Oral Presentation 23rd Annual Lorne Proteomics Symposium 2018

Discovery DIA: All Ion fragmentation on the timsTOF Pro (#67)

Daryl Wilding-McBride 1 , Giuseppe Infusini 1 , Markus Lubec 2 , Oliver Raether 2 , Andrew Webb 1
  1. The Walter & Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
  2. Bruker Daltonics, Bremen, Germany

Data Independent Acquisition (DIA) strategies, where all peptides are systematically fragmented using mass-isolation windows, are being rapidly adopted for quantitative proteomics. These approaches provide robust quantitative data, but are generally at the expense of discovering new peptides from samples being analysed. While a few DIA approaches also acquire MS1 information, all of these approaches are fundamentally limited by current MS technology, resulting in slow cycle times and reduced duty cycle. In particular, with improvements in chromatography (producing <4 sec FWHM peaks) now providing significant gains in sensitivity and peak capacity, current DIA sampling rates (~2.5 – 3.5 sec) are too slow for reliable and accurate quantitation. Furthermore, the use of narrow isolation windows (4 - 9m/z windows) restricts the duty cycle to a small fraction of the total ion current.
The recently developed trapped ion mobility spectrometry (TIMS) from Bruker adds an innovative dimension to quadrupole time-of-flight (QTOF). The second generation dual TIMS analyser in the timsTOF Pro has advantages over other IMS-QTOF configurations, where ions are released dependent on their mobility from the second section of the TIMS analyser, while the further incoming ions can be accumulated in parallel in the first part of the TIMS analyser. This parallel accumulation theoretically allows duty cycles of up to 100% to be achieved, with no ion loss. Additionally, the MS1 mobility is encoded in the MS2 data, facilitating mobility correlated extraction of MS1 and MS2 features, generating spectra that can be identified with conventional database search algorithms. Overall, this approach provides a comprehensive unbiased acquisition of samples at or near 100% duty cycle, but without the need for a spectral library.