly altered high abundance lipids in AD, exhibiting >2-fold increases (p < 0.01) in LDL/VLDL including triacylglycerol, ceramide, phosphatidylethanolamine, and diacylglycerol. Three lipid species (triacylglycerol 50:1, diacylglycerol 18:1_18:1, and phosphatidylethanolamine 36:2) showing a strong correlation with the degree of brain atrophy were found as candidate species which can be utilized to differentiate the early stage of MCI when simple Mini-Mental State Examination results were statistically incorporated. The present study elucidated lipoprotein-dependent alterations of lipids in progression of MCI and further to AD which can be utilized for the future development of lipid biomarkers to enhance the predictability of disease progress.

On-line high speed lipid extraction for nanoflow liquid chromatography-tandem mass spectrometry.

An on-line lipid extraction method is introduced by utilizing a short capillary extraction column using HILIC and C4 particles prior to nanoflow liquid chromatography-tandem mass spectrometry (nLC-MS/MS). The on-line extraction using a urine sample spiked with PL standards showed similar or slightly higher recovery values (86%-96%) of phospholipids (PLs) compared to those obtained by the conventional off-line extraction based on the Folch method with or without using the air-exposed drying process. In this study, we demonstrated that PL oxidation can occur during the air-exposed drying process of lipid extracts in standard liquid-liquid extraction procedures, which was confirmed by the oxidized PL (OxPL) molecules that were generated from an off-line extraction using a few PL standards. Quantitative comparison of these OxPL species between on- and off-line extraction followed by nLC-MS/MS with multiple reaction monitoring (MRM) analysis showed a significant decrease (2-10 fold) in unwanted OxPL species when on-line extraction was employed. While the number of identified PLs from a urine sample was somewhat lower than those by off-line extraction, the number of OxPLs was significantly reduced (from 70 to 22) with on-line extraction. The new method offers high speed (∼5min) automated extraction of PLs with nLC-MS/MS analysis and presents the possibility of handling a biological sample with a very limited amount of lipids.