Technical Challenges in Mass Spectrometry-Based Metabolomics

Abstract

Metabolomics is a strategy for analysis, and quanti cation of the complete collection of metabolites present in biological samples. Metabolomics is an emerging area of scienti c research because there are many application areas including clinical, agricultural, and medical researches for the biomarker discovery and the metabolic system analysis by employing widely targeted analysis of a few hundred preselected metabolites from 10-100 biological samples. Further improvement in technologies of mass spectrometry in terms of experimental design for larger scale analysis, computational methods for tandem mass spectrometry-based elucidation of metabolites, and speci c instrumentation for advanced bioanalysis will enable more comprehensive metabolome analysis for exploring the hidden secrets of metabolism.

The impact of genome variation and diet on the metabolic phenotype and microbiome composition of Drosophila melanogaster

“…Tissue specificity and a more fine-grained analysis of the interaction between the metabolic profile, the gut microbiome composition and the impact of environmental factors thus will be highly informative. Again, metabolomics should provide a rapid means to achieve this goal, as it was previously used to investigate the metabolome throughout the lifecycle of Drosophila 67 and in different tissues of the fly 68 , although the absolute quantifications, which we performed with the targeted assays, are still difficult to achieve using mass spectrometry based metabolomics methods 69 .…”

Current trends in isotope‐coded derivatization liquid chromatographic‐mass spectrometric analyses with special emphasis on their biomedical application

“…Based on this we can conclude that the low percentage of heavy isotope content, along with low chemical purity, could result in misinterpretation of the results and thus they should be carefully studied by the analyst. Eventually, it is noteworthy that ICD‐based metabolomics also suffer from some limitations such as false‐positive metabolites detection due to the reagent impurities and by‐products; in addition, there is no adaptation to the compounds having non‐reactive functional groups (Jiang, Jiao, & Xu, ; Matsuda, ; Scalbert et al, ). This could be overcome by using recent strategies such as universal metabolome standard (UMS) and simultaneous targeted and non‐targeted metabolomics that will be discussed in detail later (Peng, Chen, Chen, & Li, ; Takayama et al, ).…”

“…Eventually, it is noteworthy that ICD-based metabolomics also suffer from some limitations such as false-positive metabolites detection F I G U R E 1 Representative scheme for the absolute and relative quantification approaches of isotopecoded derivatization (ICD) through differential labeling of the standard or the control sample for comparison with real samples. MS/MS, tandem mass spectrometry due to the reagent impurities and by-products; in addition, there is no adaptation to the compounds having non-reactive functional groups (Jiang, Jiao, & Xu, 2016;Matsuda, 2016;Scalbert et al, 2009). This could be overcome by using recent strategies such as universal metabolome standard (UMS) and simultaneous targeted and nontargeted metabolomics that will be discussed in detail later (Peng, Chen, Chen, & Li, 2014;Takayama et al, 2019).…”

Encoding Information in Synthetic Metabolomes

“…This makes the metabolome an incredibly information-rich system, which displays diverse chemical, structural and biological dimensions [3][4][5]. Despite this complexity, improvements in protocols and e cient mass spectrometry (MS) have enabled metabolomic disease screening and drug discovery [6][7][8][9][10][11][12]. These technologies are supported by continually improving statistical tools and databases [13,14].…”