Overview

Agilent MassHunter .d is a directory, not a single file. The reader targets the modern AcqData layout (the only shape found across the 338-file PRIDE validation corpus - no legacy ChemStation DATA.MS directories were encountered):

SomeRun.d/
  AcqData/
    Contents.xml            - manifest of what's in this AcqData folder
    AcqMethod.xml            - acquisition method
    Devices.xml, DeviceConfigInfo.xml   - instrument/device config
    DefaultMassCal.xml        - default calibration
    MSActualDefs.xml           - field definitions for MSPeriodicActuals.bin
    MSScan.bin + MSScan.xsd    - per-scan index (see MSScan.bin)
    MSPeriodicActuals.bin      - instrument telemetry log
    MSProfile.bin              - profile-mode spectra (Q-TOF only, when present)
    MSPeak.bin                 - centroid/MRM spectra
    MSMassCal.bin               - per-scan calibration coefficients (Q-TOF only)
  Results/Qual/...            - post-processing outputs, not read by OpenARaw

All .xml/.xsd files are plain text, published alongside the binary data by Agilent's own acquisition software - reading them is not reverse engineering, and several of them (MSScan.xsd, MSActualDefs.xml, DefaultMassCal.xml) directly document fields inside the neighboring .bin files.

Binary files

File	Purpose	Status
MSScan.bin	Per-scan index: retention time, MS level, and byte offsets into the payload files	Confirmed
MSPeak.bin	Centroid (Q-TOF) or single-point MRM (QQQ) peak data	Confirmed
MSProfile.bin	Profile-mode intensity arrays, LZF-compressed	Confirmed
MSPeriodicActuals.bin	Instrument telemetry (pressures, temperatures, voltages, ...)	Confirmed
MSMassCal.bin	Per-scan calibration coefficient traceability (Q-TOF only)	Confirmed

See Known limitations for the specific corpus files and conditions the current reader does not handle.

Clean-room provenance

Every byte-level claim on these pages came from binary analysis of the public PRIDE corpus (see CORPUS.md) plus the plain-text .xml/.xsd schema files Agilent ships alongside its own data. No Agilent SDK, MassHunter software, or other vendor tooling was used at any point - see CONTRIBUTING.md.