Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions

MacLean, Brendan X.; Pratt, Brian S.; Egertson, Jarrett D.; MacCoss, Michael J.; Smith, Richard D.; Baker, Erin S.

doi:10.1007/s13361-018-2028-5

Title: Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions

Journal Article · Wed Jul 25 00:00:00 EDT 2018 · Journal of the American Society for Mass Spectrometry

DOI:https://doi.org/10.1007/s13361-018-2028-5· OSTI ID:1503220

MacLean, Brendan X.; Pratt, Brian S.; Egertson, Jarrett D.; MacCoss, Michael J.; Smith, Richard D.;

Recent advances in ion mobility spectrometry (IMS) have illustrated its power in determining the structural characteristics of a molecule, especially when coupled with other separations dimensions such as liquid chromatography (LC) and mass spectrometry (MS). However, these three separation techniques together greatly complicate data analyses, making better informatics tools essential for assessing the resulting data. In this manuscript, Skyline was adapted to analyze LC-IMS-CID-MS data from numerous instrument vendor datasets and determine the effect of adding the IMS dimension into the normal LC-MS molecular pipeline. For the initial evaluation, a tryptic digest of bovine serum albumin (BSA) was spiked into a yeast protein digest at seven different concentrations and Skyline was able to rapidly analyze the MS and CID-MS data for 38 of the BSA peptides. Calibration curves for the precursor and fragment ions were assessed with and without the IMS dimension. In all cases, addition of the IMS dimension removed noise from co-eluting peptides with close m/z values, resulting in calibration curves with greater linearity and lower detection limits. This study presents an important informatics development since to date LC-IMS-CID-MS data from the different instrument vendors is often assessed manually and cannot be analyzed quickly. Because these evaluations require days for the analysis of only a few target molecules in a limited number of samples, it is unfeasible to evaluate hundreds of targets in numerous samples. Thus, this study showcases Skyline’s ability to work with the multidimensional LC-IMS-CID-MS data and provide biological and environmental insights rapidly.

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Research Organization:: Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE

DOE Contract Number:: AC05-76RL01830

OSTI ID:: 1503220

Report Number(s):: PNNL-SA-133839

Journal Information:: Journal of the American Society for Mass Spectrometry, Vol. 29, Issue 11; ISSN 1044-0305

Publisher:: American Society for Mass Spectrometry

Country of Publication:: United States

Language:: English

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