Legacy .wiff.scan blocks

Status: Confirmed

.wiff.scan is a flat binary file with no container format of its own - it relies entirely on the Idx stream in the paired .wiff file (see Legacy .wiff CFBF container) to locate its data blocks.

The Idx stream

SampleSubtree/Sample1/Idx holds a 32-byte header followed by a contiguous array of 54-byte records, one per scan:

Offset	Type	Description
0x00	u32	Byte offset of the block in .wiff.scan
0x04	u32	Byte size of the block
0x0C	f32	Retention time (minutes)
0x10	u8	MS level flag (1 = MS1, 0 = MS2)
0x12	f64	Total ion current (cps)
0x1A	f64	Grid-spacing-related field (not fully resolved)

Unlike some vendor formats, the Idx stream does not store precursor m/z for MS2 scans - that lives in the not-yet-decoded DDERealTimeDataEx stream (data-dependent scans) or is defined statically in the method subtree (MRM/targeted scans).

Scan blocks

Each .wiff.scan block starts with a fixed 56-byte header (scan-specific boundaries), followed by a variable-length compressed payload.

Payload encoding

The payload is not standard LZ/entropy compression (measured entropy ~4.2-4.7 bits/byte) - it's a custom byte-level prefix encoding for an array of (delta_mz, intensity) integer pairs:

Prefix byte	Meaning
0x00-0xfb	Literal value (the byte itself)
0xfc	Next 1 byte is the value
0xfd	Next 2 bytes (little-endian)
0xfe	Next 3 bytes (little-endian)
0xff	Next 4 bytes (little-endian)

In sparse background regions, delta_mz is a large gap and intensity is baseline noise; in continuous peak regions, delta_mz is the scan's constant grid spacing and intensity is the true signal height. The reader currently exposes mz as the raw accumulated time-bin integer (not a calibrated Da value) and drops zero-intensity points as background artifacts - see Reader.