scholarly journals Shorthand notation for lipid structures derived from mass spectrometry

2013 ◽  
Vol 54 (6) ◽  
pp. 1523-1530 ◽  
Author(s):  
Gerhard Liebisch ◽  
Juan Antonio Vizcaíno ◽  
Harald Köfeler ◽  
Martin Trötzmüller ◽  
William J. Griffiths ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Shorthand Notation ◽  
Lipid Structures

scholarly journals Update on LIPID MAPS classification, nomenclature, and shorthand notation for MS-derived lipid structures

2020 ◽  
Vol 61 (12) ◽  
pp. 1539-1555 ◽  
Author(s):  
Gerhard Liebisch ◽  
Eoin Fahy ◽  
Junken Aoki ◽  
Edward A. Dennis ◽  
Thierry Durand ◽  
...  
Keyword(s):  
Hierarchical Architecture ◽  
Metabolic Labeling ◽  
Internal Standards ◽  
Shorthand Notation ◽  
Lipid Species ◽  
Lipid Mass ◽  
Standardized Reporting ◽  
Fatty Acyls ◽  
And Storage ◽  
Lipid Structures

A comprehensive and standardized system to report lipid structures analyzed by MS is essential for the communication and storage of lipidomics data. Herein, an update on both the LIPID MAPS classification system and shorthand notation of lipid structures is presented for lipid categories Fatty Acyls (FA), Glycerolipids (GL), Glycerophospholipids (GP), Sphingolipids (SP), and Sterols (ST). With its major changes, i.e., annotation of ring double bond equivalents and number of oxygens, the updated shorthand notation facilitates reporting of newly delineated oxygenated lipid species as well. For standardized reporting in lipidomics, the hierarchical architecture of shorthand notation reflects the diverse structural resolution powers provided by mass spectrometric assays. Moreover, shorthand notation is expanded beyond mammalian phyla to lipids from plant and yeast phyla. Finally, annotation of atoms is included for the use of stable isotope-labeled compounds in metabolic labeling experiments or as internal standards. This update on lipid classification, nomenclature, and shorthand annotation for lipid mass spectra is considered a standard for lipid data presentation.

scholarly journals MS-DIAL 4: accelerating lipidomics using an MS/MS, CCS, and retention time atlas

2020 ◽  
Author(s):  
Hiroshi Tsugawa ◽  
Kazutaka Ikeda ◽  
Mikiko Takahashi ◽  
Aya Satoh ◽  
Yoshifumi Mori ◽  
...  
Keyword(s):  
Cross Section ◽  
Ion Mobility ◽  
Retention Time ◽  
Collision Cross Section ◽  
Tandem Mass ◽  
Notation System ◽  
Mass Spectral ◽  
False Discovery ◽  
Shorthand Notation ◽  
Lipid Structures

To the EditorWe formulated mass spectral fragmentations of lipids across 117 lipid subclasses and included ion mobility tandem mass spectrometry (MS/MS) to provide a comprehensive lipidome atlas with retention time, collision cross section, and MS/MS information. The all-in-one solution from import of raw MS data to export of a common output format (mztab-M) was packaged in MS-DIAL 4 (http://prime.psc.riken.jp/) providing an enhanced standardized untargeted lipidomics procedure following lipidomics standards initiative (LSI) semi-quantitative definitions and shorthand notation system of lipid structures with a 1–2% estimated false discovery rate, which will contribute to harmonizing lipidomics data across laboratories to accelerate lipids research.

scholarly journals Computational mass spectrometry accelerates C=C position-resolved untargeted lipidomics using oxygen attachment dissociation

2021 ◽  
Author(s):  
Haruki Uchino ◽  
Hiroshi Tsugawa ◽  
Hidenori Takahashi ◽  
Makoto Arita
Keyword(s):  
Mass Spectrometry ◽  
Fatty Acids ◽  
Cultured Cells ◽  
Cellular Membrane ◽  
Species Level ◽  
Specific Lipids ◽  
Novel Approach ◽  
Living Organisms ◽  
Long Chain ◽  
Lipid Structures

Abstract Mass spectrometry-based untargeted lipidomics has revealed the lipidome atlas of living organisms at the molecular species level. Despite the double bond (C=C) position being a crucial factor for enzyme preference, cellular membrane milieu, and biological activity, the C=C defined structures have not yet been characterized. Here, we present a novel approach for C=C position-resolved untargeted lipidomics using a combination of oxygen attachment dissociation and computational mass spectrometry to increase the rate of annotation. We validated the accuracy of our platform as per the authentic standards of 21 lipid subclasses and the biogenic standards of 51 molecules containing polyunsaturated fatty acids (PUFAs) from the cultured cells fed with various fatty acid-enriched media. By analyzing human and mice-derived biological samples, we characterized 675 unique lipid structures with the C=C position-resolved level encompassing 22 lipid subclasses defined by LIPID MAPS. Our platform also illuminated the unique profiles of tissue-specific lipids containing n-3 and/or n-6 very long-chain PUFAs (carbon M 28 and double bonds a 4) in the eye, testis, and brain of the mouse.

Profiling of phospholipids and related lipid structures using multidimensional ion mobility spectrometry-mass spectrometry

2009 ◽  
Vol 287 (1-3) ◽  
pp. 58-69 ◽  
Author(s):  
Sarah Trimpin ◽  
Bo Tan ◽  
Brian C. Bohrer ◽  
David K. O’Dell ◽  
Samuel I. Merenbloom ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Ion Mobility Spectrometry ◽  
Ion Mobility ◽  
Lipid Structures

How SIMS microscopy can be used in medicine

1992 ◽  
Vol 50 (2) ◽  
pp. 1602-1603
Author(s):  
Philippe Fragu
Keyword(s):  
Mass Spectrometry ◽  
Biomedical Applications ◽  
Secondary Ion Mass Spectrometry ◽  
Chemical Elements ◽  
Biological Applications ◽  
The Past ◽  
Potential Source ◽  
Secondary Ion ◽  
Chemical Integrity ◽  
Scientific Endeavour

The identification, localization and quantification of intracellular chemical elements is an area of scientific endeavour which has not ceased to develop over the past 30 years. Secondary Ion Mass Spectrometry (SIMS) microscopy is widely used for elemental localization problems in geochemistry, metallurgy and electronics. Although the first commercial instruments were available in 1968, biological applications have been gradual as investigators have systematically examined the potential source of artefacts inherent in the method and sought to develop strategies for the analysis of soft biological material with a lateral resolution equivalent to that of the light microscope. In 1992, the prospects offered by this technique are even more encouraging as prototypes of new ion probes appear capable of achieving the ultimate goal, namely the quantitative analysis of micron and submicron regions. The purpose of this review is to underline the requirements for biomedical applications of SIMS microscopy.Sample preparation methodology should preserve both the structural and the chemical integrity of the tissue.

Imaging of Al-Li-Cu alloys with a Scanning Ion Microprobe

1990 ◽  
Vol 48 (2) ◽  
pp. 314-315
Author(s):  
K.K. Soni ◽  
D.B. Williams ◽  
J.M. Chabala ◽  
R. Levi-Setti ◽  
D.E. Newbury
Keyword(s):  
Mass Spectrometry ◽  
Secondary Ion Mass Spectrometry ◽  
Equilibrium Phase ◽  
Icosahedral Symmetry ◽  
Ion Microprobe ◽  
X Ray ◽  
Cu Alloys ◽  
Two Phases ◽  
The University ◽  
Secondary Ion

In contrast to the inability of x-ray microanalysis to detect Li, secondary ion mass spectrometry (SIMS) generates a very strong Li+ signal. The latter’s potential was recently exploited by Williams et al. in the study of binary Al-Li alloys. The present study of Al-Li-Cu was done using the high resolution scanning ion microprobe (SIM) at the University of Chicago (UC). The UC SIM employs a 40 keV, ∼70 nm diameter Ga+ probe extracted from a liquid Ga source, which is scanned over areas smaller than 160×160 μm2 using a 512×512 raster. During this experiment, the sample was held at 2 × 10-8 torr.In the Al-Li-Cu system, two phases of major importance are T1 and T2, with nominal compositions of Al2LiCu and Al6Li3Cu respectively. In commercial alloys, T1 develops a plate-like structure with a thickness <∼2 nm and is therefore inaccessible to conventional microanalytical techniques. T2 is the equilibrium phase with apparent icosahedral symmetry and its presence is undesirable in industrial alloys.

Applications of Time-OF-Flight Secondary Ion Mass Spectrometry (TOF-SIMS)

1990 ◽  
Vol 48 (2) ◽  
pp. 308-309
Author(s):  
Bruno Schueler ◽  
Robert W. Odom
Keyword(s):  
Mass Spectrometry ◽  
Secondary Ion Mass Spectrometry ◽  
Structural Information ◽  
Time Of Flight ◽  
Biological Tissues ◽  
Polymer Surfaces ◽  
Tof Sims ◽  
Secondary Ions ◽  
Ion Mass Spectrometry ◽  
Secondary Ion

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) provides unique capabilities for elemental and molecular compositional analysis of a wide variety of surfaces. This relatively new technique is finding increasing applications in analyses concerned with determining the chemical composition of various polymer surfaces, identifying the composition of organic and inorganic residues on surfaces and the localization of molecular or structurally significant secondary ions signals from biological tissues. TOF-SIMS analyses are typically performed under low primary ion dose (static SIMS) conditions and hence the secondary ions formed often contain significant structural information.This paper will present an overview of current TOF-SIMS instrumentation with particular emphasis on the stigmatic imaging ion microscope developed in the authors’ laboratory. This discussion will be followed by a presentation of several useful applications of the technique for the characterization of polymer surfaces and biological tissues specimens. Particular attention in these applications will focus on how the analytical problem impacts the performance requirements of the mass spectrometer and vice-versa.

Gold liposomes

1996 ◽  
Vol 54 ◽  
pp. 898-899
Author(s):  
James F. Hainfeld
Keyword(s):  
Direct Methods ◽  
Important Class ◽  
Double Bonds ◽  
Membrane Phospholipids ◽  
Essential Ingredient ◽  
Lipid Structures

Lipids are an important class of molecules, being found in membranes, HDL, LDL, and other natural structures, serving essential roles in structure and with varied functions such as compartmentalization and transport. Synthetic liposomes are also widely used as delivery and release vehicles for drugs, cosmetics, and other chemicals; soap is made from lipids. Lipids may form bilayer or multilammellar vesicles, micelles, sheets, tubes, and other structures. Lipid molecules may be linked to proteins, carbohydrates, or other moieties. EM study of this essential ingredient of life has lagged, due to lack of direct methods to visualize lipids without extensive alteration. OsO4 reacts with double bonds in membrane phospholipids, forming crossbridges. This has been the method of choice to both fix and stain membranes, thus far. An earlier work described the use of tungstate clusters (W11) attached to lipid moieties to form lipid structures and lipid probes.

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