Retention Time Alignment for Protein Turnover Studies Using Heavy Water Metabolic Labeling.

ABSTRACT: Retention time (RT) alignment has been important for robust protein identification and quantification in proteomics. In data-dependent acquisition mode, whereby the precursor ions are semistochastically chosen for fragmentation in MS/MS, the alignment is used in an approach termed matched between runs (MBR). MBR transfers peptides, which were fragmented and identified in one experiment, to a replicate experiment where they were not identified. Before the MBR transfer, the RTs of experiments are aligned to reduce the chance of erroneous transfers. Despite its widespread use in other areas of quantitative proteomics, RT alignment has not been applied in data analyses for protein turnover using an atom-based stable isotope-labeling agent such as metabolic labeling with deuterium oxide, D

SUBMITTER: Deberneh HM 

PROVIDER: S-EPMC10233748 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature