Introduction to Kuiper, a game changing new search engine for directDIA
Oliver Bernhardt, MSc (Biognosys)
Over the past years, directDIA has become the most popular workflow for processing DIA data using Spectronaut. However, for computationally challenging search spaces (e.g., unspecific searches), library-based analysis is often a more practical approach. To tackle this challenge, we created Kuiper, a new search engine designed from the ground up to efficiently process large search spaces. We report dramatic improvements in search times and identifications, particularly in the context of immunopeptidomics. In addition, this presentation will highlight other significant enhancements introduced in Spectronaut 20.
Deep dive into directDIA immunopeptidomics with Kuiper
Monika Pepelnjak, PhD (Biognosys)
While the proteomics field has largely transitioned from DDA to DIA, DDA remains widely used in immunopeptidomics. Here, we present a novel, fully integrated, library-free DIA workflow for class I and class II immunopeptidomics that is both sensitive and time-efficient. To evaluate the performance of Kuiper within this new pipeline, we compared Spectronaut 20 to Spectronaut 19 using a library-free approach across more than 25 immunopeptidomics experiments. We validated that over 90% of identified peptides were predicted to be strong binders and exhibited the expected peptide-length distribution. Furthermore, the peptide motifs derived from these binders showed high similarity across searches and aligned well with known binding motifs.
