Introduction:

ProteoScape, formerly PaSER, has been transforming into a comprehensive proteomics data analysis platform that can integrate third-party tools while utilizing the concept of data streaming to realize fully customizable real-time processing workflows including on-the fly decision making based on the data generated. Recent advances in technology have decidedly allowed the field to migrate towards fast LC gradients, allowing for increasingly larger sample cohorts in studies in both data-dependent acquisition (DDA) and data-independent acquisition (DIA) modes. "Library-free" analysis of DIA data has also grown to be an increasingly alternative to generating project specific spectral library from DDA acquisitions. A significant downside of these "library-free" workflows is longer processing times due to the increased search space, especially when PTMs are considered.

Methods & Results:

Here we"ve integrated a workflow including a Spectronaut module in Bruker ProteoScape (BPS) to take advantage of the synergistic capabilities of the two software. We show that BPS is a natural platform for faster library free analysis of dia-PASEF data using Spectronaut"s directDIA+ workflow by: 1) Allowing data to be processed at a single injection level, before combining at the project level. 2) Providing same results, including FDR control, for both single injection and project level analysis, and 3) Providing an intuitive user interface for the entire workflow. We utilize this new workflow on several dataset, including a phosphorylation enriched dataset and a multi-species dataset with know ratios to help evaluate precision and accuracy of the workflow and can show more than 80% savings in time-to-results vs analysis fully after the acquisition.

Conclusion:

ProteoScape has workflows integrating academic algorithms, such as DIA-NN, or 3rd party algorithms, such as Novor, and now Spectronaut greatly reducing time-to-results for large projects while simultaneously providing detailed results at the single injection level.