IceR improves proteome coverage and data completeness in global and single-cell proteomics.

ABSTRACT: Label-free proteomics by data-dependent acquisition enables the unbiased quantification of thousands of proteins, however it notoriously suffers from high rates of missing values, thus prohibiting consistent protein quantification across large sample cohorts. To solve this, we here present IceR (Ion current extraction Re-quantification), an efficient and user-friendly quantification workflow that combines high identification rates of data-dependent acquisition with low missing value rates similar to data-independent acquisition. Specifically, IceR uses ion current information for a hybrid peptide identification propagation approach with superior quantification precision, accuracy, reliability and data completeness compared to other quantitative workflows. Applied to plasma and single-cell

SUBMITTER: Kalxdorf M 

PROVIDER: S-EPMC8352929 | biostudies-literature | 2021 Aug

REPOSITORIES: biostudies-literature