ArticleJournal of the American Society for Mass Spectrometry2009
A signal filtering method for improved quantification and noise discrimination in fourier transform ion cyclotron resonance mass spectrometry-based metabolomics data.
Article in Journal of the American Society for Mass Spectrometry, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- The effect of perhexiline on myocardial protection during coronary artery surgery: a two-centre, randomized, double-blind, placebo-controlled trial.European journal of cardio-thoracic surgery : official journal of the European Association for Cardio-thoracic Surgery · 2015Trial
- CellMate─A Deep Learning-Assisted Single-Cell Data Processing Platform.Analytical chemistry · 2026Article
- Statistical methods and resources for biomarker discovery using metabolomics.BMC bioinformatics · 2023Review
- 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
- Fast and sensitive flow-injection mass spectrometry metabolomics by analyzing sample-specific ion distributions.Nature communications · 2020Article
- Untargeted metabolomic analysis and pathway discovery in perinatal asphyxia and hypoxic-ischaemic encephalopathy.Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism · 2019Article
- Pre-analytic Considerations for Mass Spectrometry-Based Untargeted Metabolomics Data.Methods in molecular biology (Clifton, N.J.) · 2019Article
- Detection of high-risk carbapenem-resistant Klebsiella pneumoniae and Enterobacter cloacae isolates using volatile molecular profiles.Scientific reports · 2018Article
- Parallel detection in a single ICR cell: Spectral averaging and improved S/N without increased acquisition time.International journal of mass spectrometry · 2018Article
- Bottled aqua incognita: microbiota assembly and dissolved organic matter diversity in natural mineral waters.Microbiome · 2017Article
- Comprehensive list of metabolites measured by DI-FTICR mass spectrometry in thyme plants with contrasting tolerance to drought.Data in brief · 2017Article
- Article
- Application of Passive Sampling to Characterise the Fish Exometabolome.Metabolites · 2017Article
- Metabolomics reveals an involvement of pantothenate for male production responding to the short-day stimulus in the water flea, Daphnia pulex.Scientific reports · 2016Article
- A complete workflow for high-resolution spectral-stitching nanoelectrospray direct-infusion mass-spectrometry-based metabolomics and lipidomics.Nature protocols · 2016Article
- Galaxy-M: a Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data.GigaScience · 2016Article
- Article
- Omega-3 and alpha-tocopherol provide more protection against contaminants in novel feeds for Atlantic salmon (Toxicology reports · 2016Article
- Establishing ion ratio thresholds based on absolute peak area for absolute protein quantification using protein cleavage isotope dilution mass spectrometry.The Analyst · 2014Article
- Distinguishing between the metabolome and xenobiotic exposome in environmental field samples analysed by direct-infusion mass spectrometry based metabolomics and lipidomics.Metabolomics : Official journal of the Metabolomic Society · 2014Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Direct-infusion electrospray-ionization Fourier transform ion cyclotron resonance mass spectrometry (DI ESI FT-ICR MS) is increasingly being utilized in metabolomics, including the high sensitivity selected ion monitoring (SIM)-stitching approach. Accurate signal quantification and the discrimination of real signals from noise remain major challenges for this approach, with both adversely affected by factors including ion suppression during electrospray, ion-ion interactions in the detector cell, and thermally-induced white noise. This is particularly problematic for complex mixture analysis where hundreds of metabolites are present near the noise level. Here we address relative signal quantification and noise discrimination issues in SIM-stitched DI ESI FT-ICR MS-based metabolomics. Using liver tissue, we first optimized the number of scans (n) acquired per SIM window to address the balance between quantification accuracy versus acquisition time (and thus sample throughput); a minimum of n = 5 is recommended. Secondly, we characterized and computationally-corrected an effect whereby an ion's intensity is dependent upon its location within a SIM window, exhibiting a 3-fold higher intensity at the high m/z end. This resulted in significantly improved quantification accuracy. Finally, we thoroughly characterized a three-stage filter to discriminate noise from real signals, which comprised a signal-to-noise-ratio (SNR) hard threshold, then a "replicate" filter (retaining only peaks in r-out-of-3 replicate analyses), and then a "sample" filter (retaining only peaks in >s% of biological samples). We document the benefits of three-stage filtering versus one- and two-stage filters, and show the importance of selecting filter parameters that balance the confidence that a signal is real versus the total number of peaks detected.
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Registered trials
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.