Scan Index and Data Packets
Scan index, data packets, profile, peaks
15. ScanIndexEntry
Array of scan index entries located at RunHeader.scan_index_addr. One entry
per scan. Provides the offset, size, and summary statistics for each scan's
data packet.
15.1 Version 66
| Offset | Size | Type | Field | Description |
|---|---|---|---|---|
| 0x00 | 4 | UInt32 | offset_32 | Defunct 32-bit offset |
| 0x04 | 4 | UInt32 | index | Scan number (0-based) |
| 0x08 | 2 | UInt16 | scan_event | Scan event index |
| 0x0A | 2 | UInt16 | scan_segment | Scan segment index |
| 0x0C | 4 | UInt32 | next | Index of next scan (linked list) |
| 0x10 | 4 | UInt32 | unknown_long | |
| 0x14 | 4 | UInt32 | data_size | Size of scan data packet in bytes |
| 0x18 | 8 | Float64 | start_time | Retention time (minutes) |
| 0x20 | 8 | Float64 | total_current | Total ion current |
| 0x28 | 8 | Float64 | base_intensity | Base peak intensity |
| 0x30 | 8 | Float64 | base_mz | Base peak M/z |
| 0x38 | 8 | Float64 | low_mz | Lowest M/z in scan |
| 0x40 | 8 | Float64 | high_mz | Highest M/z in scan |
| 0x48 | 8 | UInt64 | offset | File offset to ScanDataPacket (relative to data stream start) |
| 0x50 | 4 | UInt32 | unknown_long[1] | |
| 0x54 | 4 | UInt32 | unknown_long[2] |
Total size: 92 bytes per entry
15.2 Version 64
Same as v66 but without the trailing unknown_long[1] and [2]:
Total size: 84 bytes per entry
15.3 Pre-v64
No 64-bit offset field; offset at position 0x00 is the actual 32-bit offset:
Total size: 76 bytes per entry
15.4 Scan Data Location
The actual file position of scan i's data:
absolute_offset = RunHeader.data_addr + ScanIndexEntry[i].offset
16. ScanDataPacket
Each scan's raw data packet, located at the offset indicated by its ScanIndexEntry. The packet contains the mass spectrum in profile form, centroid form, or both.
16.1 Structure
| Order | Size | Type | Field | Description |
|---|---|---|---|---|
| 1 | 40 | PacketHeader | header | Sizes and M/z range (see §17) |
| 2 | header.profile_size × 4 | bytes | profile_data | Raw profile data |
| 3 | header.peak_list_size × 4 | bytes | centroid_data | Centroid peak list |
| 4 | header.descriptor_list_size × 4 | bytes | descriptor_data | Additional descriptors |
| 5 | header.unknown_stream_size × 4 | bytes | unknown_data | Unknown stream |
| 6 | header.triplet_stream_size × 4 | bytes | triplet_data | Triplet data |
All size fields in the PacketHeader are in 4-byte words (i.e., the actual byte size is 4× the stored value).
17. PacketHeader
The 40-byte header at the start of each ScanDataPacket.
| Offset | Size | Type | Field | Description |
|---|---|---|---|---|
| 0x00 | 4 | UInt32 | unknown_long[1] | |
| 0x04 | 4 | UInt32 | profile_size | Profile data size (in 4-byte words) |
| 0x08 | 4 | UInt32 | peak_list_size | Centroid data size (in 4-byte words) |
| 0x0C | 4 | UInt32 | layout | Profile layout flag: 0 or 128 |
| 0x10 | 4 | UInt32 | descriptor_list_size | Descriptor data size (in 4-byte words) |
| 0x14 | 4 | UInt32 | unknown_stream_size | Unknown data size (in 4-byte words) |
| 0x18 | 4 | UInt32 | triplet_stream_size | Triplet data size (in 4-byte words) |
| 0x1C | 4 | UInt32 | unknown_long[2] | |
| 0x20 | 4 | Float32 | low_mz | Lowest M/z in this scan |
| 0x24 | 4 | Float32 | high_mz | Highest M/z in this scan |
Total size: 40 bytes
17.1 Layout Flag
The layout field controls how ProfileChunk structures are decoded:
| Value | Meaning |
|---|---|
| 0 | No fudge factor in profile chunks (8-byte chunk preamble) |
| 128 (0x80) | Fudge factor present in profile chunks (12-byte chunk preamble) |
18. Profile
The profile data region within a ScanDataPacket. Represents the raw signal intensity as a function of frequency bins (which map to M/z values via the conversion function in the associated ScanEvent).
18.1 Structure
| Offset | Size | Type | Field | Description |
|---|---|---|---|---|
| 0x00 | 8 | Float64 | first_value | First bin's frequency (or M/z in pre-FTMS) |
| 0x08 | 8 | Float64 | step | Bin width (negative for frequency domain) |
| 0x10 | 4 | UInt32 | peak_count | Number of ProfileChunks (non-zero signal regions) |
| 0x14 | 4 | UInt32 | nbins | Total number of bins across all chunks |
Preamble size: 24 bytes
After the preamble, peak_count ProfileChunk structures follow sequentially.
18.2 Interpretation
- If
step < 0, data is in frequency domain and must be converted to M/z using the frequency-to-M/z conversion function (see §32). - If
step > 0, data is directly in M/z domain (older instruments). - "Peaks" in the profile context refers to signal peaks (regions of non-zero signal), not mass spectral peaks.
19. ProfileChunk
A contiguous run of non-zero signal values within the profile.
19.1 Layout == 0 (No Fudge)
| Offset | Size | Type | Field |
|---|---|---|---|
| 0x00 | 4 | UInt32 | first_bin |
| 0x04 | 4 | UInt32 | nbins |
| 0x08 | nbins × 4 | Float32[] | signal |
19.2 Layout > 0 (With Fudge)
| Offset | Size | Type | Field |
|---|---|---|---|
| 0x00 | 4 | UInt32 | first_bin |
| 0x04 | 4 | UInt32 | nbins |
| 0x08 | 4 | Float32 | fudge |
| 0x0C | nbins × 4 | Float32[] | signal |
19.3 M/z Calculation for a Bin
For bin index i within a chunk:
bin_index_global = chunk.first_bin + i
frequency = profile.first_value + bin_index_global * profile.step
mz = convert(frequency) # See §32
If a fudge factor is present, it is an additive m/z correction applied after conversion (it is in m/z units, typically on the order of 1e-4 to 1e-3):
mz = convert(frequency) + chunk.fudge
Applying it in the frequency domain instead shifts Orbitrap profile bins by roughly 1e-3 m/z relative to the centroid peak list.
20. Peaks
The centroid peak list within a ScanDataPacket. Contains pre-picked peaks with M/z and abundance values.
20.1 Structure
| Offset | Size | Type | Field |
|---|---|---|---|
| 0x00 | 4 | UInt32 | count |
| 0x04 | count × 8 | Peak[] | peaks |
20.2 Peak
| Offset | Size | Type | Field |
|---|---|---|---|
| 0x00 | 4 | Float32 | mz |
| 0x04 | 4 | Float32 | abundance |
Size per peak: 8 bytes