Determination of free desmosine and isodesmosine as urinary biomarkers of lung disorder using ultra performance liquid chromatography–ion mobility-mass spectrometry

► We have analyzed free DES/IDES levels in urine (Healthy vs. COPD). ► Targeting Free DES/IDES provides a significant reduction in sample preparation. ► Resolution of the free DES/IDES isomers is achieved in 6 min. ► Free DES/IDES levels have been quantified using ion mobility-mass spectrometry. ► Free DES/IDES levels in urine are significantly elevated in COPD patients. The elastin degradation products, desmosine (DES) and isodesmosine (IDES) are highly stable, cross-linking amino-acids that are unique to mature elastin. The excretion of DES/IDES in urine, in the free form and with associated peptide fragments, provides an indicator of lung damage in chronic obstructive pulmonary disease (COPD). A quantitative ion mobility-mass spectrometry (IM-MS) method has been developed for the analysis of free DES/IDES in urine with deuterated IDES as an internal standard. Resolution of DES/IDES isomers was achieved in less than five minutes using ultra performance liquid chromatography (UPLC) combined with ion pairing. The optimized UPLC–IM-MS method provided a linear dynamic range of 10–300 ng/mL and a limit of quantitation of 0.028 ng/mL for IDES and 0.03 ng/mL for DES (0.55 ng and 0.61 ng on column respectively). The method reproducibility (%RSD) was