_PROCnnn.DAT / _PROCnnn.IDX / _PROCnnn.STS / _PROCnnn.MAX

Post-processed spectrum data created by MassLynx peak-processing step. Found only in SYNAPT G2-Si IMS acquisitions in the corpus; not present in non-IMS or native-MS-only datasets.

Status: Partially Decoded (Phase 3)

Core structure decoded. MAX file internals and PROC number assignment scheme are not fully understood.

Corpus Presence

Dataset	PROC files	Notes
PXD058812 (Q-TOF Ultima, non-IMS)	None
PXD066594 (WANG.raw, SYNAPT G2-Si, IMS)	PROC 002,003,005,006,008,009
PXD068881 (CtpA, SYNAPT G2-Si, IMS)	None
PXD075602 (DHPR, Xevo G2-XS, non-IMS)	None

CtpA is also SYNAPT G2-Si but has no PROC files; PROC file generation is apparently optional or controlled by MassLynx processing settings.

PROC Number Scheme

PROC numbers observed: 2, 3, 5, 6, 8, 9 (no 1, 4, 7). Numbers appear to be assigned in pairs sharing the same retention time:

PROC pair	RT (min)	DAT size	MAX file
002 + 003	0.2027	120000 + 551772	PROC002.MAX
005 + 006	1.3864	120000 + 544488	PROC005.MAX
008 + 009	1.3864	120000 + 540948	PROC008.MAX

Within each pair, one file has a fixed 120000-byte DAT (with MAX) and one has a variable-size DAT (without MAX). The two members appear to represent complementary projections or resolution levels of the same IMS-MS data.

The PROC numbers skip 1, 4, 7; these gaps may correspond to _FUNC001 and to IMS reference functions that are not processed into PROC files.

_PROCnnn.IDX

30-byte records, same stride as _FUNCnnn.IDX Variant B. Always exactly one record per PROC file (one "processed spectrum" per file).

Offset	Type	Description
0x00	u32	Flags (always 0)
0x04	u16	Record count (= n_records in paired .DAT)
0x06	u8	Type byte: 0x78 for fixed-size DAT (with MAX), 0x58 for variable-size DAT
0x07	u8	0x00
0x08	u32	Hardware counter; pairs at same RT share high 2 bytes
0x0C	f32	Retention time of the processed spectrum (minutes)
0x10	u16	Scan-varying count (13945-27076 in WANG corpus); purpose unclear; may be a peak count or hardware reference
0x12	u16	Small for fixed-size type (738-741 in corpus), large for variable-size (21680-50355); purpose unclear
0x14	u16	Same value for PROC pairs at identical RT; differs between RT points (34646-56336 in corpus); may be a scan-level TIC or hardware register
0x16	u32	DAT byte offset (always 0; each PROC has its own .DAT file)
0x1A	u32	0

_PROCnnn.DAT

12-byte records packed sequentially with no header. Record count is given by u16@0x04 in the paired .IDX file.

struct ProcRecord {
    u32 intensity;      // raw intensity (varies)
    u32 position;       // packed (mz_bin << 16) | dt_bin
    u32 tag;            // 0x40000000 (= f32 2.0) when intensity > 0, else 0
};

Fixed-size DAT (002/005/008 type, with MAX)

10000 records. Coarse 2D grid of mz x drift:

• 1250 unique mz_bin values
• 8 dt_bin steps per mz_bin, spaced 0x2000 (= 8192) apart
• dt_bin range: 0x0000 to 0xE000 (step 0x2000)

Position field decoding:

`mz_bin = position >> 16`
dt_bin = position & 0xFFFF

The 1250 mz_bins form a contiguous range starting from a calibration-dependent offset (e.g. mz_bin=29922 for PROC002 with RT=0.2027 in WANG.raw).

Variable-size DAT (003/006/009 type, no MAX)

~45000 records per file. Finer dt_bin spacing (step = 1712 vs 8192), more mz_bins covered:

• First observed mz_bin = 22278 (smaller than fixed-type start of 29922)
• dt_bin increments of 0x06B0 = 1712

The variable-size type likely represents the full-resolution IMS-MS peak list while the fixed-size type is a downsampled or projected version.

_PROCnnn.STS

Waters Parameter Table format (same as _FUNCnnn.STS). Always exactly one data record per file (n_desc=54, rec_size=157 bytes, n_records=1).

The 54 channels include both standard ESI/TOF fields (Cone, Collision Energy, TIC Trace A/B, Scan Push Count, Lock mass correction, Pusher Frequency) and MALDI-specific legacy fields (Linear Detector Voltage, Laser Repetition Rate, Laser Energy Coarse/Fine, Aim X/Y Position, Sample Plate Voltage, PSD fields, Source Region 1/2). The MALDI fields appear to be a fixed schema present in all Waters STS files regardless of instrument type; their values in an ESI dataset are expected to be zero or default.

See 07-func-sts.md for the Waters Parameter Table format description.

Notable channels in PROC STS:

• TIC Trace A/B (f32): TIC for this processed spectrum
• Scan Push Count (u32): number of IMS pushes summed into this spectrum
• Collision Energy (f32): collision energy used
• Cone (i16): cone voltage
• PIC Function Number (f32): back-reference to source function
• PIC Channel Number (f32): back-reference to source channel
• PIC Retention Time (f32): RT of peak apex

_PROCnnn.MAX

Present only alongside fixed-size DAT files (002/005/008 type). File sizes: 1105024, 1090456, 1083376 bytes.

Structure:

• Bytes 0-3: f32 = record count of the paired .DAT file (e.g. 10000.0)
• Bytes 4-7: zeros
• Remaining data: purpose unknown; likely full-resolution IMS mobility profiles for each (mz_bin, dt_bin) pair, enabling maximal projection along the drift axis

The .MAX suffix and the "maximum" naming convention in MassLynx processing suggest this stores the maximum-intensity projection data from Apex3D or a related peak-detection algorithm.

Interpretation

PROC files represent post-processed "peak apex" spectra extracted by MassLynx from the raw _FUNC001.DAT IMS data. Each PROC file corresponds to one discrete retention time of interest (e.g. a detected chromatographic peak). The PROC number does not correspond to a function number in _FUNCTNS.INF; rather, it is an internal MassLynx index assigned during data processing.

The paired structure (fixed + variable size at the same RT) suggests:

• Fixed-size / MAX: coarse Apex3D projection grid for visualization
• Variable-size: full list of detected (drift, mz) peak centroids