_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.
Key Fields for m/z Decoding
These fields are required to convert a stored TOF bin index to 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 field used to convert a bin index to a raw flight
time:
t_raw_us = tof_bin * (PusherInterval / 65536)
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- standard MS1 or MS2 survey scanTOF PARENT FUNCTION- survey + auto-MS/MS (DDA)TOF PRODUCT FUNCTION- MS/MS fragment scanTOF CALIBRATION FUNCTION- lock-mass reference channel
Key per-function fields:
| Field | Units | Description |
|---|---|---|
Start Mass | Da | Acquisition m/z lower limit |
End Mass | Da | Acquisition m/z upper limit |
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 |
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 |
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) |
Reference Sources
- Corpus files: all
_extern.inffiles in PXD058812, PXD066594, PXD068881, PXD075602 - Used by:
_HEADER.TXTcalibration polynomial,_FUNCnnn.DATEncoding A/C m/z decode