Analysis of protein mixtures by matrix-assisted laser desorption ionization-ion mobility-orthogonal-time-of-flight mass spectrometry

Abstract

Matrix-assisted laser desorption ionization (MALDI)-ion mobility (IM)-time-of-flight (TOF) mass spectrometry (MS) has been applied to the analysis of enzymatically digested protein mixtures. The IM-TOF MS technique is rapid relative to other approaches to coupling separation methods with mass spectrometry (e.g., LC–MS, CE–MS, etc.), and MALDI-IM-TOF MS retains the advantage of reduced chemical noise which makes chromatography–mass spectrometry such a powerful analytical method. The use of IM separation prior to mass analysis also facilitates the use of internal calibration. MALDI-IM-TOF MS was evaluated by analyzing low picomole amounts of single proteins and mixtures of proteins digested with trypsin, without using time consuming “clean-up” procedures (e.g., lyophilization, dialysis, etc.). In all cases, a larger number of predicted digest fragments and higher amino acid coverages are obtained by MALDI-IM-TOF MS when compared with a conventional MALDI-TOF MS analysis. There also appears to be less signal suppression in high pressure MALDI compared to high vacuum MALDI. For example, the ratio of lysine-to-arginine terminated digest fragments appears to be higher in high-pressure MALDI relative to high-vacuum MALDI.