New software will accelerate data-independent acquisition (DIA) proteomics experiments

Biognosys has announced a major update to Spectronaut 13, which will allow scientists to build libraries from PASEF (DDA) and analyze diaPASEF (DIA) data acquired using the timsTOF Pro.

Incorporating the ion mobility dimension into the data acquisition, timsTOF Pro allows for up to 100% sampling of the peptide precursor ion current using the new ion mobility-based Parallel Accumulation-Serial Fragmentation (PASEF) workflow.

This is an ideal complement to data-independent acquisition (DIA), a parallel data acquisition method that captures fragment ions over a large precursor mass range.

Analyzing such multidimensional, highly convoluted data requires new algorithms and workflows. At Biognosys, in collaboration with Bruker, we have been busy adding support for this data format into Spectronaut. An initial evaluation has demonstrated excellent performance in terms of speed, sensitivity, and quantitative results.

Support for PASEF (DDA) and the complete workflow analysis of diaPASEF comes with the latest update of Spectronaut 13:

  • Generation of an ion mobility enhanced library from PASEF DDA data using our Pulsar search engine algorithm.
  • Targeted analysis of diaPASEF runs using the ion mobility enhanced library.

If you are not yet a Spectronaut user, you can request a free trial by emailing [email protected] The upgrade is available for all current users of Spectronaut 13 with an active update and support plan.

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