Metabolomics

Metabolic Dynamics and Prediction of Gestational Age and Time to Delivery in Pregnant Women

Metabolism during pregnancy is a dynamic and precisely programmed process, the failure of which can bring devastating consequences to the mother and fetus. To define a high-resolution temporal profile of metabolites during healthy pregnancy, we analyzed the untargeted metabolome of 784 weekly blood samples from 30 pregnant women. Using linear models, we built a metabolic clock with five metabolites that time gestational age in high accordance with ultrasound (R = 0.92). Furthermore, two to threemetabolites can identify when labor occurs (time to delivery within two, four, and eight weeks, AUROCR0.85). Our study represents a weekly characterization of the human pregnancy metabolome, providing ahigh-resolution landscape for understanding pregnancy with potential clinical utilities.

MetNormalizer

MetNormalizer is used to normalize large scale metabolomics data.

deepPseudoMSI

The deepPseudoMSI project is the first method that convert LC-MS raw data to “images” and then process them using deep learning method for diagnosis.

metflow2

metflow2 is a R package which is used for untargeted metabolomics data processing and analysis.

metID

metID is a R packge which is used for metabolite identification based on in-house database and public database based on accurate mass, rentention time and/or MS2 spectra.

TidyMass

TidyMass project is a comprehensive computational framework that can process the whole workflow of data processing and analysis for LC-MS-based untargeted metabolomics using tidyverse principles.

Development of a Correlative Strategy To Discover Colorectal Tumor Tissue Derived Metabolite Biomarkers in Plasma Using Untargeted Metabolomics

The metabolic profiling of biofluids using untargeted metabolomics provides a promising choice to discover metabolite biomarkers for clinical cancer diagnosis. However, metabolite biomarkers discovered in biofluids may not necessarily reflect the pathological status of tumor tissue, which makes these biomarkers difficult to reproduce. In this study, we developed a new analysis strategy by integrating the univariate and multivariate correlation analysis approach to discover tumor tissue derived (TTD) metabolites in plasma samples. Specifically, untargeted metabolomics was first used to profile a set of paired tissue and plasma samples from 34 colorectal cancer (CRC) patients. Next, univariate correlation analysis was used to select correlative metabolite pairs between tissue and plasma, and a random forest regression model was utilized to define 243 TTD metabolites in plasma samples. The TTD metabolites in CRC plasma were demonstrated to accurately reflect the pathological status of tumor tissue and have great potential for metabolite biomarker discovery. Accordingly, we conducted a clinical study using a set of 146 plasma samples from CRC patients and gender-matched polyp controls to discover metabolite biomarkers from TTD metabolites. As a result, eight metabolites were selected as potential biomarkers for CRC diagnosis with high sensitivity and specificity. For CRC patients after surgery, the survival risk score defined by metabolite biomarkers also performed well in predicting overall survival time (p = 0.022) and progression-free survival time (p = 0.002). In conclusion, we developed a new analysis strategy which effectively discovers tumor tissue related metabolite biomarkers in plasma for cancer diagnosis and prognosis.

Predicting the pathological response to neoadjuvant chemoradiation using untargeted metabolomics in locally advanced rectal cancer

A panel of metabolites has been identified to facilitate the prediction of tumor response to NCRT in LARC, which is promising for the generation of personalized treatment strategies for LARC patients.

Large-Scale Prediction of Collision Cross-Section Values for Metabolites in Ion Mobility-Mass Spectrometry

The use of collision cross-section (CCS) values derived from ion mobility–mass spectrometry (IM–MS) has been proven to facilitate lipid identifications. Its utility is restricted by the limited availability of CCS values. Recently, the machine-learning algorithm-based prediction (e.g., MetCCS) is reported to generate CCS values in a large-scale. However, the prediction precision is not sufficient to differentiate lipids due to their high structural similarities and subtle differences on CCS values. To address this challenge, we developed a new approach, namely, LipidCCS, to precisely predict lipid CCS values.

MetDNA

MetDNA characterizes initial seed metabolites using a small tandem spectral library, and utilize their experimental MS2 spectra as surrogate spectra to annotate their reaction-paired neighbor metabolites which are subsequently served as the basis for recursive analysis.