Relative quantification of proteins and post-translational modifications in proteomic experiments with shared peptides: a weight-based approach.

ABSTRACT:

Motivation

Bottom-up mass spectrometry-based proteomics studies changes in protein abundance and structure across conditions. Since the currency of these experiments are peptides, i.e. subsets of protein sequences that carry the quantitative information, conclusions at a different level must be computationally inferred. The inference is particularly challenging in situations where the peptides are shared by multiple proteins or post-translational modifications. While many approaches infer the underlying abundances from unique peptides, there is a need to distinguish the quantitative patterns when peptides are shared.

Results

We propose a statistical approach for estimating protein abundances, as well as site occupancies of post-translational modifications, based on quantitat

SUBMITTER: Staniak M 

PROVIDER: S-EPMC11879648 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature