Peak labeling customizes the display of the selected Spectrum view. Use the Labels area in the Display Option dialog box to add or remove labels that appear above the spectrum peaks. By default, the application labels each mass spectrum peak with its corresponding m/z value. The following table shows different options for peak labels.

Options for peak labels

Option

Description

Mass

Adds an m/z label to each peak in the spectrum.

Flags

Displays one of the following letters or symbols for the flagged peaks:

  • S—Saturated peaks are peaks with a signal too large to measure; that is, the signal is so high that it exceeds the dynamic range of the detector, and causes saturation.
  • R—Reference peaks are peaks from a reference compound used for an internal recalibration.
  • L—Lock peaks are local references used to calculate the accurate mass of nearby peaks.
  • E—Exception peaks are peaks from a reference compound that are not used for recalibration. These are typically small isotopes or fragments of the main references.
  • #—Mathematically modified peaks are peaks whose masses are recalculated by the instrument, usually due to a calibration process.
  • M—Merged peaks consist of peaks that were close together before being combined by the centroider.
  • F—Fragmented peaks are peaks that were originally merged together but were separated into multiple peaks by the centroider.
  • T—Top peak in the cluster that is identified by the Advanced Peak Determination algorithm.
  • U—Isotopically unresolved peaks, where the resolution setting used to acquire the data is insufficient to resolve isotopes.

Resolution

Adds a peak resolution label to each peak in the spectrum. The abbreviation R next to a value indicates the peak resolution.

Charge

Adds a charge state label to each peak in the spectrum. The abbreviation z next to a value indicates the charge state.

Baseline

Adds a baseline label to each peak in the spectrum. The abbreviation B next to a value indicates the baseline.

Noise

Adds a noise magnitude label to each peak in the spectrum. The abbreviation N next to a value indicates the noise.

Width (m/r)

Adds a width label to each peak in the spectrum. The width equals the mass, in mmu units, divided by the peak resolution. The abbreviation W next to a value indicates the width label.

Monoisotopic Mass

Displays the monoisotopic mass and peak label (MM) in the Spectrum view.

  • For peaks in the cluster that are not monoisotopic, the label is shown as MM:1335.
  • For the monoisotopic peak in the cluster, the label is shown as MM=1335.

Species ID

Displays a species ID label (S) above mass spectral peaks that belong to the same chemical species (with the same species ID). The application does not label peaks with a species ID label if they do not have an assigned species ID.

Reference and Exception Peaks

Shows or hides the reference peaks and exception peaks in the Spectrum view.

Precursor Flag

A marker () present on a peak that contain data-dependent scans.

Nearby Precursor

A marker () that denotes spectrum peaks with related data-dependent scans within the specified time range of the current scan. A related data-dependent scan is an MSn+1 stage data-dependent scan for a precursor ion that matches the m/z value of the current peak within the specified mass tolerance.

In the Nearby Precursor area, you can specify the search for the data-dependent scans using the following options:

  • Entire File: When selected, sets the search to every scan in the file (no time range limit). By default, this option is selected.
  • Backward RT: Specifies the first time point for the search, RTcurrent scan – Specified time in minutes
  • By default, 1.00 min; range: 0.00 to 10.00 min.
  • NOTE This field is not available when the Entire File checkbox is selected.
  • Forward RT: Specifies the last time point for the search, RTcurrent scan +Specified time in minutes
  • By default, 1.00 min; range: 0.00 to 10.00 min.
  • NOTE This field is not available when the Entire File checkbox is selected.

Label Threshold

Sets the percentage of the base peak so that the application labels only the peaks above that percentage. For example, if the base peak is 100 percent and the label threshold setting is 50 percent, the application labels only the peaks in the Spectrum view or MultiSpectrum view that are at or above 50 percent.

Range: 0–100; default: 0%