Filters








99 Hits in 11.4 sec

MOESM1 of Comprehensive identification of sphingolipid species by in silico retention time and tandem mass spectral library

Hiroshi Tsugawa, Kazutaka Ikeda, Wataru Tanaka, Yuya Senoo, Makoto Arita, Masanori Arita
2017 Figshare  
Figure S1 The fragment assignments of 12 sphingolipid classes. The annotations were combinatorially performed by hydrogen rearrangement rules in combination with substantial manual curation.  ...  The original spectra were obtained from LC/MS data of some biological samples including human cells, mouse tissues, and plant species.  ... 
doi:10.6084/m9.figshare.c.3718279_d1 fatcat:y74ehhiyyngozmkdnoixjykw54

Comprehensive identification of sphingolipid species by in silico retention time and tandem mass spectral library

Hiroshi Tsugawa, Kazutaka Ikeda, Wataru Tanaka, Yuya Senoo, Makoto Arita, Masanori Arita
2017 Journal of Cheminformatics  
Compound identification relies on similarity matching of the retention time (RT), precursor m/z, isotopic ratio, and MS/MS spectrum with reference compounds.  ...  Liquid chromatography coupled with electrospray ionization tandem mass spectrometry (LC-ESI-MS/ MS) is used for comprehensive metabolome and lipidome analyses.  ...  Tobias Kind for the support of LipidBlast template. We also thank Mr. Shu Yasuda for the preparation of HEK and HeLa cells.  ... 
doi:10.1186/s13321-017-0205-3 pmid:28316657 pmcid:PMC5352698 fatcat:dmjcn54rpnffreolc2a2bkkm7q

Mass spectral databases for LC/MS- and GC/MS-based metabolomics: State of the field and future prospects

Maria Vinaixa, Emma L. Schymanski, Steffen Neumann, Miriam Navarro, Reza M. Salek, Oscar Yanes
2016 TrAC. Trends in analytical chemistry  
Finally, future prospects for mass spectral databases are discussed in terms of the needs posed by novel applications and instrumental advancements.  ...  The main characteristics of the mass spectral databases currently used in MS-based metabolomics, are reviewed in this paper, underlining the advantages and limitations of each.  ...  Acknowledgements We thank the financial support from the Spanish Biomedical Research Centre in Diabetes  ... 
doi:10.1016/j.trac.2015.09.005 fatcat:ngzm3daq4naurcled4t3l6zmyy

Advances in structure elucidation of small molecules using mass spectrometry

Tobias Kind, Oliver Fiehn
2010 Bioanalytical Reviews  
The importance of mass spectral library search algorithms for tandem mass spectra and multiple-stage MS(n) mass spectra as well as mass spectral tree libraries that combine multiple-stage mass spectra  ...  The successive chapter discusses mass spectral fragmentation pathways, biotransformation reactions and drug metabolism studies, the mass spectral simulation and generation of in silico mass spectra, expert  ...  A comprehensive review covered the identification of known endogenous and exogenous metabolites by applying accurate mass, isotopic pattern filter, retention indices, and mass spectral fragmentation in  ... 
doi:10.1007/s12566-010-0015-9 pmid:21289855 pmcid:PMC3015162 fatcat:yuvii4d4xfd2rgmxjl34bfbqja

Advances in structure elucidation of small molecules using mass spectrometry [chapter]

Tobias Kind, Oliver Fiehn
2010 Frontiers of Bioanalytical Chemistry  
The importance of mass spectral library search algorithms for tandem mass spectra and multiple-stage MS(n) mass spectra as well as mass spectral tree libraries that combine multiple-stage mass spectra  ...  The successive chapter discusses mass spectral fragmentation pathways, biotransformation reactions and drug metabolism studies, the mass spectral simulation and generation of in silico mass spectra, expert  ...  A comprehensive review covered the identification of known endogenous and exogenous metabolites by applying accurate mass, isotopic pattern filter, retention indices, and mass spectral fragmentation in  ... 
doi:10.1007/978-3-642-36303-0_7 fatcat:3nekzqs4kza33hwmoxb7sw6kae

Annotation of the human cerebrospinal fluid lipidome using high resolution mass spectrometry and a dedicated data processing workflow

Alexandre Seyer, Samia Boudah, Simon Broudin, Christophe Junot, Benoit Colsch
2016 Metabolomics  
In addition, an automatic annotation using an in silico lipid database and several MS/MS experiments were performed to identify CSF lipid species.  ...  Objectives This study explored the CSF lipidome in order to generate a robust mass spectral database using an untargeted lipidomic approach.  ...  , and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.  ... 
doi:10.1007/s11306-016-1023-8 pmid:27110228 pmcid:PMC4824825 fatcat:2srvfbbkkbewhgqc3al6qwskau

Lipidomics from sample preparation to data analysis: a primer

Thomas Züllig, Martin Trötzmüller, Harald C. Köfeler
2019 Analytical and Bioanalytical Chemistry  
Lipidomics is the science of the large-scale determination of individual lipid species, and the underlying analytical technology that is used to identify and quantify the lipidome is generally mass spectrometry  ...  , ion-mobility spectrometry, MS, and data processing by various software packages.  ...  MS/MS fragmentations are compared with libraries of experimental and/or computationally generated MS/MS data such as the NIST Tandem Mass Spectral Library, MassBank [104] , Massbank of North America (  ... 
doi:10.1007/s00216-019-02241-y pmid:31820027 fatcat:2vpmhuly7rhpviagvo72kc634i

Computational solutions in redox lipidomics – Current strategies and future perspectives

Zhixu Ni, Laura Goracci, Gabriele Cruciani, Maria Fedorova
2019 Free Radical Biology & Medicine  
Here we discuss the main principles of high-throughput identification of lipids and their modified forms and review the main software tools currently available in redox lipidomics.  ...  specific identification of already discovered and yet unknown modified lipids.  ...  Acknowledgments Financial support from German Federal Ministry of Education and Research (BMBF) within the framework of the e:Med research and funding concept for SysMedOS project (to MF) and the EU H2020  ... 
doi:10.1016/j.freeradbiomed.2019.04.027 pmid:31035005 fatcat:xxqgyuksvvghth2t6xqhen7htq

LipidFrag: Improving reliability of in silico fragmentation of lipids and application to the Caenorhabditis elegans lipidome

Michael Witting, Christoph Ruttkies, Steffen Neumann, Philippe Schmitt-Kopplin, Monika Oberer
2017 PLoS ONE  
In contrast to shotgun lipidomics, LC-MS based lipidomics uses chromatographic separation of lipid species followed by mass spectrometric detection, which allows differentiation of isomeric lipid species  ...  Lipid identification is a major bottleneck in high-throughput lipidomics studies. However, tools for the analysis of lipid tandem MS spectra are rather limited.  ...  C. elegans samples were kindly provided by Steve Garvis, ENS Lyon. We thank Emma Schymanski (Eawag, Dübendorf, Switzerland) for fruitful and intensive discussions and comments on the manuscript.  ... 
doi:10.1371/journal.pone.0172311 pmid:28278196 pmcid:PMC5344313 fatcat:n2qeeif3n5hd5frbv7e3f2ielm

Challenges in Identifying the Dark Molecules of Life

María Eugenia Monge, James N. Dodds, Erin S. Baker, Arthur S. Edison, Facundo M. Fernández
2019 Annual Review of Analytical Chemistry  
In this review, we critically discuss the state-of-the-art in metabolite identification with specific applications in metabolomics and how technologies such as mass spectrometry, ion mobility, chromatography  ...  Because metabolites do not follow a molecular alphabet as proteins and nucleic acids do, their identification is much more time consuming, with a high failure rate.  ...  In particular, Fiehn and collaborators (30) have greatly contributed to the metabolomics field by building FiehnLib libraries comprising mass spectra and retention indices from quadrupole and time-of-flight  ... 
doi:10.1146/annurev-anchem-061318-114959 pmid:30883183 pmcid:PMC6716371 fatcat:xp2ey4drrncp5dzdcqxuk7m7ti

Opti-nQL: An Optimized, Versatile and Sensitive Nano-LC Method for MS-Based Lipidomics Analysis

Angela Cattaneo, Giuseppe Martano, Umberto Restuccia, Laura Tronci, Michele Bianchi, Angela Bachi, Vittoria Matafora
2021 Metabolites  
Lipidomics is the comprehensive analysis of lipids in a given biological system.  ...  MS analysis showed that theOpti-nQL method increases the number of identified lipids, which is evidenced by injecting 20 times less material than in microflow based chromatography, being more reproducible  ...  Lipid identification was based on exact mass, retention time, and MS/MS pattern. Lipid species based on precursor fragment ions were determined using a comprehensive targets list in LipidView.  ... 
doi:10.3390/metabo11110720 pmid:34822378 pmcid:PMC8623082 fatcat:d7cd4zwr6ra6zjyw5rnas4jtgu

The state of the art in plant lipidomics

Cheka Kehelpannala, Thusitha Rupasinghe, Thomas Hennessy, David Bradley, Berit Ebert, Ute Roessner
2021 Molecular Omics  
In this review, we provide a critical appraisal of the key developments, current state and future trends in liquid-chromatography–mass spectrometry-based workflows for plant lipid analysis.  ...  Most of the developed software tools use in silico lipid libraries, which can be rapidly generated by computing all possible combinations of fatty acids, head groups, linkages and backbones with fragments  ...  of double bonds. 76 In general, the retention time of lipids increases with increasing carbon number and decreases with increasing number of double bonds.  ... 
doi:10.1039/d1mo00196e pmid:34699583 fatcat:mewggdqftngfndapfnm5pbu6tm

A Comprehensive Proteomic SWATH-MS Workflow for Profiling Blood Extracellular Vesicles: A New Avenue for Glioma Tumour Surveillance

Susannah Hallal, Ali Azimi, Heng Wei, Nicholas Ho, Maggie Yuk Ting Lee, Hao-Wen Sim, Joanne Sy, Brindha Shivalingam, Michael Edward Buckland, Kimberley Louise Alexander-Kaufman
2020 International Journal of Molecular Sciences  
(SWATH-MS) and data extraction was performed by aligning against a custom 8662-protein library.  ...  Plasma-EVs isolated from pre-operative glioma grade II–IV patients (n = 41) and controls (n = 11) were sequenced by Sequential window acquisition of all theoretical fragment ion spectra mass spectrometry  ...  To ensure accurate assignment of the SWATH-MS peaks, the retention times of the SWATH-MS peaks were aligned to the IDA spectral library using an indexed retention time (iRT) calculator Assembling a Spectral  ... 
doi:10.3390/ijms21134754 pmid:32635403 pmcid:PMC7369771 fatcat:7eshiewbcvegnprsppvdv4kj3i

Development and Application of Multidimensional Lipid Libraries to Investigate Lipidomic Dysregulation Related to Smoke Inhalation Injury Severity [article]

Kaylie I Kirkwood, Michael W Christopher, Jefferey L Burgess, Sally R Littau, Brian S Pratt, Nicholas Shulman, Kaipo Tamura, Michael J. MacCoss, Brendan X MacLean, Erin S Baker
2021 bioRxiv   pre-print
such as indexed retention time (iRT) for retention time prediction and IMS drift time filtering for increased sensitivity and selectivity.  ...  Here, we have overcome these challenges by developing sample-specific multidimensional libraries using the freely available software Skyline.  ...  ACKNOWLEDGEMENTS All measurements were performed in the Molecular Education, Technology and Research Innovation Center (METRIC) at NC State University.  ... 
doi:10.1101/2021.10.13.464246 fatcat:eatn5owpnndxpfshrwhq5kpm6i

Greazy: Open-Source Software for Automated Phospholipid Tandem Mass Spectrometry Identification

Michael A. Kochen, Matthew C. Chambers, Jay D. Holman, Alexey I. Nesvizhskii, Susan T. Weintraub, John T. Belisle, M. Nurul Islam, Johannes Griss, David L. Tabb
2016 Analytical Chemistry  
Lipid identification from data produced with high-throughput technologies is essential to the elucidation of the roles played by lipids in cellular function and disease.  ...  We assess Greazy's performance against the NIST 2014 metabolomics library, observing high accuracy in a search of multiple lipid classes.  ...  Xiaoli Gao in the metabolomics component of the UTHSCSA Mass Spectrometry Laboratory, supported by UTHSCSA and by NIH grant 1S10RR031586-01 (STW).  ... 
doi:10.1021/acs.analchem.6b00021 pmid:27186799 pmcid:PMC4996967 fatcat:gh2jene3pnhvviyceqxjf5auwq
« Previous Showing results 1 — 15 out of 99 results