Peak identification and isotope measurements

The peak identification tool helps to identify a peak by comparing its measured mass-to-charge ratio (m/z) with a catalog of atomic isotope ions. You can then associate a candidate with a signal or create a signal from the peak. Isotope measurements compare selected signals within the current region and viewing frames.

WarningImportant Limitations

The catalog searches single-atom isotope ions only. It does not suggest molecular or cluster ions, such as a dimer (two atoms of the same element), ions containing hydrogen or hydroxyl groups, or organic molecular fragments. The charge and polarity filters do include multiply charged single atoms, which are different from dimers.

Different species can have similar or overlapping m/z values. A listed atomic candidate is therefore a possible match, not a confirmed identification, and an unlisted molecular ion could contribute to the same peak. Consider other peaks, isotope patterns, mass resolution, and independent evidence when interpreting a result. Measured signal shares are not quantitative composition. See this review of mass interference in FIB-TOF-SIMS for more detail.

Open the identification tools

Use Identify peak or Isotope measurements above the mass spectrum.

Open identification and isotope measurements from the mass spectrum header.

Find isotope candidates

1. Open Identify peak, then click a peak in the identification spectrum to search for potential matches. Alternatively, enter an exact Measured m/z and select Find candidates.
2. Adjust the tolerance and its unit, or the charge and polarity, to change the search. The default absolute tolerance is 0.3 m/z; changing these settings refreshes the candidates.
3. Review the candidate table, which shows predicted m/z, mass error, and natural abundance. Select a candidate to use it in the actions below.

By default, candidates with known natural abundance are ordered by abundance within the tolerance. Use Candidate order to choose closest-mass ordering, or include isotopes without tabulated natural abundance. The identification spectrum starts with a logarithmic intensity scale; source and reference information are available in the dialog.

The identification dialog compares a measured peak with isotope candidates.

Assign or create a signal

After selecting a candidate, you can choose one of these actions:

• Assign an isotope to an existing signal: choose a signal and select Assign isotope to signal. This records the candidate and reference information for isotope measurements and saved analyses; it does not change the signal’s name, mass window, or intensities, or confirm the identification.
• Create a signal from this peak: enter the mass window and select Apply window to open an assigned draft that you can tweak further, or Add signal to immediately calculate a new signal across all acquisition frames.

Measure isotope signals

Warning

Isotope measurement is a pre-alpha feature and has not been thoroughly tested. If this is a feature you are interested in helping to test, please contact us!

1. Open Isotope measurements and choose the signals to measure.
2. Select Measure. Results use original-resolution data over the current ROI and viewing frames, restricted to the signals’ common coverage.
3. Review the percentage shares and results, region and frame summary, and any explanations for zero intensity or missing isotope assignments. Expand the calculation details and provenance for more information.

A measurement compares two selected signals across the displayed region and frames.

The results describe ratios within the selected signal set; they are not quantitative composition. Fractions are suppressed when mass windows overlap. If inputs change, captured measurements are marked out of date until you select Measure again.

Isotope CSV exports the measurement scope, mass errors, uncertainties, and provenance. Save as and reopening the saved analysis also preserve isotope assignments and captured results.