Impact of the Identification Strategy on the Reproducibility of the DDA and DIA Results.

ABSTRACT: Data-independent acquisition (DIA) is a promising technique for the proteomic analysis of complex protein samples. A number of studies have claimed that DIA experiments are more reproducible than data-dependent acquisition (DDA), but these claims are unsubstantiated since different data analysis methods are used in the two methods. Data analysis in most DIA workflows depends on spectral library searches, whereas DDA typically employs sequence database searches. In this study, we examined the reproducibility of the DIA and DDA results using both sequence database and spectral library search. The comparison was first performed using a cell lysate and then extended to an interactome study. Protein overlap among the technical replicates in both DDA and DIA experiments was 30% higher with libra

SUBMITTER: Fernandez-Costa C 

PROVIDER: S-EPMC7898222 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature