How Data Analysis finds MS ... (Data Analysis)
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How Data Analysis finds MS compounds and qualifiers

When you add or update MS compounds to an MS processing method, the application automatically analyzes the data as follows:

For Scan data:

  1. In the TIC SCAN chromatogram, extract a background subtracted MS spectrum for each integrated peak.

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

  2. Find qualifier ions (see About qualifier ions) and list them in the processing method.

  3. If a library has been selected in the method, conduct the search for each MS spectrum, and use names of the best library matches as compound names.

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

  5. For each base peak's m/z value, extract an EIC and find the closest peak to the TIC SCAN peak (only internally, not visible to the user).

  6. The TIC SCAN signal is added as a compound signal to the compound table. The compound name is either the best library match or created from the retention time, for example peak@1.001min. The TIC SCAN is set as the signal for all compounds. EIC signals are available in the drop-down list.

    Each compound has a signal assigned that corresponds to a TIC SCAN.

For SIM or SIM/Scan data:

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

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

  3. 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.

    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.

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

See Also