MSConnect: Open-Source, End-to-End Platform for Automated Mass Spectrometry Data Management, Analysis, and Visualization.

The scale of mass spectrometry-based proteomics data sets continues to increase, and the analysis workflows are becoming more complex as various steps are carried out using a multitude of software programs developed by both commercial providers and the research community. Manually shepherding data across multiple programs and in-house-developed scripts can be error prone and labor intensive. It is also difficult for others to follow the same steps, leading to poor repeatability. We have developed an integrated data management and analysis platform termed MSConnect that enables simple and traceable processing workflows across multiple programs, thus improving repeatability and automating common backup and analysis steps from the point of data collection through summarization and visualization. The open nature of the MSConnect platform enables the diverse omics community to seamlessly integrate third-party tools or develop and automate their own unique workflows. With an open license and design architecture, MSConnect has the potential to become a community-driven platform serving a wide range of MS-based omics researchers.