Overview

SCIEX legacy acquisitions are a pair of files: sample.wiff (metadata, methods, and the scan index) and sample.wiff.scan (the actual spectrum payload). Neither file is self-describing on its own - .wiff.scan has no container format at all, and relies entirely on an index stream inside the paired .wiff file to locate its data blocks.

sample.wiff         - CFBF/OLE2 container: methods, sample metadata, Idx stream
sample.wiff.scan    - flat binary file: global header + variable-length scan blocks

.wiff uses Microsoft's public Compound File Binary Format (CFBF/OLE2) - reading its stream tree is not reverse engineering SCIEX's own work, only the contents and layout of the streams inside it are.

Files

File	Purpose	Status
Legacy .wiff CFBF container	Method/sample metadata stream tree, including the Idx scan index	Confirmed
Legacy .wiff.scan blocks	Block index layout and the custom token-stream payload encoding	Confirmed
.wiff2 container	SCIEX's newer, self-contained, proprietary-encrypted format	Unsolved, not readable

Clean-room provenance

Every byte-level claim on these pages came from binary analysis of the public PRIDE corpus (see CORPUS.md) plus the public CFBF/OLE2 container specification. No SCIEX SDK, Analyst software, or other vendor tooling was used at any point - see CONTRIBUTING.md.