Enabling re-executable workflows with near-realtime visualization, provenance capture and advanced querying for mass spectrometry data

Mass spectrometry imaging (MSI) enables simultaneous spatially-resolved analysis of numerous ionizable molecules on a sample surface. Ambient ionization techniques are attractive because they enable imaging without sample pretreatment. The current analysis pipeline involves analyzing the data coming off the instrument using a tool called MSI Quickview and saving the results onto a storage drive before moving on to the next experiment. While this works well for single datasets, there is a demand for more scalable, flexible workflows that are re-executable across datasets, support extensive querying and ease collaboration. Here, we present a workflow that moves data analysis from a mere desktop application for single experiments to a more general capability that can be possibly extended to perform multi-modal analysis across datasets. The core components of the workflow include (1) MSI Quickview, a desktop application for the near-real time visualization and analysis of mass spectrometry data; (2) Provenance Environment (ProvEn), a provenance production and collection framework that provides components supporting the production and collection of provenance information for distributed application environments; (3) Elasticsearch, a readily-scalable, broadly-distributable, enterprise-grade search engine that is accessible through an elaborate and extensive API to power extremely fast indexing and searches that support your data discovery applications; (4) Logstash, processing of log files; and (5) Kibana, a platform to visualize, analyze and explore data from multiple sources including Elasticsearch and Logstash.