Selection of Features with Consistent Profiles Improves Relative Protein Quantification in Mass Spectrometry Experiments.

ABSTRACT: In bottom-up mass spectrometry-based proteomics, relative protein quantification is often achieved with data-dependent acquisition (DDA), data-independent acquisition (DIA), or selected reaction monitoring (SRM). These workflows quantify proteins by summarizing the abundances of all the spectral features of the protein (e.g. precursor ions, transitions or fragments) in a single value per protein per run. When abundances of some features are inconsistent with the overall protein profile (for technological reasons such as interferences, or for biological reasons such as post-translational modifications), the protein-level summaries and the downstream conclusions are undermined. We propose a statistical approach that automatically detects spectral features with such inconsistent patter

SUBMITTER: Tsai TH 

PROVIDER: S-EPMC7261813 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature