A simple tool extends TIMSTOF compatibility with historic data processing tools and enables ion mobility-enhanced spectral libraries

Abstract

AbstractTrapped ion mobility mass spectrometry is proving to be a disruptive technology in LCMS based proteomics. One primary drawback of this hardware is the lack of compatibility with the hundreds of data processing pipelines historically in use. This study describes a simple data conversion tool that “folds” the TIMSTOF ion mobility data into the MS2 fragmentation spectra allowing simple downstream processing. Little to no detriment in the assignment of peptide spectral matches is observed when “folding” the 1/k0 value into the low mass region. To demonstrate one utility of TIMS Folding, spectral libraries are provided in multiple common formats that were constructed from the same files both with and without folded ion mobility data. When new data is acquired and folded using the same parameters prior to data processing the folded ion mobility data can be used as an additional metric for peptide match confidence against folded spectral libraries.