Non-target analysis (NTA) employing high-resolution mass spectrometry (HRMS) coupled with liquid chromatography is increasingly being used to identify chemicals of biological relevance. HRMS datasets are large and complex making the identification of potentially relevant chemicals extremely challenging. As they are recorded in vendor-specific formats, interpreting them is often reliant on vendor-specific software that may not accommodate advancements in data processing. Here we present InSpectra, a vendor independent automated platform for the systematic detection of newly identified emerging chemical threats. InSpectra is web-based, open-source/access and modular providing highly flexible and extensible NTA and suspect screening workflows. As a cloud-based platform, InSpectra exploits parallel computing and big data archiving capabilities with a focus for sharing and community curation of HRMS data. InSpectra offers a reproducible and transparent approach for the identification, tracking and prioritisation of emerging chemical threats.