ArticleAnalytical chemistry2012
Data preprocessing method for liquid chromatography-mass spectrometry based metabolomics.
Article in Analytical chemistry, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
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- Regulation of PSAT1 and PHGDH by m6A in endocrine-resistant breast cancer cells.Biochimica et biophysica acta. Molecular basis of disease · 2026Article
- MetScribeR: A Semiautomated Tool for Data Processing of In-House LC-MS Metabolite Reference Libraries.Journal of proteome research · 2025Article
- Targeting PGM3 abolishes SREBP-1 activation-hexosamine synthesis feedback regulation to effectively suppress brain tumor growth.Science advances · 2025Article
- A novel human specific lncRNA MEK6-AS1 regulates adipogenesis and fatty acid biosynthesis by stabilizing MEK6 mRNA.Journal of biomedical science · 2025Article
- Multiomics Studies on Metabolism Changes in Alcohol-Associated Liver Disease.Journal of proteome research · 2024Article
- Toxicometabolomics-based cardiotoxicity evaluation of Thiazolidinedione exposure in human-derived cardiomyocytes.Metabolomics : Official journal of the Metabolomic Society · 2024Article
- Article
- Towards inferring absolute concentrations from relative abundance in time-course GC-MS metabolomics data.Molecular omics · 2023Article
- Activated Protein C Strengthens Cardiac Tolerance to Ischemic Insults in Aging.Circulation research · 2022Article
- Chronic Kidney Disease Cohort Studies: A Guide to Metabolome Analyses.Metabolites · 2021Review
- SCOUR: a stepwise machine learning framework for predicting metabolite-dependent regulatory interactions.BMC bioinformatics · 2021Article
- Discrepancies in metabolomic biomarker identification from patient-derived lung cancer revealed by combined variation in data pre-treatment and imputation methods.Metabolomics : Official journal of the Metabolomic Society · 2021Article
- Combined exposure to polychlorinated biphenyls and high-fat diet modifies the global epitranscriptomic landscape in mouse liver.Environmental epigenetics · 2021Article
- miR-375 prevents high-fat diet-induced insulin resistance and obesity by targeting the aryl hydrocarbon receptor and bacterial tryptophanase (Theranostics · 2021Article
- Integrating Two-Dimensional Gas and Liquid Chromatography-Mass Spectrometry for Untargeted Colorectal Cancer Metabolomics: A Proof-of-Principle Study.Metabolites · 2020Article
- Mass Spectrometry-Based Metabolomics Combined with Quantitative Analysis of the Microalgal Diatom (Marine drugs · 2020Article
- Mining for Peaks in LC-HRMS Datasets Using Finnee - A Case Study with Exhaled Breath Condensates from Healthy, Asthmatic, and COPD Patients.ACS omega · 2020Article
- Cardiospecific Overexpression of ATPGD1 (Carnosine Synthase) Increases Histidine Dipeptide Levels and Prevents Myocardial Ischemia Reperfusion Injury.Journal of the American Heart Association · 2020Article
- Human Melanoma-Cell Metabolic Profiling: Identification of Novel Biomarkers Indicating Metastasis.International journal of molecular sciences · 2020Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
A set of data preprocessing algorithms for peak detection and peak list alignment are reported for analysis of liquid chromatography-mass spectrometry (LC-MS)-based metabolomics data. For spectrum deconvolution, peak picking is achieved at the selected ion chromatogram (XIC) level. To estimate and remove the noise in XICs, each XIC is first segmented into several peak groups based on the continuity of scan number, and the noise level is estimated by all the XIC signals, except the regions potentially with presence of metabolite ion peaks. After removing noise, the peaks of molecular ions are detected using both the first and the second derivatives, followed by an efficient exponentially modified Gaussian-based peak deconvolution method for peak fitting. A two-stage alignment algorithm is also developed, where the retention times of all peaks are first transferred into the z-score domain and the peaks are aligned based on the measure of their mixture scores after retention time correction using a partial linear regression. Analysis of a set of spike-in LC-MS data from three groups of samples containing 16 metabolite standards mixed with metabolite extract from mouse livers demonstrates that the developed data preprocessing method performs better than two of the existing popular data analysis packages, MZmine2.6 and XCMS(2), for peak picking, peak list alignment, and quantification.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.