Users can set the Display options to add customized peak labels to the selected Spectrum view. By default, the application labels each mass spectrum peak with its corresponding m/z value. The following table shows different parameters that users can add to peak labels.
Parameter | Subparameter | Description |
|---|---|---|
Mass | N/A | Adds an m/z label to each peak in the spectrum. |
Flags | N/A | Displays a letter or a symbol for each flagged peak. |
S | Specifies saturated peaks. These are peaks with a signal too large to measure; that is, the signal is so high that it exceeds the detector’s dynamic range and causes saturation. | |
R | Specifies reference peaks, which is a reference compound used for an internal recalibration. | |
L | Specifies lock peaks, which are local references used to calculate the accurate mass of nearby peaks. | |
E | Specifies exception peaks from a reference compound that are not used for recalibration. These are typically small isotopes or fragments of the main references. | |
# | Specifies mathematically modified peaks whose masses are recalculated by the instrument, usually due to a calibration process. | |
M | Specifies merged peaks that were close together before being combined by the centroider. | |
F | Specifies fragmented peaks that were originally merged but were separated into multiple peaks by the centroider. | |
T | Specifies the top peak in the cluster that is identified by the Advanced Peak Determination algorithm. | |
U | Specifies isotopically unresolved peaks, where the resolution setting used to acquire the data is insufficient to resolve isotopes. | |
Resolution | N/A | Adds a peak resolution label (R) to each peak in the spectrum. |
Charge | N/A | Adds a charge state label (z) to each peak in the spectrum. |
Baseline | N/A | Adds a baseline label (B) to each peak in the spectrum. |
Noise | N/A | Adds a noise magnitude label (N) to each peak in the spectrum. |
Width (m/r) | N/A | Adds a width label (W) to each peak in the spectrum. The width equals the mass, in mmu units, divided by the peak resolution. |
Reference and Exception Peaks | N/A | Displays the reference peaks and exception peaks in the Spectrum view. |
Precursor Flag | N/A | Adds a marker ( |
Monoisotopic Mass | N/A | Adds the monoisotopic mass and peak label (MM) in the Spectrum view. |
Species ID | N/A | Adds 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. |
Nearby Precursor | N/A | Adds a marker ( NOTE: The Nearby Precursor is disabled for an averaged Spectrum view. |
| Turn on for Entire File | Allows users to set the search to every scan in the file (for the entire RT range). By default, this toggle is turned off. |
| Backward RT (min) | Specifies the first time point for the search using the following equation: RTcurrent scan – Specified time (in minutes). Range: 0.00−10.00 min; default: 1.00 min. |
| Forward RT (min) | Specifies the last time point for the search using the following equation: RT current scan +Specified time (in minute). Range: 0.00−10.00 min; default: 1.00 min. |
Plot Type | Specifies whether double-clicking a marker in the precursor survey scan opens the following options:
Default: Average. | |
Label Threshold | N/A | Allows users to set 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% |
) on a peak that contains data-dependent scans.
) that denotes spectrum peaks with related data-dependent scans within the specified time range of the current scan. A related data-dependent scan is MSn+1 stage data-dependent.