HEADER.TXT

Plain ASCII key-value file. Always present. Encodes run-level metadata and per-function TOF calibration polynomials.

Status: Fully Known

HEADER.TXT is human-readable and straightforward to parse. Its presence and basic structure are consistent across all known instrument generations.

Example Content

$$ Sample Description:
$$ Acquired Date: 10-Sep-2019
$$ Acquired Time: 14:23:07
$$ Instrument: SYNAPT G2-Si#WAA123456789
$$ Operator: operator
$$ MS Method: D:\Projects\...\method.EXP
$$ Cal Function 1: -3.072e-2,9.999e-1,8.393e-5,-2.360e-6,2.529e-8,T1
$$ Cal Function 2: -3.072e-2,9.999e-1,8.393e-5,-2.360e-6,2.529e-8,T1

Observations

• Lines beginning with $$ are metadata fields
• Field name and value are separated by :
• Fields are not always present; treat all as optional
• Character encoding is 7-bit ASCII; no BOM observed
• Line endings are CRLF on Windows-generated files

Calibration Polynomial Fields

Each MS function has a corresponding $$ Cal Function N: line where N matches the 1-based function number. The value is a comma-separated list of floating-point polynomial coefficients followed by a calibration-type code.

Format

$$ Cal Function N: c0,c1,c2,...,ck,TYPE

• N = 1-based function index
• c0..ck = polynomial coefficients (5 or 6 coefficients observed)
• TYPE = calibration type: T0 (none/identity), T1 (standard TOF polynomial)
  • T0 means no calibration (identity); all coefficients will be zero or absent
  • T1 means the polynomial is applied to the raw TOF time before m/z conversion

T1 Polynomial Definition

Given the raw TOF flight time t_raw (in microseconds), the calibrated flight time is computed as a polynomial in t_raw:

t_cal = c0 + c1·t_raw + c2·t_raw² + c3·t_raw³ + ... + ck·t_raw^k

The calibrated time is then converted to m/z using the TOF physics formula:

mz = (t_cal / A_us)²

where A_us is the TOF constant derived from instrument geometry:

A_us = sqrt(m_proton · L_eff / (2 · e · V_eff)) × 10⁶

• m_proton = 1.6726219 × 10⁻²⁷ kg
• L_eff = effective flight path length in metres (from _extern.inf → Lteff field, convert mm → m)
• e = 1.6021766 × 10⁻¹⁹ C
• V_eff = effective accelerating voltage in volts (from _extern.inf → Veff field)

And the raw time t_raw in µs is derived from the stored TOF bin index:

t_raw = tof_bin × (pusher_cycle_us / 65536)

where pusher_cycle_us comes from _extern.inf (field Pusher Cycle Time or ADC Pusher Frequency, both in µs).

Observed Coefficients

Dataset	Instrument	c0	c1	c2	c3	c4	c5	Type
PXD058812	QTOF (native MS)	−3.072e-2	9.999e-1	8.393e-5	−2.360e-6	2.529e-8	(absent)	T1
PXD075602	Xevo G2-XS QTof	−4.778e-3	1.000e0	4.431e-6	−1.461e-7	−2.191e-10	5.119e-11	T1

Note: the number of coefficients can vary between 5 and 6 (at least); parsers must be tolerant of variable-length coefficient lists before the type code.

Per-Function Calibration

When multiple MS functions are present, each function has its own Cal Function N: line. In PXD075602, all three functions share the same coefficients (applied once at acquisition time from the same lock-mass reference run).

CoVar Fields

Additional lines $$ Cal CoVar N: contain the calibration covariance matrix as a flat comma-separated list of 21 floats (row-major upper triangle of a 6×6 matrix). These are used for mass accuracy estimation and are not required for basic decoding.

StdDev Fields

$$ Cal StdDev Function N: gives the calibration residual standard deviation (Da). A value of 0.0 indicates a perfect fit or a static calibration with no fit data.

Reference Sources

• PXD058812/molecular_mass_P15_01.raw _HEADER.TXT (5-coefficient T1)
• PXD075602/DHPR_11257-1.raw _HEADER.TXT (6-coefficient T1, 3 functions)
• _extern.inf (Lteff, Veff, pusher cycle time)