Analysis of biopharmaceutical proteins in biological matrices by LC-MS/MS II. LC-MS/MS analysis

•Overview of topics relating to the bioanalysis of biopharmaceutical proteins.•Biological matrices, notably blood serum and plasma.•Quantitative LC-MS analysis with low-resolution and high-resolution MS.•Signature peptide and internal standards.•Data-independent acquisition (DIA) collects all data in a single analysis.

The first section of Part II describes the current strategies for mass spectrometric (MS) detection in the selected reaction monitoring (SRM) mode which has become the method of choice to quantify peptides. We then discuss the selection of signature peptides, SRM transitions and labeled internal-standard peptides to obtain the best assay selectivity. We also present improved assay selectivity on triple-quadrupole linear ion trap using MS3 and differential mobility MS. We dedicate the final section to alternative approaches based on high-resolution data-independent acquisition.