omicsMIC: a comprehensive benchmarking platform for robust comparison of imputation methods in mass
Weiqiang Lin1, Jiadong Ji2, Kuan-Jui Su1
1Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA.
NAR Genomics and Bioinformatics
|June 17, 2024
Summary
Mass spectrometry omics data often contain missing values, hindering biomarker discovery. A new platform, omicsMIC, compares 28 imputation methods to aid researchers in selecting the best strategy for their data.
Area of Science:
- Biomedical data analysis
- Computational biology
- Mass spectrometry-based omics
Background:
- Mass spectrometry is crucial for proteomics, lipidomics, and metabolomics, but missing values complicate biomarker identification and biological process elucidation.
- Existing imputation methods for omics data lack comprehensive comparison, leaving researchers without clear guidance for selection.
Purpose of the Study:
- To address the challenge of missing values in mass spectrometry-based omics data.
- To provide a platform for comparing various imputation methods to aid researchers in selecting the most appropriate strategy.
Main Methods:
- Development of omicsMIC, an interactive platform for evaluating 28 different imputation methods.
- Benchmarking imputation methods using real-time visualizations of outcomes.
- Facilitating data-driven decisions in imputation method selection.
Main Results:
- omicsMIC offers a versatile framework for assessing imputation method performance.
- The platform acknowledges data heterogeneity and dataset-specific attributes.
- Empowers researchers to choose imputation strategies based on visualized results.
Conclusions:
- omicsMIC provides a valuable tool for the scientific community working with mass spectrometry-based omics data.
- Facilitates informed selection of imputation methods, improving the reliability of omics data analysis.
- Enhances the comprehensive identification of biomarkers and elucidation of biological processes.
More Related Videos
11:00Untargeted Metabolomics from Biological Sources Using Ultraperformance Liquid Chromatography-High Resolution Mass Spectrometry UPLC-HRMS
Published on: May 20, 2013
22.5K
07:34Large Scale Non-targeted Metabolomic Profiling of Serum by Ultra Performance Liquid Chromatography-Mass Spectrometry UPLC-MS
Published on: March 14, 2013
12.7K
Related Concept Videos
01:19Mass Spectrometry: Overview
5.0K
Mass spectrometry is an analytical technique used to determine the molecular mass and molecular formula of a compound. The basic principle of mass spectrometry is to generate ions from the analyte molecule and measure these ion abundances against their molecular mass. One common type of ionization, known as electrospray ionization or EI, bombards the analyte molecules in the gas phase with high-energy electron beams. The electron beams displace an electron from the molecule and leave...
5.0K
02:54Evolutionary Relationships through Genome Comparisons
5.7K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.7K
01:33Peptide Identification Using Tandem Mass Spectrometry
6.4K
Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
6.4K
01:21Mass Spectrometry: Complex Analysis
743
Mass spectrometry is an important technique for the identification of pure compounds. However, it has some limitations for the analysis of complex mixtures, often due to excessive fragmentation making the spectrum too complicated to decipher. Mass spectrometry can be combined with suitable separation methods in sequence, forming hyphenated methods, which are useful in the analysis of complex mixtures.
GC–MS is a powerful hyphenated method commonly used in forensics and environmental...
GC–MS is a powerful hyphenated method commonly used in forensics and environmental...
743
01:19MALDI-TOF Mass Spectrometry
4.8K
Mass spectrometry is a powerful characterization technique that can identify and separate a wide variety of compounds ranging from chemical to biological entities, based on their mass-to-charge ratio (m/z). The instruments that allow this detection, known as mass spectrometers, have three components: an ion source, a mass analyzer, and a detector. These spectrometers differ based on the nature of their ion source and analyzers.
Matrix-assisted laser desorption ionization (MALDI) is a commonly...
Matrix-assisted laser desorption ionization (MALDI) is a commonly...
4.8K