Erin Baker, Ph.D., is a bioanalytical chemist with more than 14 years’ experience utilizing ion mobility spectrometry in conjunction with mass spectrometry (IMS-MS) to study biological systems. In the last 8 years she has worked primarily on IMS-MS applications in the field of proteomics and more recently she has studied IMS-MS metabolomic and lipidomic separations. Her research involves the development and evaluation of high-throughput IMS-MS, FAIMS-IMS-MS and LC-IMS-MS analyses to quickly study numerous samples in a short time period without losing valuable biological information. She has previously evaluated short LC gradients for use with IMS-MS in proteomic and lipidomic analyses, and is presently working with the Informatics team to design and implement software tools that automatically analyze the complex multidimensional data.

Utilizing Skyline to Analyze Multidimensional LC-IMS(CID)-MS Data

Ion mobility spectrometry (IMS) in conjunction with liquid chromatography separations and mass spectrometry offers a range of possibilities for analyzing complex biological samples.  While a number of informatic tools exist to analyze LC-MS-based proteomics data, many of these tools do not have the unique requirements for analyzing the 3-dimensional LC-IMS-MS data. Over the last year, Skyline has successfully incorporated IMS information into their LC-MS analyses allowing better characterization of LC-IMS(CID)-MS data. In this presentation I will illustrate how Skyline has helped us understand the differences between acquiring LC-IMS(CID)-MS data taken in an all-ions fragmentation mode versus using a SWATH approach.