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Quantitative protein analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS) in the selected reaction monitoring (SRM) mode is developing into a major alternative to current immunochemical assays.In order to quantify human matrix metalloprotease-9 (MMP-9) in bronchoalveolar lavage fluid (BALF) from patients having undergone lung transplantation, we developed an SRM assay for microfluidics-based nanoLC-MS/MS on a triple quadrupole mass spectrometer based on two signature peptides: AVIDDAFAR and AFALWSAVTPLTFTR.