Peak identification
Quantitate chooses which integrated peak is the analyte, then which quant result is reported. The quant choice is in Quantitation. This page is the peak choice.
Expected retention time
The analyte has an expected RT and a time window (default 0.5 minutes). The allowed distance is half the window on each side. The window is absolute minutes, not a percent of RT.
The time used for the comparison is the peak on the quantifier signal. If that peak is missing, the tallest peak on the candidate is used.
Candidates inside the window are preferred. If none are inside, the closest candidates outside the window can still be selected so you have a peak to review. The retention-time failure is still flagged when the distance is larger than the window.
Relative retention uses time-reference analytes on the sample. After you update expected retention times, Quanto queues that time-reference correction. An ISTD does not replace the expected RT by itself; it normalizes the response. You can still use an RT-reference analyte when the method has one.
Which peak is chosen
The method’s identification setting is one of:
| Setting | Choice |
|---|---|
| Best retention time | The candidate closest to the expected RT. |
| Preferred qualified, best retention time | The closest candidate that passed qualifier ratios, if any; otherwise the closest. |
| Largest response | The largest quantifier response (or the largest peak if there is no quantifier peak). |
| Best Q value | The best qualifier / library Q. |
A candidate you rejected is skipped. A manual pin on the compound is kept and automatic identification does not replace it.
If no candidate has a quantifier peak, a peak-less candidate can still be kept so you can review, comment, and integrate by hand.
Qualifiers and library match
Qualifier ratios are tested on the chosen peak. See Qualifiers.
For SCAN analytes, a spectrum match (Spec match) is computed against the spectrum stored on the analyte. Library search in Compound Discovery reports Match, RMatch, Prob, and PBM %. See Library search. Those library columns are the discovery hit list. The result’s stored Q is the ion-ratio Q, and Spec match is the comparison with the method spectrum.
Not found or uncertain
- No quantifier peak: nothing is auto-selected as the identified peak; a placeholder candidate can remain for review.
- Peak outside the time window: it can still be selected, and the retention-time check fails.
- Qualifier ratio outside tolerance: that qualifier is too low or too high. Identity fails when Q is below the confirmation threshold.
- Q of 0: a qualifier peak was missing or a ratio could not be formed.
- Above the top of the curve: the concentration flag is too high. That is a range check, not a failed identification.
Outliers collects these flags. See Checks.