How does "Add/Update MS Compounds" work?

When you run Add/Update MS compounds, the application automatically analyzes the focused injection as follows. The result depends on the settings in the method under Compounds  >  Identification > > Qualifier Setup.

For Scan data with no qualifiers (Number of qualifiers used for scan data set to zero)
NOTE: It is essential that integration of TIC SCAN and EIC signals was set up correctly.

1. In the TIC SCAN chromatogram, extract an MS spectrum for each integrated peak (as configured in the  method under Extraction  >  Spectrum  > MS).

   These MS spectra are automatically set as MS reference spectra in the Compounds > Spectra method section.

   In each MS spectrum, identify the base peak (most abundant ion).

2. If a library has been selected in the method under Spectral Analysis > MS Library Search, conduct the search for each MS spectrum, and use names of the best library matches as compound names.

3. Either TIC SCAN or base peak EIC signal is added as a compound signal to the compound table (depending on the For scan-only data, add/update compounds on). The compound name is either the best library match or created from the retention time, for example peak@1.001min.

   Both TIC SCAN and base peak EIC signals are available in the signals drop-down list in the method.

For Scan data with one or more qualifiers (Number of qualifiers used for scan data set to 1 or more), additional steps are executed to add qualifiers.

• Use the 2^nd to n^th highest peaks in each spectrum as qualifier candidates.

• Verify that the corresponding EICs have integrated peaks.

• Only add the qualifier if it fits into the qualifier retention time window (set via Qualifier RT window ( ± min )).

• Calculate the response ratio Rsp %. The formula depends on the values you configured in the method. See MS qualifier calculations

For SIM or SIM/Scan data:
NOTE: It is essential that the acquisition method and integration of SIM signals were set up correctly.

1. Take compounds directly from defined SIM targets in the acquisition method.

2. Verify that TIC SIM and SIM signals have at least one integrated peak.

3. In each SIM signal, identify the most abundant peak.

4. If SIM signals are labeled with different names in the acquisition method, all SIM signals will be added to the compound table as target compounds.

   If SIM signals are labeled with the same name, the most abundant one will be the target compound. The other signals will be assigned as qualifiers if they meet the qualifier requirements. The ones that fail the qualifier requirements will be highlighted to mark them as invalid, and the retention time will remain blank.

   Qualifier ratios are always calculated as Qualifier SIM response/Base peak SIM response.

   If SIM signals are not labeled with a name, the compound name will be m/z # .

   If Data Analysis cannot find a peak for a given SIM Signal, the retention time will not be filled in the compound table. The table row is highlighted to mark it as invalid. You must add the missing information manually before you can save the processing method.

5. If a compound is specified as an ISTD, it will be an ISTD in the compound table.