Analysis of peptides by denaturing ultrafiltration and LC-MALDI-TOF-MS.

The dynamic range of complex biological samples represents a challenge for mass spectrometric -characterization. Removal of high abundant proteins is a prerequisite for a successful mass spectrometric analysis of low abundant analytes. In particular, plasma and serum proteome span at least ten orders of magnitude and represent a major challenge for biomarker discovery. Immunoaffinity depletion is the most common methods of removal of high abundant proteins. Here we describe coupling of denaturing ultrafiltration, an alternative depletion strategy, with reverse-phase fractionation and mass spectrometry for characterization of low-molecular-weight proteins and peptides.