Common extract, add-in, and license problems. For install layout see Installation and folders. For vendor formats see ChemStation, SCIEX, and Shimadzu.

MassHunter: AcqData, MSTree2.bin

MassHunter .D samples need an AcqData folder. Indexed extract looks for:

sample.d\AcqData\MSTree2.bin

If that file is missing, Quanto writes the index into the sample.D. The Windows account needs write permission on the .D folder.

Index conversion is MassHunter only. ChemStation .D reads natively via MSDChem (ChemStation vendor notes).

ConvertResult outcomes (MassHunter index)

When Quanto runs or skips conversion, typical outcomes are:

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

Write permissions on .D

Symptom Check
Convert fails / index not written NTFS write on the sample .D (and parent share)
Read-only network snapshot Copy to a writable local or study folder, or pre-index on the acquisition PC

ChemStation vs MassHunter .D provider

Both use .D folders, but different add-ins and file layouts:

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

Wrong expectations (waiting for index conversion on ChemStation data, or opening MH data without AcqData/index) cause empty or failed extracts. Confirm which vendor created the folder.

SCIEX: MRM-centric extract

SCIEX WIFF extract is MRM-centric (transitions from the WIFF via Clearcore2). Empty or unexpected chromatograms often mean the method ions do not match what is in the file, or the multi-sample #n selection is wrong.

Sample data files not found: rows named 0455.wiff#n still use 0455.wiff in the batch folder. #n is the injection index, not part of the filename. See SCIEX vendor notes.

Shimadzu: MRM/SRM-centric extract

Shimadzu .lcd extract is MRM/SRM-centric (Q1 / Q3 / CE from LabSolutions IO). Empty chromatograms often mean the method ions do not match the file, or VendorSupportFiles\Shimadzu is missing. See Shimadzu vendor notes.

Empty chromatogram in Auto mode

Internal acquisition mode is Auto, Scan, Sim, or MsMs. Auto detects from the file and tries alternates if a channel comes back empty. If the chrom stays empty:

  1. Confirm the Quant ion / transition exists in that sample.
  2. Force Scan / Sim / MsMs on the Quant if Auto picked the wrong mode.
  3. Confirm the correct data provider (MH vs ChemStation vs SCIEX vs Shimadzu).
  4. For MH, confirm AcqData\MSTree2.bin exists or conversion succeeded (Success / Already indexed).
  5. For ChemStation, confirm data.ms / dataSim.ms are present.

Add-in failed to load

Add-ins load from C:\Program Files\Quanto\AddIns\:

Folder Role
DataProvider\ Raw data readers
Integrator\ Peak detection
MethodImporter\ Vendor methods
View\ External review grids
VendorSupportFiles\Agilent\ / Sciex\ / Shimadzu\ Native vendor DLLs

Checks:

See also Creating add-ins.

License blocks save

After the 21-day installation grace, save is blocked when recent samples (acquired within 30 days) lack an instrument serial license. Unlicensed serials are highlighted earlier. Details: Licensing.

Cloudflare / web cache

Quanto is a desktop app. Browser Cloudflare cache, CDN, or site cookies do not affect Analyze, licenses, or local .qtb files. Website downloads of example zips are separate from the running application.