AlphaPept: a modern and open framework for MS-based proteomics.

ABSTRACT: In common with other omics technologies, mass spectrometry (MS)-based proteomics produces ever-increasing amounts of raw data, making efficient analysis a principal challenge. A plethora of different computational tools can process the MS data to derive peptide and protein identification and quantification. However, during the last years there has been dramatic progress in computer science, including collaboration tools that have transformed research and industry. To leverage these advances, we develop AlphaPept, a Python-based open-source framework for efficient processing of large high-resolution MS data sets. Numba for just-in-time compilation on CPU and GPU achieves hundred-fold speed improvements. AlphaPept uses the Python scientific stack of highly optimized packages, reducing the co

SUBMITTER: Strauss MT 

PROVIDER: S-EPMC10924963 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature