Method

A method is the list of analytes, ions or channels, expected retention times, calibration levels, integration settings, checks, and libraries used to process a batch. It is stored with the batch and can also be saved as a .qtm file.

Open it with Method → Edit method… (F10).

Analytes and quants

An analyte is the compound you report (the name, the expected retention time, the acquisition key, and the role). A quant is one quantitative measurement of that analyte: one channel or transition, its own curve, its own qualifiers, and its own response.

One analyte often has several quants. Typical reasons, all of which the method supports:

• Different ions or channels for the same compound (a low-range ion and a high-range ion, or a quantifier and extra confirming channels that are themselves quants).
• Different calibration ranges. The reported quant is the one whose calibration range just covers the sample. See Which quant is reported.
• A quant that uses another quant’s curve (reference curve) with a multiplier.
• The same compound name acquired under more than one acquisition key. Those are separate analyte rows that share a name. The sample’s acquisition key decides which row applies. See Acquisition keys.

An analyte is not split into a separate row just because it is an internal standard or because of the matrix. The role is Target, ISTD, or Surrogate on the analyte. Matrix and limit groups are chosen on the sample and in Limit groups, not by adding another quant. See Limit groups.

The analyte’s selected quant (MSelectedQuant in the method) is the primary quant used when a screen needs one quantifier channel. On a result, the reported quant can still be a different quant on that same analyte when the calibration-range rule or a manual pin says so.

Ions, retention time, and acquisition key

In the method editor, View opens Analytes, Quants, Quant channels, Channels, and AcqKeys.

• RT is the expected retention time, in minutes. Time window is the full window around that time (default 0.5 minutes). Identification uses half of that window on each side.
• A quant channel is the ion or transition used for the amount. A qualifier is a confirming ion on that quant. See Qualifiers.
• AcqKey groups the channels and analytes that belong to one acquisition method. The default name is 1.

Add in the method editor can insert an analyte (Compound Discovery), a blank analyte row, an analyte name, an acquisition key, a channel, a quant, a qualifier, a dose, a response, or a sample type.

Calibration

Each analyte has dose levels. The concentration at a level is on View → Analyte doses. The level names are on View → Doses. See Doses.

On a new quant that is not an internal standard, the curve is Linear, origin Force, weighting Equal. An ISTD quant uses Average of response factors. Saved curves are left as they were. See Calibration curves.

Internal standards are analytes of type ISTD. A target quant points at the ISTD quant that normalizes its response. Surrogates are type Surrogate.

Integration and libraries

Each channel has an integrator (default name Quanto) and integrator settings. Savitzky–Golay smoothing is on the channel. See Integration and Smoothing.

Library files used by library search are stored on the method. Choose them in Compound Discovery with Libraries. See Library search.

Creating a method from SCAN data

While the open method has no live analyte, the editor shows this path:

1. Add SCAN samples.
2. Select a sample (for example the calibration sample).
3. Open Edit method, then Compound Discovery.
4. Deconvolute a range or the whole run.
5. Create analytes from all.

The button is Open Compound Discovery. Details are in Compound Discovery. A full walk-through is in Set up a method from scratch.

Other method commands

Method → Properties… opens method properties. Qualifier tolerances… edits the general ion-ratio table. Propose SG width suggests a Savitzky–Golay window from the current sample. Create doses from sample dose builds dose rows from the dose names already on the samples. Convert qualifiers to quants turns qualifier ions into their own quants. Validate method checks the method.

Method → Load or import… loads a .qtm, imports a vendor method (replace), or appends analytes under a different acquisition key. Method → Save method… writes the package. Make Readonly stops that file from being overwritten.