The Experts below are selected from a list of 17820 Experts worldwide ranked by ideXlab platform

Xianlin Han - One of the best experts on this subject based on the ideXlab platform.

  • RECOGNITION AND AVOIDANCE OF ION SOURCE-GENERATED ARTIFACTS IN Lipidomics ANALYSIS.
    Mass Spectrometry Reviews, 2020
    Co-Authors: Wenqing Luo, Xianlin Han
    Abstract:

    Lipid research is attracting more and more attention as various key roles and novel biological functions of lipids have been demonstrated and discovered in the organism. Mass spectrometry (MS)-based Lipidomics approaches are the most powerful and effective tools for analysis of cellular lipidomes with very high sensitivity and specificity. However, the artifacts generated from in-source fragmentation are always present in all kinds of ion sources, even soft ionization techniques (i.e., electrospray ionization and matrix-assisted laser desorption/ionization [MALDI]). These artifacts can cause many problems for Lipidomics, especially when the fragment ions correspond to/are isomeric species of other endogenous lipid species in complex biological samples. These commonly observed artifacts could lead to misannotation, false identification, and consequently, incorrect attribution of phenotypes, and will have negative impact on any MS-based Lipidomics research including but not limited to biomarker discovery, drug development, etc. Liquid chromatography-MS, shotgun Lipidomics, and MALDI-MS imaging are three representative Lipidomics approaches in which ion source-generated artifacts are all manifested and are comprehensively summarized in this article. The strategies on how to avoid/reduce the artifacts of in-source fragmentation on Lipidomics analysis are also discussed in detail. We believe that with the recognition and avoidance of ion source-generated artifacts, MS-based Lipidomics approaches will provide better accuracy on comprehensive analysis of biological samples and will make greater contribution to the research on metabolism and translational/precision medicine (collectively termed functional Lipidomics). © 2020 John Wiley & Sons Ltd. Mass Spec Rev.

  • Strategies to Improve/Eliminate the Limitations in Shotgun Lipidomics
    Proteomics, 2019
    Co-Authors: Qiao Duan, Xianlin Han
    Abstract:

    Direct infusion-based shotgun Lipidomics is one of the most powerful and useful tools in comprehensive analysis of lipid species from lipid extracts of various biological samples with high accuracy/precision. However, despite many advantages, the classical shotgun Lipidomics suffers some general dogmas of limitations, such as ion suppression, ambiguous identification of isobaric/isomeric lipid species, and ion source-generated artifacts, restraining the applications in analysis of low-abundance lipid species, particularly those less ionizable or isomers that yield almost identical fragmentation patterns. This article reviews the strategies (such as modifier addition, prefractionation, chemical derivatization, charge feature utilization) that have been employed to improve/eliminate these limitations in modern shotgun Lipidomics approaches (e.g., high mass resolution mass spectrometry-based and multidimensional mass spectrometry-based shotgun Lipidomics). Therefore, with the enhancement of these strategies for shotgun Lipidomics, comprehensive analysis of lipid species including isomeric/isobaric species is achieved in a more accurate and effective manner, greatly substantiating the aberrant lipid metabolism, signaling trafficking, and homeostasis under pathological conditions.

  • Tutorial on Lipidomics.
    Analytica Chimica Acta, 2019
    Co-Authors: Jianing Wang, Chunyan Wang, Xianlin Han
    Abstract:

    Abstract The mainstream of Lipidomics involves mass spectrometry-based, systematic, and large-scale studies of the structure, composition, and quantity of lipids in biological systems such as organs, cells, and body fluids. As increasingly more researchers in broad fields are beginning to pay attention to and actively learn about the lipidomic technology, some introduction on the topic is needed to help the newcomers to better understand the field. This tutorial seeks to introduce the basic knowledge about Lipidomics and to provide readers with some core ideas and the most important approaches for studying the field.

  • Novel strategies for enhancing shotgun Lipidomics for comprehensive analysis of cellular lipidomes
    TrAC Trends in Analytical Chemistry, 2019
    Co-Authors: Chunyan Wang, Xianlin Han
    Abstract:

    Abstract Shotgun Lipidomics is one of the most powerful tools in analysis of cellular lipidomes in Lipidomics, which directly analyzes lipids from lipid extracts of diverse biological samples with high accuracy/precision. However, despite its great advances in high throughput analysis of cellular lipidomes, low coverage of poorly ionized lipids, especially those species in very low abundance, and some types of isomers within complex lipid extracts by shotgun Lipidomics remains a huge challenge. In the past few years, many strategies have been developed to enhance shotgun Lipidomics for comprehensive analysis of lipid species. Chemical derivatization represents one of the most attractive and effective strategies, already receiving considerable attention. This review focuses on novel advanced derivatization strategies for enhancing shotgun Lipidomics. It is anticipated that with the development of enhanced strategies, shotgun Lipidomics can make greater contributions to biological and biomedical research.

  • Is the clinical Lipidomics a potential goldmine
    Cell Biology and Toxicology, 2018
    Co-Authors: Linlin Zhang, Xianlin Han, Xiangdong Wang
    Abstract:

    Clinical Lipidomics is a new extension of Lipidomics to study lipid profiles, pathways, and networks by characterizing and quantifying the complete lipid molecules in cells, biopsy, or body fluids of patients. It undoubtfully has more values if Lipidomics can be integrated with the data of clinical proteomic, genomic, and phenomic profiles. A number of challenges, e.g., instability, specificity, and sensitivity, in Lipidomics have to be faced and overcome before clinical application. The association of Lipidomics data with gene expression and sequencing of lipid-specific proteins/enzymes should be furthermore clarified. Therefore, clinical Lipidomics is expected to be more stable during handling, sensitive in response to changes, specific for diseases, efficient in data analyses, and standardized in measurements, in order to meet clinical needs. Clinical Lipidomics will become a more important approach in clinical applications and will be the part of “natural” measures for early diagnosis and progress of disease. Thus, clinical Lipidomics will be one of the most powerful approaches for disease-specific diagnosis and therapy, once the mystery of lipidomic profiles and metabolic enzymes is deciphered.

Kim Ekroos - One of the best experts on this subject based on the ideXlab platform.

  • ms based Lipidomics of human blood plasma a community initiated position paper to develop accepted guidelines
    Journal of Lipid Research, 2018
    Co-Authors: Oztekin Urla, Makoto Arita, Masanori Arita, Anne K End, Amaury Cazenavegassio, Kazutaka Ikeda, Edward A. Dennis, Kim Ekroos, Gerhard Liebisch
    Abstract:

    Human blood is a self-regenerating lipid-rich biological fluid that is routinely collected in hospital settings. The inventory of lipid molecules found in blood plasma (plasma lipidome) offers insights into individual metabolism and physiology in health and disease. Disturbances in the plasma lipidome also occur in conditions that are not directly linked to lipid metabolism; therefore, plasma Lipidomics based on MS is an emerging tool in an array of clinical diagnostics and disease management. However, challenges exist in the translation of such lipidomic data to clinical applications. These relate to the reproducibility, accuracy, and precision of lipid quantitation, study design, sample handling, and data sharing. This position paper emerged from a workshop that initiated a community-led process to elaborate and define a set of generally accepted guidelines for quantitative MS-based Lipidomics of blood plasma or serum, with harmonization of data acquired on different instrumentation platforms across independent laboratories as an ultimate goal. We hope that other fields may benefit from and follow such a precedent.

  • analysis of lipid experiments alex a software framework for analysis of high resolution shotgun Lipidomics data
    PLOS ONE, 2013
    Co-Authors: Peter Husen, Kim Ekroos, Kirill Tarasov, Maciej Katafiasz, Elena Sokol, Johannes Vogt, Jan Baumgart, Robert Nitsch, Christer S Ejsing
    Abstract:

    Global Lipidomics analysis across large sample sizes produces high-content datasets that require dedicated software tools supporting lipid identification and quantification, efficient data management and lipidome visualization. Here we present a novel software-based platform for streamlined data processing, management and visualization of shotgun Lipidomics data acquired using high-resolution Orbitrap mass spectrometry. The platform features the ALEX framework designed for automated identification and export of lipid species intensity directly from proprietary mass spectral data files, and an auxiliary workflow using database exploration tools for integration of sample information, computation of lipid abundance and lipidome visualization. A key feature of the platform is the organization of Lipidomics data in ”database table format” which provides the user with an unsurpassed flexibility for rapid lipidome navigation using selected features within the dataset. To demonstrate the efficacy of the platform, we present a comparative neuroLipidomics study of cerebellum, hippocampus and somatosensory barrel cortex (S1BF) from wild-type and knockout mice devoid of the putative lipid phosphate phosphatase PRG-1 (plasticity related gene-1). The presented framework is generic, extendable to processing and integration of other lipidomic data structures, can be interfaced with post-processing protocols supporting statistical testing and multivariate analysis, and can serve as an avenue for disseminating Lipidomics data within the scientific community. The ALEX software is available at www.msLipidomics.info.

  • High throughput quantitative molecular Lipidomics
    Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, 2011
    Co-Authors: Hye R. Jung, Tuulia Sylvänne, Kaisa M. Koistinen, Kirill Tarasov, Dimple Kauhanen, Kim Ekroos
    Abstract:

    Applications in biomedical research increasingly demand detailed lipid molecule information acquired at high throughput. Although the recent advances in Lipidomics offer to delineate the lipidomes in detail, the challenge remains in performing such analyses at the requested quality and to maintain the quality also in a high throughput setting. In this review we describe a high throughput molecular lipidomic solution based on robotic assisted sample preparation and lipid extraction and multiple lipidomic platforms integrated with a sophisticated bioinformatics system. As demonstrated, the virtue of this lipidomic toolkit lies in its high throughput delivery of comprehensive quantitative lipidomic outputs at the molecular lipid level, its ease of scalability and its capability to serve in a regulatory setting. We anticipate that this toolkit will contribute to basic research, nutritional research and promote the discovery of new disease biomarkers, disease related mechanisms of actions and drug targets. This article is part of a Special Issue entitled Lipodomics and Imaging Mass Spectrometry.

  • Lipidomics: a tool for studies of atherosclerosis.
    Current Atherosclerosis Reports, 2010
    Co-Authors: Kim Ekroos, Kirill Tarasov, Minna Jänis, Reini Hurme, Reijo Laaksonen
    Abstract:

    Lipids, abundant constituents of both the vascular plaque and lipoproteins, play a pivotal role in atherosclerosis. Mass spectrometry-based analysis of lipids, called Lipidomics, presents a number of opportunities not only for understanding the cellular processes in health and disease but also in enabling personalized medicine. Lipidomics in its most advanced form is able to quantify hundreds of different molecular lipid species with various structural and functional roles. Unraveling this complexity will improve our understanding of diseases such as atherosclerosis at a level of detail not attainable with classical analytical methods. Improved patient selection, biomarkers for gauging treatment efficacy and safety, and translational models will be facilitated by the lipidomic deliverables. Importantly, lipid-based biomarkers and targets should lead the way as we progress toward more specialized therapeutics.

  • high throughput shotgun Lipidomics by quadrupole time of flight mass spectrometry
    Journal of Chromatography B, 2009
    Co-Authors: Marcus Stahlman, Kirill Tarasov, Christer S Ejsing, Jeanna Perman, Jan Boren, Kim Ekroos
    Abstract:

    Technological advances in mass spectrometry and meticulous method development have produced several shotgun lipidomic approaches capable of characterizing lipid species by direct analysis of total lipid extracts. Shotgun Lipidomics by hybrid quadrupole time-of-flight mass spectrometry allows the absolute quantification of hundreds of molecular glycerophospholipid species, glycerolipid species, sphingolipid species and sterol lipids. Future applications in clinical cohort studies demand detailed lipid molecule information and the application of high-throughput Lipidomics platforms. In this review we describe a novel high-throughput shotgun lipidomic platform based on 96-well robot-assisted lipid extraction, automated sample infusion by mircofluidic-based nanoelectrospray ionization, and quantitative multiple precursor ion scanning analysis on a quadrupole time-of-flight mass spectrometer. Using this platform to compile comprehensive lipid arrays associated with metabolic dysfunctions is a powerful strategy for pinpointing the mechanistic details by which alterations in tissue-specific lipid metabolism are directly linked to the etiology of many lipid-mediated disorders.

Qiuhui Xuan - One of the best experts on this subject based on the ideXlab platform.

  • Recent advances in analytical strategies for mass spectrometry-based Lipidomics
    Analytica chimica acta, 2020
    Co-Authors: Qiuhui Xuan
    Abstract:

    Lipids are vital biological molecules and play multiple roles in cellular function of mammalian organisms such as cellular membrane anchoring, signal transduction, material trafficking and energy storage. Driven by the biological significance of lipids, Lipidomics has become an emerging science in the field of omics. Lipidome in biological systems consists of hundreds of thousands of individual lipid molecules that possess complex structures, multiple categories, and diverse physicochemical properties assembled by different combinations of polar headgroups and hydrophobic fatty acyl chains. Such structural complexity poses a huge challenge for comprehensive lipidome analysis. Thanks to the great innovations in chromatographic separation techniques and the continuous advances in mass spectrometric detection tools, analytical strategies for Lipidomics have been highly diversified so that the depth and breadth of Lipidomics have been greatly enhanced. This review will present the current state of mass spectrometry-based analytical strategies including untargeted, targeted and pseudotargeted Lipidomics. Recent typical applications of Lipidomics in biomarker discovery, pathogenic mechanism and therapeutic strategy are summarized, and the challenges facing to the field of Lipidomics are also discussed.

  • development of a high coverage pseudotargeted Lipidomics method based on ultra high performance liquid chromatography mass spectrometry
    Analytical Chemistry, 2018
    Co-Authors: Qiuhui Xuan, Lichao Wang, Yang Zhou, Xinjie Zhao, Xiaoli Hou
    Abstract:

    Lipid coverage is crucial in comprehensive Lipidomics studies challenged by high diversity in lipid structures and wide dynamic range in lipid levels. Current state-of-the-art Lipidomics technologies are mostly based on mass spectrometry (MS), including direct-infusion MS, chromatography-MS, and matrix-assisted laser desorption ionization (MALDI) imaging MS, each with its pros and cons. Due to the need or favorability for measurement of isomers and isobars, chromatography-MS is preferable for lipid profiling. The ultra-high performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS)-based nontargeted Lipidomics approach and UHPLC-tandem MS (UHPLC-MS/MS)-based targeted approach are two representative methodological platforms for chromatography-MS. In the present study, we developed a high coverage pseudotargeted Lipidomics method combining the advantages of nontargeted and targeted Lipidomics approaches. The high coverage of lipids was achieved by integration of the detected lipids der...

Richard W. Gross - One of the best experts on this subject based on the ideXlab platform.

  • The evolution of Lipidomics through space and time.
    Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, 2017
    Co-Authors: Richard W. Gross
    Abstract:

    Although the foundations of mass spectrometry-based Lipidomics have been practiced for over 30 years, recent technological advances in ionization modalities in conjunction with robust increases in mass accuracy and resolution have greatly accelerated the emergence, growth and importance of the field of Lipidomics. Moreover, advances in the separation sciences, bioinformatic strategies and the availability of robust databases have been synergistically integrated into modern lipidomic technologies leading to unprecedented improvements in the depth, penetrance and precision of lipidomic analyses and identification of their biological and mechanistic significance. The purpose of this "opinion" article is to briefly review the evolution of Lipidomics, critique the platforms that have evolved and identify areas that are likely to emerge in the years to come. Through seamlessly integrating a rich repertoire of mass spectrometric, chemical and bioinformatic strategies, the chemical identities and quantities of tens of thousands to hundreds of thousands of different lipid molecular species and their metabolic alterations during physiologic or pathophysiologic perturbations can be obtained. Thus, the field of Lipidomics which already has a distinguished history of exciting new discoveries in many disease states holds unparalleled potential to identify the pleiotropic roles of lipids in health and disease at the chemical level. This article is part of a Special Issue entitled: BBALIP_Lipidomics Opinion Articles edited by Sepp Kohlwein.

  • Multi-dimensional mass spectrometry-based shotgun Lipidomics and novel strategies for lipidomic analyses
    Mass Spectrometry Reviews, 2012
    Co-Authors: Xianlin Han, Kui Yang, Richard W. Gross
    Abstract:

    Since our last comprehensive review on multi-dimensional mass spectrometry-based shotgun Lipidomics (Mass Spectrom. Rev. 24 (2005), 367), many new developments in the field of Lipidomics have occurred. These developments include new strategies and refinements for shotgun lipidomic approaches that use direct infusion, including novel fragmentation strategies, identification of multiple new informative dimensions for mass spectrometric interrogation, and the development of new bioinformatic approaches for enhanced identification and quantitation of the individual molecular constituents that comprise each cell's lipidome. Concurrently, advances in liquid chromatography-based platforms and novel strategies for quantitative matrix-assisted laser desorption/ionization mass spectrometry for lipidomic analyses have been developed. Through the synergistic use of this repertoire of new mass spectrometric approaches, the power and scope of Lipidomics has been greatly expanded to accelerate progress toward the comprehensive understanding of the pleiotropic roles of lipids in biological systems.

  • shotgun Lipidomics electrospray ionization mass spectrometric analysis and quantitation of cellular lipidomes directly from crude extracts of biological samples
    Mass Spectrometry Reviews, 2005
    Co-Authors: Xianlin Han, Richard W. Gross
    Abstract:

    Lipidomics, after genomics and proteomics, is a newly and rapidly expanding research field that studies cellular lipidomes and the organizational hierarchy of lipid and protein constituents mediating life processes. Lipidomics is greatly facilitated by recent advances in, and novel applications of, electrospray ionization mass spectrometry (ESI/MS). In this review, we will focus on the advances in ESI/MS, which have facilitated the development of shotgun Lipidomics and the utility of intrasource separation as an enabling strategy for utilization of 2D mass spectrometry in shotgun Lipidomics of biological samples. The principles and experimental details of the intrasource separation approach will be extensively discussed. Other ESI/MS approaches towards the quantitative analyses of global cellular lipidomes directly from crude lipid extracts of biological samples will also be reviewed and compared. Multiple examples of lipidomic analyses from crude lipid extracts employing these approaches will be given to show the power of ESI/MS techniques in Lipidomics. Currently, modern society is plagued by the sequelae of lipid-related diseases. It is our hope that the integration of these advances in multiple disciplines will catalyze the development of Lipidomics, and such development will lead to improvements in diagnostics and therapeutics, which will ultimately result in the extended longevity and an improved quality of life for humankind.

Huwei Liu - One of the best experts on this subject based on the ideXlab platform.

  • Recent advances in Lipidomics for disease research.
    Journal of separation science, 2015
    Co-Authors: Li Yang, Yu Bai, Yabing Shan, Sensen Shen, Huwei Liu
    Abstract:

    Lipidomics is an important branch of metabolomics, which aims at the detailed analysis of lipid species and their multiple roles in the living system. In recent years, the development of various analytical methods for effective identification and characterization of lipids has greatly promoted the process of Lipidomics. Meanwhile, as many diseases demonstrate a remarkable alteration in lipid profiles compared with that of healthy people, Lipidomics has been extensively introduced to disease research. The comprehensive lipid profiling provides a chance to discover novel biomarkers for specific disease. In addition, it plays a crucial role in the study of lipid metabolism, which could illuminate the pathogenesis of diseases. In this review, after brief discussion of analytical methods for Lipidomics in clinical research, we focus on the recent advances of Lipidomics related to four types of diseases, including cancer, atherosclerosis, diabetes mellitus, and Alzheimer's disease.

  • Analytical methods in Lipidomics and their applications.
    Analytical Chemistry, 2013
    Co-Authors: Li Yang, Yu Bai, Huwei Liu
    Abstract:

    ■ CONTENTS Analytical Methods of Lipidomics 162 Extraction Methods of Lipids 163 Direct-Infusion MS-Based Lipidomics Analysis 163 Electrospray Ionization (ESI) MS 163 Matrix-Assisted Laser Desorption Ionization (MALDI) MS 164 Other Ionization Techniques Used in Lipidomics Analysis 164 Mass Spectrometry Imaging (MSI) in Lipidomics 165 Chromatography-Based Lipidomics Analysis 165 TLC 166 GC 166 HPLC 166 SFC 167 CE 167 Spectroscopy 167 Nuclear Magnetic Resonance (NMR) 167 Raman Spectroscopy 168 Applications of Lipidomics Analysis in Life Science 168 Lipidomics of Cancers 168 Lipidomics of Alzheimer’s Disease (AD) 168 Cellular Lipidomics 168 Plants 168 Conclusions 170 Author Information 170 Corresponding Author 170 Notes 170 Biographies 170 Acknowledgments 171 References 171

  • Recent advances of chromatography and mass spectrometry in Lipidomics.
    Analytical and Bioanalytical Chemistry, 2010
    Co-Authors: Zhigui Zhou, Yu Bai, Honggang Nie, Huwei Liu
    Abstract:

    Lipidomics, as a novel branch of metabolomics, which is aimed at comprehensive analysis of lipids and their biological roles with respect to health and diseases, has attracted increased attention from biological and analytical scientists. As a result of the complexity and diversity of lipids, accurate identification and efficient separation are required for Lipidomics analysis. Mass spectrometry (MS) and chromatography have been extensively developed in the past few decades and hold a distinguished position in qualification and separation science. They are powerful and indispensable tools for Lipidomics. Herein, we present the recent advancement of MS, chromatography, and their hyphenation technologies in Lipidomics.