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

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.