CometFIAdapter: Integration into Quantms and Evaluation

Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China

^* Corresponding author: This email address is being protected from spambots. You need JavaScript enabled to view it.

Abstract

As the scale of mass spectrometry-based proteomics data continues to grow, the computational cost of database searching has become a major bottleneck in high-throughput data analysis. Comet is a widely used open-source database search engine in proteomics, and its recent introduction of a fragment ion indexing mechanism (Comet-FI) provides a new strategy for accelerating large-scale spectral searches. However, existing OpenMS-based standardized workflows still lack systematic support for Comet-FI at both the tool and workflow levels. To address this limitation, we designed and implemented CometFIAdapter, which extends the original database search functionality by supporting fragment ion index generation and invocation. Furthermore, CometFIAdapter was integrated into the quantms workflow, enabling the practical use of Comet-FI in standardized proteomics analysis pipelines. Benchmark experiments on public datasets showed that, on the PXD005486 dataset, Comet-FI reduced the mean database search runtime by 46.9% and reduced the mean CPU usage by 17.5%. On an additional dataset, Comet-FI reduced the mean runtime by 21.7%. Although the indexing mechanism has a limited impact on identification results, it achieves an overall favorable balance between computational efficiency and result consistency overall. In summary, these results show that CometFIAdapter provides a practical route for incorporating Comet-FI into OpenMS-based workflows, including quantms, for large-scale proteomics data analysis.