Quanto user guideAll documentation

Set up a method from scratch

This walk-through uses the menu names in Quanto. Each step links to the topic page.

1. Start a batch

File → New batch… creates the batch. In Batch properties, leave the calibration mode on Initial unless you need partial updates or brackets. See Bracketing.

The new method has no analytes yet. The editor shows the SCAN hint until you add one.

2. Add samples and set types and levels

File → Add samples… and choose the data files. See Supported data.

In View → Samples:

  • Set Type to Calibration, QC, CCV, Blank, Solvent, or Sample (the unknown). CCV is a continuing calibration verification. See Continuing calibration verification.
  • Set Dose to the level name (L1, L2, IS, …). Create the names later under Doses if they are not there yet.
  • Set dilution, limit group, and calibration group when you use them.

Save with File → Save batch….

3. Create analytes

Method → Edit method… (F10).

  • From a chromatogram: Add → Analyte… opens Compound Discovery. See Compound Discovery and the starting points below.
  • By hand: Add → Analyte (blank row) inserts an empty analyte. Type the name, the expected RT, and the acquisition key.

Create analytes from all in Compound Discovery adds every discovered compound (or the rows you selected).

4. Quants, qualifiers, and retention windows

In the method editor, open Quants, Channels, and the qualifier list.

  • The quant channel is the ion or transition used for the amount.
  • Add qualifier ions, or use Add from spectrum on a selected stick. See Qualifiers.
  • Set RT and the time window (default 0.5 minutes). See Peak identification.

5. Internal standards

Set the analyte type to ISTD. On each target quant, choose that ISTD quant as the internal standard. Give the ISTD a dose named IS with the spike concentration. ISTD curves use Average of response factors. See Quantitation.

6. Calibration levels

View → Doses holds the level names. View → Analyte doses holds the concentration of each analyte at each level. Turn Use off for a level that should not enter the curve.

Method → Create doses from sample dose builds rows from the dose names already on the samples. See Doses.

7. Curve fit

On a new target quant the fit is already Linear, origin Force, weighting Equal. Change Fit, Origin, or Weight only when the method needs a different model. See Calibration curves.

8. Integration and thresholds

On the channel, set the integrator (default Quanto) and, if the trace is noisy, the Savitzky–Golay length and order. Propose SG width suggests a length from the current sample.

Set Threshold absolute on the channel, or Threshold % of dose response and Threshold dose on the quant. Calibration and QC ignore the threshold. See Integration and Smoothing.

9. Checks and limit groups

View → Limit groups adds a group. Assign it on the sample. On Limits, enter recovery, concentration, minimum R², and qualifier limits for each analyte name. See Limit groups and Checks.

Method → Qualifier tolerances… chooses GCMS(EI), China GB, or Other.

10. Save, process, review, report

Method → Save method… writes the .qtm. File → Save batch… writes the .qtb.

Then:

  1. Analyze → Get signals
  2. Analyze → Integrate
  3. Analyze → Quantitate

Review in Results, Sample details, Result details, and Calibration. See Sample review and Analyte review.

View → Report runs the workbook. See Report templates.

Starting points

All of these go through Method → Load or import… unless the subsection says Compound Discovery. Load replaces the method. Append adds analytes under another acquisition key.

1. MRM acquisition method

Supported when the file is a quant method or an MRM method file:

  • MassHunter .m or .quantmethod.xml that already contains MRM compounds.
  • ChemStation .M with qdb.mth.
  • Shimadzu .lcm, .gcm, or .qgm (MRM/SRM compounds).

Method → Load or import…, choose the file, and import (replace or append).

What you get: compound names, transitions (precursor and product), and the retention times stored in that method. MassHunter and ChemStation quant methods also bring ISTD links, curve settings, and levels when the file has them. Shimadzu method files bring the MRM/SRM compounds; check levels and the curve afterwards.

Then check qualifier ratios, the time window, doses, and the fit. New quants you add yourself still default to Linear, Force, Equal. Imported fits stay as they were imported.

A SCIEX .msm acquisition method is not imported. Use the .wiff data file (below) or build the analytes by hand.

2. SIM acquisition method

There is no importer whose only job is a SIM acquisition method. SIM compounds are imported when they are already inside a MassHunter quant method or a ChemStation qdb.mth. A SIM-only acquisition method that is not one of those quant files is not a supported starting point.

For SIM data, use the SIM data-file path below.

3. MassHunter quant method

Supported. Method → Load or import… and choose the .m folder or the .quantmethod.xml file (quantitative.xml in the method folder is the same content).

What you get: the quant method’s compounds, ions or transitions, names, expected RT, ISTD relationships, calibration levels, and curve settings, as far as the file contains them. Group names from the MassHunter compound group are mapped onto the analyte group.

Afterwards: confirm the acquisition key (it follows the method file name when you append), qualifier tolerances, limit groups (Quanto does not invent your reporting limits), and libraries. Save the method as .qtm.

4. MRM data file

Supported. The method is built from transitions in the data file, not from a quant method.

  • Agilent MassHunter .D that contains MRM transitions. Duplicate folders are skipped.
  • SCIEX .wiff (MRM transitions). .msm is not used.
  • Waters .raw (MRM compounds).
  • Shimadzu .lcd, .gcd, .qgd, or .lrd (MRM/SRM compounds).

Method → Load or import… and point at that file or folder.

What you get: names when the file has them, transitions, and retention times stored with the acquisition. You do not get a finished calibration table, ISTD assignments, or limits unless that vendor file stored them. Enter doses, ISTD links, the curve (or accept Linear, Force, Equal on quants you add), qualifiers, and limit groups.

Add the same files again with File → Add samples… so the batch can quantitate them. Importing the method does not add the injections as samples.

5. SIM data file

Not a method import. None of the method-from-data readers build a method from SIM channels alone. MassHunter data-as-method looks for MRM transitions. SCIEX, Waters, and Shimadzu method-from-data read MRM/SRM.

What you can do: File → Add samples…, select the sample, Method → Edit method…, Compound Discovery, turn on SIM, then Deconvolute or Deconvolute all, then Create analytes from all. You then fill doses, ISTD, and the curve yourself. See Compound Discovery.

6. SCAN data file

Not a method-file import. This is the Compound Discovery path:

  1. File → Add samples…
  2. Select the sample.
  3. Method → Edit method…, then Compound Discovery (or Add → Analyte…).
  4. Turn on SCAN.
  5. Set From and To, or use Deconvolute all.
  6. Libraries if you want names from a .L or .mslibrary.xml.
  7. Create analytes from all.

What you get: an analyte per component, expected RT at the apex, a quant channel, acquisition key from the sample, and the default curve. Qualifier percent starts at 100. Levels, ISTD links, and limits are still empty until you enter them. See SCAN deconvolution and Library search.