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

Mass spectrometry (MS) is widely used in proteomics research in recent years. In practice, MS is often coupled with liquid chromatography or gas chromatography to analyze complex mixtures. Retention time (RT) is a critical feature that distinguishes different components in mixtures. And RT alignment is one of the crucial methods for correlating identical components across different samples. This review provides a broad perspective of RT alignment methods and tools used in proteomics and metabolomics. Firstly, we categorize these methods and tools into four types based on the information they employ, and introduce them, respectively. Subsequently, we present the application of RT alignment in proteomics. We have emphasized that the identification-free strategy might be a potential application of RT alignment. Finally, we summarize the limitations of current methods and discuss the future direction of RT alignment.