Introduction

It also offers an updated implementation of the original Mass Spectrometry File Converter, replacing its former CWL-based architecture with a cleaner, modular system based on individual microservices managed by a centralized controller. It includes detailed setup instructions for running locally, deploying via Docker, and managing Kubernetes installations—covering both manual and Helm chart-based configurations for scalability. The system notably replaces traditional shared drives with S3 object storage, utilizing multi-part upload to stream large files in customizable chunks that are reassembled upon completion. This architecture ensures resilient, high-performance processing, as each chunk uploads independently—allowing parallel transfers and isolated retries without restarting the entire file transfer.