_extern.inf

ASCII key-value instrument parameter file. Always present. Records the instrument geometry constants and per-function acquisition method parameters needed to decode TOF time bins into m/z values.

Status: Fully Known

_extern.inf is plain text and human-readable. It is the primary source for the calibration constants Lteff, Veff, and PusherInterval that appear in every m/z decoding formula documented in this project.

Encoding

Windows-1252. Contains characters such as µ (0xB5) and ° (0xB0). Line endings are CRLF on Windows-generated files.

File Structure

The file is divided into labelled sections. Sections begin with a line ending in : (no leading whitespace). Fields within a section are indented with one or more spaces:

Parameters for <method_file_path>
Created by <masslynx_version>
<Section Heading>:
  Field Name                    value
  ...
Function Parameters - Function 1 - <FUNCTION_TYPE>
  Field Name                    value
  ...
Function Parameters - Function 2 - <FUNCTION_TYPE>
  ...

There is no strict alignment requirement; fields are whitespace-separated with the field name (possibly multi-word, possibly containing parentheses and units) on the left and the value on the right.

Flight-Time Geometry Fields

No _FUNCnnn.DAT encoding stores a TOF bin; every encoding stores m/z directly and only the _HEADER.TXT polynomial is applied. These fields describe the flight-time geometry. They are used to check the ADC sample spacing of Encoding D records (t = A_us * sqrt(m/z)), not to decode m/z. All are in the Instrument Configuration: section unless noted.

Field Name	Units	Description
Lteff	mm	Effective TOF flight path length
Veff	V	Effective accelerating voltage
PusherInterval	µs	Actual pusher cycle period (authoritative value)

PusherInterval is the pusher cycle period. Several other field names encode the same physical quantity but appear in different instrument generations or contexts:

Also observed	Notes
Pusher Cycle Time (µs)	In older Instrument Parameters sections; may read Automatic (ignore if so)
ADC Pusher Frequency (µs)	Per-function override; use if present for that function

When Pusher Cycle Time (µs) reads Automatic, use PusherInterval from the Instrument Configuration: section.

Instrument Configuration Section

Present in all observed datasets. Key fields:

Field	Observed values	Description
Lteff	1800.0-1997.94 mm	Effective flight path length
Veff	6328.24-9100.0 V	Effective accelerating voltage
Resolution	4000-22000	Nominal resolving power
Min Points in Peak	2	Minimum peak points for centroiding
Acquisition Device	WatersADC	ADC type (always seen)
PusherInterval	60.25-88.0 µs	Authoritative pusher cycle time
PusherOffset	0.0-0.25 µs	Pusher timing offset
EDC Delay Coefficient	1.33-1.40	Enhanced Duty Cycle delay constant
EDC Delay Offset	0.40 µs	EDC delay offset

IMS-capable instruments (SYNAPT G2-Si) additionally have:

Field	Description
ADC Pushes Per IMS Increment	Pushes accumulated per mobility bin (always 1)
IMS Wave Velocity (m/s)	Travelling wave velocity
IMS Wave Height (V)	Travelling wave amplitude
Trap Wave Velocity (m/s)	Trap region wave velocity
Transfer Wave Velocity (m/s)	Transfer region wave velocity
Drift Time Bins	Number of IMS drift bins (0 = auto)

Instrument Parameters Section

Contains per-run electrode voltages and source conditions. Key fields:

Field	Units	Description
Polarity	-	ES+ or ES- (electrospray polarity)
Capillary (kV)	kV	Spray capillary voltage
Sampling Cone	V	Cone voltage
Source Temperature (°C)	°C	Desolvation source temp
Desolvation Temperature (°C)	°C	Desolvation gas temp
Pusher	V	Pusher electrode voltage
Puller	V	Puller electrode voltage
Flight Tube (kV)	kV	Main flight tube voltage
Reflectron (kV)	kV	Reflectron voltage
Collision Energy	eV	Default collision energy
Detector	V	Detector voltage (MCP bias)

Function Parameters Sections

One section per MS function. Format: Function Parameters - Function N - <TYPE>

where TYPE is one of:

• TOF MS FUNCTION - MS1 scan; some MSe acquisitions also label their high-energy function this way (see "MS level" below)
• TOF PARENT FUNCTION - MSe/HDMSe low- or high-energy scan (broadband, non-selective fragmentation - [INCLUDE]'s Precursor Selection reads Everything, so there is no discrete precursor to report; see docs/format/00-overview.md's Function Concept table)
• TOF MSMS FUNCTION - MS/MS. Targeted (one fixed precursor) or data-dependent. Carries a Set Mass field (see below).
• TOF SURVEY FUNCTION, MOBILITY SURVEY FUNCTION, MOBILITY FAST DDA FUNCTION - data-dependent (DDA) acquisition: function 1 is the MS1 survey, the following functions are the MS/MS slots, each with Set Mass 0.0
• TOF DAUGHTER FUNCTION - DDA fragment scan, same Set Mass semantics as TOF MSMS FUNCTION
• TOF PRODUCT FUNCTION - MS/MS fragment scan
• TOF CALIBRATION FUNCTION - lock-mass reference channel

Key per-function fields:

Field	Units	Description
Start Mass	Da	Acquisition m/z lower limit. Not parsed into a struct field - see note below
End Mass	Da	Acquisition m/z upper limit (MSMS/DAUGHTER sections instead use MSMS End Mass, which is not recognised by the parser either). Not parsed into a struct field - see note below
Start Time (mins)	min	Acquisition start retention time
End Time (mins)	min	Acquisition end retention time
Scan Time (sec)	s	Duration of one scan
Interscan Time (sec)	s	Dead time between scans
Data Format	-	Continuum or Centroid. Not parsed. Every function in the corpus that declares it says Continuum, including lock-mass functions whose DAT holds centroids (see _FUNCnnn.DAT, "Profile or centroid")
Analyser	-	Resolution Mode or Sensitivity Mode
ADC Sample Frequency (GHz)	GHz	ADC sampling rate
ADC Pusher Frequency (µs)	µs	Per-function pusher cycle override (if set)
Calibration	-	Calibration mode: Dynamic 2 = lock-mass, Static = fixed
Set Mass	Da	Precursor m/z of an MS/MS function. Present on MS/MS sections (TOF MSMS, TOF DAUGHTER, and the DDA MS/MS slots labelled TOF SURVEY / MOBILITY SURVEY); absent from every TOF PARENT FUNCTION (MSe) section. DDA slots store 0.0, which the parser reports as absent (set_mass_da = None), never as m/z 0. In DDA bundles a non-zero value is a method default, not each scan's precursor (PXD001123, PXD010569: one value per function while the scans' precursors differ); the per-scan precursor is the Set Mass channel of _FUNCnnn.STS
... Collision Energy Ramp Start / ... Ramp End	eV	Collision-energy ramp of the function, e.g. Transfer Collision Energy Ramp Start (eV) 27.0
... Collision Energy Low / ... High	eV	Same, other spelling, e.g. Transfer MS Collision Energy Low (eV) 25.0
... Collision Energy (eV) <a> (Ramping to <b>)	eV	Same, on one line, e.g. Using Auto Transfer MS Collision Energy (eV) 15.0000 (Ramping to 25.0000)

The three ramp spellings are parsed into ExternFunction::collision_energy_ramp_ev = Some((start, end)) when end > start (a 0.0 to 0.0 ramp is no ramp).

No charge state or isolation-width field has been found on any function type in any corpus sample; Set Mass is the only precursor field _extern.inf exposes. Per-scan collision energy for MS/MS-classified functions (both targeted and MSe) comes from a separate file - see 07 - _FUNCnnn.STS's "Collision Energy" channel.

Start Mass / End Mass are not decoded. Spectrum decoding uses _FUNCTNS.INF's FunctionInfo::mz_low / mz_high. The corpus has not established whether the two pairs are aliases or bounds with different meanings, and TOF MSMS FUNCTION sections use an MSMS End Mass key instead of End Mass (Sigilweaver/OpenWRaw#24).

MS Level

Reader::ms_level assigns each function an MS level from the section label, the section's collision-energy ramp and the function's position:

1. REFERENCE: MS1.
2. TOF MSMS, TOF DAUGHTER: MS2.
3. TOF MS: MS2 only when the section records a collision-energy ramp and another non-lock-mass TOF MS function of the same bundle records none (the low-energy half of an MSe pair). Otherwise MS1.
4. Any other label (TOF PARENT, TOF SURVEY, MOBILITY SURVEY, ...): function 1, or the only function, is MS1; later functions are MS2.

Rule 3 is deliberately narrow. A ramp on a TOF MS function with no unramped partner, or a pair of TOF MS functions with no collision-energy fields at all, stays MS1, because the file then gives no unambiguous sign of which function fragments. In the public corpus rule 3 applies to 3 bundles: PXD009047 (function 2, Transfer Collision Energy Ramp Start/End 27 to 50 eV) and both PXD078353 bundles (function 2, 15.0000 (Ramping to 25.0000)). The 45 Vion bundles exported by UNIFI (PXD081045) have two TOF MS functions and no collision-energy field in _extern.inf or any _FUNCnnn.STS, so both are reported as MS1 even though function 2 is probably the high-energy function. PXD066594 has one TOF MS function with a fixed 30 eV transfer collision energy and stays MS1.

The two functions of an MSe pair have byte-identical _FUNCTNS.INF records (PXD009047, PXD078353, PXD081045), so that file does not help.

Version Line

Created by <version_string> gives the MassLynx version that wrote the file:

Observed	Instrument
4.1 SCN 965	SYNAPT G2-Si (PXD068881)
4.2 SCN1003	Q-TOF non-IMS (PXD058812)
4.2 SCN1003	SYNAPT G2-Si (PXD066594)
MassLynx v4.2 SCN966	Xevo G2-XS QTof (PXD075602)

SCN = software change notice (patch level within the major release).

Corpus Cross-Reference

Corpus	Instrument	Lteff (mm)	Veff (V)	Pusher (µs)
PXD058812/molecular_mass_P15_01.raw	Q-TOF non-IMS	1997.85	9100.0	88 (Cycle Time) → bin→t: 88/65536
PXD066594/WANG.raw	SYNAPT G2-Si IMS	1800.0	7202.70	69.0 (PusherInterval)
PXD068881/CtpA.raw	SYNAPT G2-Si IMS	1800.0	7198.65	69.0 (PusherInterval)
PXD075602/DHPR_11257-1.raw	Xevo G2-XS QTof	1800.0	6328.24	60.25 (PusherInterval)
PXD035818/17122018_TNFA_PEPTIDE_GSHH_MSMS_884.raw	SYNAPT G2-S	1800.0	7189.15	69.0 (PusherInterval)

The PXD035818 sample is the first targeted MS/MS (TOF MSMS FUNCTION) file in the corpus (Sigilweaver/OpenWRaw#13); Function 1's Set Mass reads 884.9.

Reference Sources

• Corpus files: all _extern.inf files in PXD058812, PXD066594, PXD068881, PXD075602, PXD035818
• Used by: Reader::ms_level (labels, collision-energy ramps) and Reader::precursor_mz (Set Mass, when the scan's STS file has no non-zero Set Mass). ExternInf::a_us() (flight-time constant from Lteff/Veff) is parsed but not used by any DAT decoder, since every encoding stores m/z directly