How Quanto reads Agilent MassHunter .D folders (AcqData layout), builds or uses the MSTree2.bin index, and imports MassHunter quant methods or methods from data. For classic ChemStation .D, see ChemStation / MSD. For OpenLab CDS (.dx / .pmx), see OpenLab CDS — do not treat OpenLab as MassHunter.

Raw data layout

Item Notes
Sample .D folder (MassHunter acquisition)
Acquisition data AcqData\ inside the sample folder
Index (for extract) sample.d\AcqData\MSTree2.bin
Modes Detector classifies SingleQuadrupole vs QQQ / MRM / SIM / SCAN from the embedded acquisition method and scan types

Reader add-in: AgilentMassHunterDataProvider (DLL AgilentMHData.dll). Vendor native libraries ship under:

C:\Program Files\Quanto\AddIns\VendorSupportFiles\Agilent\

Do not mix these DLLs with another Quanto build.

Indexing and MSTree2.bin

MassHunter extract needs the index file:

sample.d\AcqData\MSTree2.bin

If it is missing, Quanto’s built-in conversion writes MSTree2.bin into the sample .D. The Windows account needs write permission on that folder (and parent share). ChemStation .D does not use this step — see contrast below.

Typical conversion outcomes:

Outcome Meaning
Success Index written; extract can proceed
Already indexed MSTree2.bin (or equivalent) was already present
Error strings Corrupt MSScan or conversion failure — repair or re-acquire the .D, or re-run conversion on a writable copy

First-time indexing is usually well under a few seconds with Quanto’s native indexer (see table below and Hardware and performance). Antivirus scanning of *.d / MSTree2.bin during Analyze is a common cause of slow or failed conversion.

Native indexer vs TDAConverterConsole (measured)

Bench on laptop L (2026-09-16): fresh copies of each .D, wipe MSTree2.bin, then time Agilent TDAConverterConsole.exe vs Quanto AcqData.IndexConvert (overwrite, parallel). Two runs per mode; table shows the faster run.

Mode Sample MSScan.bin TDAConverter Quanto native Speed-up
MRM (LC QQQ) 10ppb.d (FastPositive demo) 11.6 MB 2.60 s 0.12 s ~21×
SIM (GC-MSD) B2092-Pesticide-SIM-fromQuant-1.d 0.82 MB 0.55 s 0.019 s ~29×
SCAN (GC-MSD) PesticideScan-B2079-5977-4.D 0.58 MB 0.34 s 0.050 s ~7×

Quanto’s built-in path does not need MassHunter Quant installed. Use vendor TDAConverterConsole.exe only when you prefer pre-indexing on an acquisition PC or when a lab policy requires the Agilent tool.

When MassHunter Quant / TDAConverter is needed

Quanto does not install Agilent MassHunter. Built-in conversion writes MSTree2.bin when the sample folder is writable. Lab checklist guidance: install MassHunter Quant / TDAConverterConsole.exe only if instruments do not already write MSTree2.bin and you prefer vendor-side indexing (for example on the acquisition PC) before analysts open read-only copies. For read-only network snapshots, copy to a writable study folder or pre-index on the acquisition PC.

Method import

Source Add-in (class) What you point at What comes in
MassHunter quant method AgilentMhMethod .m method folder (…\DaMethod\Quant\quantitative.xml) or .quantmethod.xml Compounds, ISTD flags, transitions, expected RT, curve hints
MassHunter method from data AgilentMassHunterDataMethod .D data folder Method inferred from acquisition / MRM content in the data file

Import: Method → Load / Import — Replace or Append (Method design). Vendor methods do not set Quanto’s Calibration mode; new work defaults to Initial calibration unless you change it.

SQ vs QQQ / SIM / MRM / SCAN

For MassHunter .D, Quanto classifies single quadrupole vs triple quadrupole (QQQ) and the acquisition modes SIM, MRM, and SCAN from the embedded acquisition method and scan types. Internally, chromatogram extraction uses ChromatogramAcquisitionMode: Auto, Scan, Sim, MsMs. Auto detects from the file and tries alternates if a channel comes back empty.

If a chromatogram stays empty: confirm the Quant ion / transition exists in that sample; force Scan / Sim / MsMs if Auto picked the wrong mode; confirm AcqData\MSTree2.bin exists or conversion returned Success / Already indexed.

Contrast: ChemStation (no index step)

Kind Provider Needs Conversion
MassHunter AgilentMassHunterDataProvider AcqData\ (+ MSTree2.bin for indexed access) Writes MSTree2.bin if missing
ChemStation / MSD AgilentChemStationDataProvider data.ms and/or dataSim.ms Native MSDChem — no index conversion

Both use .D folders but different layouts. Waiting for index conversion on ChemStation data, or opening MassHunter data without AcqData/index, causes empty or failed extracts. Details: ChemStation / MSD.

OpenLab CDS is separate

OpenLab CDS uses .dx sample/result data and .pmx processing methods via AgilentOpenLabDataProvider / AgilentOpenLabMethod. That is not MassHunter. See OpenLab CDS and Compatibility.

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