A quality control of proteomic experiments based on multiple isotopologous internal standards

[Display omitted] •Toward harmonization of proteomic data.•Simple protocol for internal quality control.•Use of multiple variants of isotopically labeled peptides. The harmonization of proteomics experiments facilitates the exchange and comparison of results. The definition of standards and metrics ensures reliable and consistent data quality. An internal quality control procedure was developed to assess the different steps of a proteomic analysis workflow and perform a system suitability test. The method relies on a straightforward protocol using a simple mixture of exogenous proteins, and the sequential addition of two sets of isotopically labeled peptides added to reference samples. This internal quality control procedure was applied to plasma samples to demonstrate its easy implementation, which makes it generic for most proteomics applications.