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Updating a stored spectrum

Each SCAN analyte can keep a reference spectrum. Identification compares the sample spectrum with that stored spectrum (Spec match). Compound Discovery and the channel spectrum chart can show it beside the measured sticks. It is also the source you pick ions from when you Add from spectrum.

It is not the library file. Libraries are searched separately. See Library search.

Commands

Update → Selection → Spectrum and Update → All analytes → Spectrum copy a spectrum from the selected samples onto the analyte. The dialog previews the analytes that have a spectrum. Apply does not average several spectra. One spectrum is stored.

Which sample is used:

  1. The sample pinned for that analyte in Key Review, when it has a spectrum.
  2. Otherwise the first selected sample whose acquisition key matches the analyte and that has a spectrum.
  3. Otherwise the first selected sample that has a spectrum.

The spectrum that is copied is the apex SCAN spectrum read for that analyte on that sample (the result spectrum when it is already stored, otherwise the spectrum read from the data file). This command does not store a deconvoluted component spectrum and it does not subtract background. Deconvoluted and background-subtracted spectra are the origins used inside library search. See Library search.

Update analyte in Compound Discovery writes the selected discovered component onto an existing analyte, including the acquisition key of the sample you discovered from. Use that when the spectrum you want is the deconvoluted component rather than the raw apex from Update → Spectrum.

Add from spectrum in Channels adds the ion you clicked as a qualifier or a channel. It does not replace the whole stored spectrum. See Qualifiers.

Acquisition key

Update → Spectrum sets the analyte’s acquisition key from the one sample whose spectrum was copied. That overwrite always uses that sample’s key. It is not the “only when every sample shares a key” rule, because only one sample is the source.

What it is used for

  • Spec match during identification for SCAN analytes.
  • The reference overlay on the spectrum chart.
  • Picking qualifier ions with Add from spectrum.

Qualifier ratios and expected RT are not changed by storing a spectrum. Use Retention time update and Updating qualifier ratios for those.

Undo

Edit → Undo does not restore the previous stored spectrum. It only undoes review actions (approve, zero, undo manual integration). Save the method first if you may want the old spectrum back.