Discovery of N-Acyl Amino Acids and Novel Related N-, O-Acyl Lipids by Integrating Molecular Networking and an Extended In Silico Spectral Library.

Research on novel bioactive lipids has garnered increasing interest. Although lipids can be identified by searching mass spectral libraries, the discovery of novel lipids remains challenging as the query spectra of such lipids are not included in libraries. In this study, we propose a strategy to discover novel carboxylic acid-containing acyl lipids by integrating molecular networking with an extended in silico spectral library. Derivatization was performed to improve the response of this method. The tandem mass spectrometry spectra enriched by derivatization facilitated the formation of molecular networking and 244 nodes were annotated. We constructed consensus spectra for these annotations based on molecular networking and developed an extended in silico spectral library based on these consensus spectra. The spectral library included 6879 in silico molecules covering 12,179 spectra. Using this integration strategy, 653 acyl lipids were discovered. Among these, O-acyl lactic acids and N-lactoyl amino acid-conjugated lipids were annotated as novel acyl lipids. Compared with conventional methods, our proposed method allows for the discovery of novel acyl lipids, and extended in silico libraries significantly increase the size of the spectral library.

[1]  Zemin Fang,et al.  Isoenzyme N-Acyl-l-Amino Acid Amidohydrolase NA Increases Ochratoxin A Degradation Efficacy of Stenotrophomonas sp. CW117 by Enhancing Amidohydrolase ADH3 Stability , 2022, Microbiology spectrum.

[2]  Liang Li,et al.  Segment Scan Mass Spectral Acquisition for Increasing the Metabolite Detectability in Chemical Isotope Labeling Liquid Chromatography-Mass Spectrometry Metabolome Analysis. , 2022, Analytical chemistry.

[3]  Liang Li,et al.  High-Coverage Quantitative Metabolomics of Human Urine: Effects of Freeze-Thaw Cycles on the Urine Metabolome and Biomarker Discovery. , 2022, Analytical chemistry.

[4]  K. Y. Loh,et al.  An exercise-inducible metabolite that suppresses feeding and obesity , 2022, Nature.

[5]  Julia A. Bubis,et al.  A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics , 2022, bioRxiv.

[6]  D. Raftery,et al.  Extending the Scope of 1H NMR-Based Blood Metabolomics for the Analysis of Labile Antioxidants: Reduced and Oxidized Glutathione. , 2021, Analytical chemistry.

[7]  Xia Zhao,et al.  In-silico-library-based method enables rapid and comprehensive annotation of cardiolipins and cardiolipin oxidation products using high resolution tandem mass spectrometer. , 2021, Analytica chimica acta.

[8]  D. Raftery,et al.  Expanding Urinary Metabolite Annotation through Integrated Mass Spectral Similarity Networking. , 2021, Analytical chemistry.

[9]  William Stafford Noble,et al.  Large-scale tandem mass spectrum clustering using fast nearest neighbor searching , 2021, bioRxiv.

[10]  Yutaka Yamada,et al.  A lipidome atlas in MS-DIAL 4 , 2020, Nature Biotechnology.

[11]  O. Fiehn,et al.  Retip: retention time prediction for compound annotation in untargeted metabolomics. , 2020, Analytical chemistry.

[12]  O. Fiehn,et al.  An in-silico generated library for sensitive detection of 2-dimethylaminoethylamine derivatized FAHFA lipids using high-resolution tandem mass spectrometry. , 2020, Analytical chemistry.

[13]  Julie C. Lumeng,et al.  Global chemical effects of the microbiome include new bile-acid conjugations , 2020, Nature.

[14]  T. Bisogno,et al.  N-Acyl Amino Acids: Metabolism, Molecular Targets, and Role in Biological Processes , 2019, Biomolecules.

[15]  R. Smoum,et al.  HU-671, a Novel Oleoyl Serine Derivative, Exhibits Enhanced Efficacy in Reversing Ovariectomy-Induced Osteoporosis and Bone Marrow Adiposity , 2019, Molecules.

[16]  Christine M. Aceves,et al.  Reproducible molecular networking of untargeted mass spectrometry data using GNPS , 2019, Nature Protocols.

[17]  P. Dorrestein,et al.  Investigation of Premyrsinane and Myrsinane Esters in Euphorbia cupanii and Euphobia pithyusa with MS2LDA and Combinatorial Molecular Network Annotation Propagation. , 2019, Journal of natural products.

[18]  D. Westaway,et al.  Development of chemical isotope labeling LC-MS for tissue metabolomics and its application for brain and liver metabolome profiling in Alzheimer's disease mouse model. , 2019, Analytica chimica acta.

[19]  R. Vandenberg,et al.  Development of an N-Acyl Amino Acid That Selectively Inhibits the Glycine Transporter 2 To Produce Analgesia in a Rat Model of Chronic Pain. , 2019, Journal of medicinal chemistry.

[20]  Amir I. Mina,et al.  Ablation of PM20D1 reveals N-acyl amino acid control of metabolism and nociception , 2018, Proceedings of the National Academy of Sciences.

[21]  B. Spiegelman,et al.  Discovery of Hydrolysis-Resistant Isoindoline N-Acyl Amino Acid Analogues that Stimulate Mitochondrial Respiration. , 2018, Journal of medicinal chemistry.

[22]  Kristian Fog Nielsen,et al.  Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking , 2016, Nature Biotechnology.

[23]  Ruixu Yang,et al.  N-Stearoyltyrosine protects primary cortical neurons against Aβ(1-40)-induced injury through inhibiting endocannabinoid degradation. , 2015, Life sciences.

[24]  Kazuki Saito,et al.  LipidBlast Templates As Flexible Tools for Creating New in-Silico Tandem Mass Spectral Libraries , 2014, Analytical chemistry.

[25]  Chris Morley,et al.  Open Babel: An open chemical toolbox , 2011, J. Cheminformatics.

[26]  Pavel A. Pevzner,et al.  Spectral Archives: Extending Spectral Libraries to Analyze both Identified and Unidentified Spectra , 2011, Nature Methods.

[27]  CHUN WEI YAP,et al.  PaDEL‐descriptor: An open source software to calculate molecular descriptors and fingerprints , 2011, J. Comput. Chem..

[28]  H. Bradshaw,et al.  Oleoyl serine, an endogenous N-acyl amide, modulates bone remodeling and mass , 2010, Proceedings of the National Academy of Sciences.

[29]  Ruedi Aebersold,et al.  Building consensus spectral libraries for peptide identification in proteomics , 2008, Nature Methods.

[30]  OUP accepted manuscript , 2021, Nucleic Acids Research.