Spectronaut in the Cloud: Scalable Solutions for Large-Scale Proteomics

The advancement of liquid chromatography and mass spectrometry instrumentation has enabled the rapid acquisition of large-scale proteomics datasets. Furthermore, data-independent acquisition (DIA) has become the de facto standard for shotgun proteomics. The advantages of DIA-based proteomics are well-established, with numerous successful studies demonstrating its efficacy to answer biological questions.

However, one major challenge of large-scale DIA proteomics is the sheer volume of data generated and the substantial computational power required for analysis. Additionally, the steps required for a complete analysis of DIA data each require different amounts of computational power, memory or time.

Collectively, the acquisition and maintenance of large-scale self-hosted computing infrastructure is becoming increasingly impractical. This makes cloud computing presents a viable and scalable solution. Here, we demonstrate the analysis of a 2,899-sample dataset using Spectronaut in a cloud environment.