Improving Proteomics Mass Accuracy by Dynamic Offline Lock Mass

Abstract

Several methods to obtain low-ppm mass accuracy have been described. In particular, online or offline lock mass approaches can use background ions, produced by electrospray under ambient conditions, as calibrants. However, background ions such as protonated and ammoniated polydimethylcyclosiloxane ions have relatively weak and fluctuating intensity. To address this issue, we implemented dynamic offline lock mass (DOLM). Within every MS1 survey spectrum, DOLM dynamically selected the strongest n background ions for statistical treatments and m/z recalibration. We systematically optimized the mass profile abstraction method to find one single m/z value to represent an ion and the number of calibrants. To assess the influence of the intensity of the analyte ions, we used tandem mass spectroscopy (MS/MS) datasets obtained from MudPIT analyses of two protein samples with different dynamic ranges. DOLM outperformed both external mass calibration and offline lock mass that used predetermined calibrant ions, especially in the low-ppm range. The unique dynamic feature of DOLM was able to adapt to wide variations in calibrant intensities, leading to averaged mass error center at 0.03 ± 0.50 ppm for precursor ions. Such consistently tight mass accuracies meant that a precursor mass tolerance as low as 1.5 ppm could be used to search or filter post-search DOLM-recalibrated MS/MS datasets.