Developing IMS-IMS-MS for rapid characterization of abundant proteins in human plasma

A drift tube mass spectrometer that utilizes back-to-back ion mobility regions separated by a collisional activation zone and new autosampling [R.T. Kurulugama, S.J. Valentine, R.A. Sowell, D.E. Clemmer, Development of a high-throughput IMS-IMS-MS approach for analyzing mixtures of biomolecules, J. Proteomics 71 (3) (2008) 318-331] and data acquisition techniques [S. Trimpin, D.E. Clemmer, Ion mobility spectrometry/mass spectrometry snapshots for assessing the molecular compositions of complex polymeric systems, Anal. Chem. 80 (23) (2008) 9073-9083; C. Becker, K.N. Qian, D.H. Russell, Molecular weight distributions of asphaltenes and deasphaltened oils studied by laser desorption ionization and ion mobility mass spectrometry, Anal. Chem. 80 (22) (2008) 8592-8597; S.I. Merenbloom, S.L. Koeniger, B.C. Bohrer, S.J. Valentine, D.E. Clemmer, Improving the efficiency of IMS-IMS by a combing technique, Anal. Chem. 80 (6) (2008) 1918-1927; M.E. Belov, B.H. Clowers, D.C. Prior, W.F. Danielson III, A.V. Liyu, B.O. Petritis, R.D. Smith, Dynamically multiplexed ion mobility time-of-flight mass spectrometry, Anal. Chem. 80 (15) (2008) 5873-5883] is used to analyze tryptic peptides from proteins obtained from 70 individual human plasma samples. The combination of methods allows ions to be efficiently separated in an initial drift region (based on differences in mobilities that arise from initial conformations), activated (in order to alter conformations), and then separated again in a second drift region, prior to detection in a mass spectrometer. The two-dimensional ion mobility separation makes it possible to create a large analytical peak capacity for the complex mixture. Additionally, the mobility distributions of the ions in different states (precursor and post-activation) provide a signature that is valuable in verifying that the same ions are being examined across the distribution of individuals. Finally, because this characterization is carried out in the gas phase it is possible to obtain information in a high-throughput fashion. Here, we develop and assess an analysis that requires ~4 min per sample. While this prototype approach is at a very early stage several thousand peaks can be resolved and detected for each sample. From a comparison of 15 plasma samples analyzed with IMS-IMS-MS and LC-MS/MS techniques we find that an average of 262 +/- 54 (1[sigma]) unique peptides assigned in the latter analyses are also observed in the former. On average, these assigned peptides represent 63 +/- 9 proteins. The utility of the approach as a means of characterizing physiologies in a state-to-state fashion is discussed.