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A Review of Retention Time Alignment Methods and Tools for Proteomics Data.

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  • 1State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.

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|March 10, 2025
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Summary
This summary is machine-generated.

Retention time (RT) alignment is crucial for correlating components in mass spectrometry (MS) based proteomics and metabolomics. This review categorizes RT alignment methods, discusses their applications, and explores future directions.

Keywords:
bioinformaticsmass spectrometryproteomicsretention time alignment

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Area of Science:

  • Analytical Chemistry
  • Biochemistry
  • Proteomics
  • Metabolomics

Background:

  • Mass spectrometry (MS) is a key technology in modern proteomics and metabolomics.
  • Chromatographic separation coupled with MS is essential for analyzing complex biological mixtures.
  • Retention time (RT) is a critical parameter for component identification and sample comparison.

Purpose of the Study:

  • To provide a comprehensive overview of retention time (RT) alignment methods and tools.
  • To categorize existing RT alignment strategies based on employed information.
  • To discuss the applications and future potential of RT alignment in omics research.

Main Methods:

  • Categorization of RT alignment methods into four types based on information utilization.
  • Review of existing RT alignment tools and software.
  • Discussion of RT alignment applications in proteomics and metabolomics.

Main Results:

  • RT alignment methods are classified into four distinct categories.
  • Various RT alignment tools are presented with their underlying principles.
  • The application of RT alignment in proteomics, including identification-free strategies, is highlighted.

Conclusions:

  • RT alignment is a vital technique for cross-sample component correlation in omics studies.
  • Identification-free strategies represent a promising application area for RT alignment.
  • Current limitations and future research directions for RT alignment are identified.