Achieving a Simplified, Multi-omics Workflow


Viewing posts tagged metabolomics

Achieving a Simplified, Multi-omics Workflow

An article by Yuchen He et. al. titled “Multi-omic Single-Shot Technology for Integrated Proteome and Lipidome Analysis” was recently published as one of the cover stories in Analytical Chemistry.

This article describes a technology to achieve broad and deep coverage of multiple molecular classes simultaneously through Multi-omics (proteome, lipidome, and metabolome) single-shot technology (MOST), requiring only one column, one LC-MS instrument, and a simplified workflow.

Li lab identifies metabolite and protein biomarkers to identify prostatic inflammation with lower urinary tract symptoms

Lower urinary tract symptoms (LUTS) are common among aging men. Since inflammation is one of its indicators, it is plausible that urinary metabolite and protein biomarkers could be used to identified and diagnose inflammation-induced LUTS. In this study, the Li lab used Mass spectrometry (MS)-based multi-omics analysis to characterize the urine metabolome and proteome in a mouse model. By comparing their findings with urinary biomarkers associated with LUTS in older men, they identified creatine, haptoglobin, immunoglobulin kappa constant and polymeric Ig receptor as conserved biomarkers for prostatic inflammation associated with LUTS.

The full article, Urinary metabolomic and proteomic analyses in a mouse model of prostatic inflammation, can be viewed here.

Collaboration with Puglielli lab reveals AT-1 acts as metabolic regulator for acetyl-CoA

In a paper titled Acetyl-CoA Flux Regulates the Proteome and Acetyl-Proteome to Maintain Intracellular Metabolic Crosstalk, Inca Dieterich et al. of Prof Luigi Puglielli’s lab investigated two models of AT-1 dysregulation and altered acetyl-CoA flux: AT-1S113R/+ mice, a model of AT-1 haploin sufficiency, and AT-1 sTg mice, a model of AT-1 overexpression. The animals display distinct metabolic adaptation across intracellular compartments, including reprogramming of lipid metabolism and mitochondria bioenergetics. Our results suggest that AT-1 acts as an important metabolic regulator that maintains acetyl-CoA homeostasis by promoting functional crosstalk between different intracellular organelles.

Collaboration Yields Insight on Role of Metabolism in Bacterial Growth

Bacterial biofilms are everywhere in nature and play an important role in many clinical, industrial, and ecological settings. Although much is known about the transcriptional regulatory networks that control biofilm formation in model bacteria such as Bacillus subtilis, very little is known about the role of metabolism in this process. To address this important knowledge gap, this study used a time-resolved analysis of the metabolic changes associated with bacterial biofilm development in B. subtilis by combining metabolomic, transcriptomic, and proteomic analyses. This report serves as a unique resource for future studies and will be relevant to future research in microbial physiology and metabolism. The full publication can be found here.

Metandem, a free and online software for MS-based isobaric labeling metabolomics

Hao et al. (2019) recently published a paper in Analytica Chimica Acta detailing the utility of Metandem, a data analysis software which is aids in isobaric labeling-based metabolomics.

While mass spectrometry-based stable isotope labeling is advantageous compared to other methods of isotope labeling due to its multiplexing and accurate quantification capabilities, its data analysis requires specifically customized bioinformatic tools. However, Metandem, a free, unique and online software, can aid in the analysis of stable isotope labeling-based metabolomics data.

Metandem has a number of different features that assist in MS-based isobaric labeling, such as integrating feature extraction, metabolite quantification and identification, batch processing of multiple data files, online parameter optimization for custom datasets, data normalization and statistical analysis.

Metatandem is available free and online at

Graphical abstract for Metandem paper published by Hao et al in Analtica Chimica Acta demonstrating the software's utility in  isobaric labeling, integrating feature extraction, and metabolite quantification.