Sirius Zodiac Score Filtering

SIRIUS Zodiac Score Filtering

Summary

Apply a minimum ZodiacScore threshold (default 0.9) to SIRIUS compound annotations to retain only high-confidence structural identifications in metabolomics annotation tables. This confidence-based filtering removes low-scoring rows while preserving all original columns for retained annotations.

When to use

After running SIRIUS on a mass spectrometry feature set and obtaining compound_identification.tsv output containing Zodiac and Cosmic confidence scores, apply this filter to eliminate low-confidence SIRIUS annotations before downstream prioritization or chemical class analysis. Use when your annotation workflow requires high-stringency structural predictions or when preparing data for the INVENTA prioritization pipeline.

When NOT to use

• Input annotations are not from SIRIUS (e.g., ISDB or other in silico tools use different confidence metrics)
• Analysis goal requires exploratory examination of all SIRIUS predictions including low-confidence ones
• Zodiac scores are unavailable or missing from the annotation table

Inputs

• SIRIUS compound_identification.tsv file (tabular format with Zodiac and Cosmic score columns)
• min_ZodiacScore threshold parameter (numeric, default 0.9)
• min_ConfidenceScore threshold parameter (numeric, optional, default 0.0)

Outputs

• Filtered annotation table (TSV format)
• High-confidence SIRIUS annotations (rows with Zodiac score ≥ min_ZodiacScore)
• Annotation row count (reduced relative to input)

How to apply

Load the SIRIUS annotations file (compound_identification.tsv format) into a tabular parser and extract the Zodiac score column. Apply a minimum threshold filter (min_ZodiacScore = 0.9 by default) to retain only rows where the Zodiac score is ≥ 0.9. Optionally apply an additional ConfidenceScore cut-off (min_ConfidenceScore = 0.0 by default) as a secondary filter criterion. Write the filtered annotation table to a new TSV file, retaining all original columns for the retained rows. The rationale is that ZodiacScore reflects SIRIUS's molecular formula and structure ranking confidence; a threshold of 0.9 operationalizes a conservative confidence cutoff standard in natural products metabolomics.

Related tools

• SIRIUS (Generates compound_identification.tsv with Zodiac scores for structural confidence ranking) — https://bio.informatik.uni-jena.de/software/sirius/
• INVENTA (Downstream prioritization pipeline that accepts filtered SIRIUS annotations as optional input for Feature Component calculation) — https://github.com/luigiquiros/inventa
• CANOPUS (Complementary SIRIUS output (chemical taxonomy) that may be used in tandem with Zodiac-filtered annotations for class-level analysis) — https://github.com/kaibioinfo/canopus_treemap

Examples

# In INVENTA notebook: min_ZodiacScore = 0.9; then load compound_identification.tsv and filter df = df[df['Zodiac_score'] >= min_ZodiacScore]; df.to_csv('filtered_sirius_annotations.tsv', sep='\t')

Evaluation signals

• Output file contains only rows where Zodiac score ≥ min_ZodiacScore (inspect min value in output Zodiac column)
• Output row count is less than or equal to input row count (no rows added, only removed)
• All original columns retained in output TSV (schema validation: same header as input)
• No NULL or NaN values introduced in retained rows
• Filtered annotation table successfully integrates into INVENTA or downstream chemical class analysis without schema errors

Limitations

• ZodiacScore threshold is heuristic; optimal cutoff may vary by organism, ionization mode, or MS instrument
• Filtering alone does not validate spectral-to-structure match; relies on SIRIUS's underlying Zodiac ranking algorithm
• If min_ZodiacScore is set too high (e.g., > 0.95), may exclude valid annotations for lower-abundance or ambiguous features
• SIRIUS annotations must have been recomputed or obtained from a version supporting Zodiac scoring; older project spaces may lack this metric

Evidence

• [other] The min_ZodiacScore filtering mechanism applies a cut-off threshold of 0.9 to retain only SIRIUS annotations meeting or exceeding this confidence score, removing lower-scoring rows from the annotation table.: "min_ZodiacScore filtering mechanism applies a cut-off threshold of 0.9 to retain only SIRIUS annotations meeting or exceeding this confidence score"
• [other] Load the SIRIUS annotations file (compound_identification.tsv format) containing Zodiac and Cosmic scores using a tabular file reader. Parse the Zodiac score column and apply a minimum threshold filter (min_ZodiacScore = 0.9) to retain only rows where Zodiac score is ≥ 0.9. Optionally apply the ConfidenceScore cut-off (min_ConfidenceScore = 0.0 by default) as an additional filter criterion if present. Write the filtered annotation table to a new TSV file, retaining all original columns for retained rows.: "Load the SIRIUS annotations file (compound_identification.tsv format) containing Zodiac and Cosmic scores using a tabular file reader. Parse the Zodiac score column and apply a minimum threshold"
• [other] Verify the output file contains only rows with Zodiac score ≥ 0.9 and row count is less than or equal to the input row count.: "Validation: verify the output file contains only rows with Zodiac score ≥ 0.9 and row count is less than or equal to the input row count"
• [other] min_ZodiacScore = 0.9 #cut-off filter for considering a sirius annotation valable: "min_ZodiacScore = 0.9 #cut-off filter for considering a sirius annotation valable"
• [readme] Recompute your project space from Sirius using the following code: "Recompute your project space from Sirius using the following code"