Annotations¶
mzmine uses a variety of annotation methods. These methods include spectral library matches, compound database annotations, lipid annotations, and manual annotation.
Spectral library matches¶
To annotate compounds by matching experimental MS2 (or MSn) spectra against spectral libraries using the Spectral library search module. mzmine supports several open library formats (see here) and also features a workflow to build your own spectral libraries.
Compound database annotations¶
The compound database annotation matches experimental MS1 data (m/z, RT, CCS, RI) against a library using the Local compound database search module. This library may be downloaded or generated in-house.
Lipid annotations¶
mzmine's lipid annotations are a rule-based fragmentation framework to confidently annotate lipids based on MS2 and/or MS1 data using the Lipid annotation module. You can also define custom lipids and create your own annotation rules.
Manual annotation¶
To annotate compounds manually use the the context menu in the feature table (right click on a row) and select "Identification" → "Annotate manually". The result is stored as a compound database match.
Preferred annotation¶
The preferred annotation is a combination of spectral library matches, compound database annotations, and lipid annotations. The most confident annotation is chosen according to a set of community guidelines. mzmine supports ranking of annotations based on
the MSI minimum reporting standards,
the Schymanski et. al. scale and default mzmine sorting.
Ranking according to MSI scale¶
See: https://link.springer.com/article/10.1007/s11306-007-0082-2
Level 4 - Unknown compounds: Not annotated, m/z-only compound database annotation (no RT, RI, CCS)
Level 3 - Putatively characterised compound classes: Compound database annotation backed by Sirius CSI:FingerId, Lipid annotation based on MS1 data
Level 2 - Putatively annotated compounds: Spectral library match to reference libraries, Lipid annotations with MS2 information, Compound database matches with m/z and RT or RI information.
Level 1 - Identified compounds: At least two orthogonal metrics confirmed with standards in the same laboratory. This annotation level is not achieved in mzmine, as it would require differentiation between lab-internal and lab-external RT and RI measurements.
Ranking according to Schymanski et. al. scale¶
See: https://pubs.acs.org/doi/10.1021/es5002105
Level 5 - Exact mass of interest: Not annotated, compound database annotation (m/z only, without isotope matching), MS1 only lipid annotation.
Level 4 - Unequivocal molecular formula: Compound database match with isotope score >= 0.75
Level 3 - Tentative candidates: Compound database match confirmed with Sirius CSI:FingerId
Level 2b - by diagnostic fragments: MS2-based species level lipid annotation
Level 2a - by a library spectrum match: Spectral library match to a reference library, molecular species level lipid annotation.
Level 1 - Confirmed structure: Spectral library match to a reference library including RT or RI matching.
Default annotation ranking in mzmine¶
The default sorting algorithm in mzmine is adapted from the Schymanski levels, but specifically weights a lipid annotation with diagnostic fragments higher than a spectral library match without RT matching. This is done because this lowers false positive molecular species level annotations and prefers species level annotations, if diagnostic fragments of multiple molecular species are present.
We want to point out that we neither prefer or disregard the MSI or Schymanski et. al. scale, but believe the more granular approach of the Schymanski et. al. scale allows a more intuitive user experience when sorting the feature table by annotation confidence.