DIAlignR Provides Precise Retention Time Alignment Across Distant Runs in DIA and Targeted Proteomics.

ABSTRACT: Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra (SWATH-MS) is widely used for proteomics analysis given its high throughput and reproducibility, but ensuring consistent quantification of analytes across large-scale studies of heterogeneous samples such as human plasma remains challenging. Heterogeneity in large-scale studies can be caused by large time intervals between data acquisition, acquisition by different operators or instruments, and intermittent repair or replacement of parts, such as the liquid chromatography column, all of which affect retention time (RT) reproducibility and, successively, performance of SWATH-MS data analysis. Here, we present a novel algorithm for RT alignment of SWATH-MS data based on direct alignment of raw MS2 chromatograms usin

SUBMITTER: Gupta S 

PROVIDER: S-EPMC6442363 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature