An understanding of what happens to therapeutic antibodies in vivo after subcutaneous injection is of high interest. Therefore, we applied the open flow microperfusion technique to extract interstitial fluid from the subcutaneous tissue. In order to analyze those biological samples, a specific and sensitive workflow was required. In this study, we present a complete workflow that enables full characterization of therapeutic antibodies after subcutaneous injection. Compared to classical pharmacokinetic approaches where only a limited number of peptides are detected, our workflow provides full sequence coverage and even enables the identification of potential quality attributes. The efficiency to purify therapeutic antibodies from biological matrixes of two different antibody capture molecules and two types of magnetic beads was compared. Furthermore, several desalting protocols were tested in the development of a miniaturized peptide map procedure. The best results were achieved using a commercial anti-human capture mAb fragment in combination with streptavidin coated magnetic beads, providing capture efficiencies of 90-100%. The optimized peptide map protocol that requires <1 μg of mAb includes two desalting steps and showed sequence coverages of 95-100%. The final method was successfully used for analysis of interstitial fluid and serum samples after a subcutaneous injection of a therapeutic antibody into a domestic pig.