Spectrus: Differentiating isobaric compounds using MS/MS in Spectrus

Description
Isobaric compounds (same nominal mass) can produce overlapping parent peaks in MS. MS/MS fragmentation patterns, however, can often distinguish between them. Spectrus supports viewing and comparing MS/MS spectra for this purpose.

Solution

1. Import or open xC/UV/MS data that includes MS/MS (MS2) information.
2. Select the chromatographic peak of interest in the TIC or XIC.
3. Display the associated MS/MS spectrum (for example, by double‑clicking the MS2 icon above a peak or selecting the MS2 spectrum from the LC/UV/MS legend).
4. For suspected isobars:
   • Compare MS/MS spectra at different retention times that share the same precursor m/z.
   • Look for diagnostic fragment ions or patterns that differ between components.
5. Use these differences to:
   • Annotate which peaks correspond to which structures.
   • Support identification, especially when MS1 data alone is ambiguous.