# Fragment Ion Mass Matching With Tolerance

> Use when denoising MS/MS spectra and you have: (1) a precursor ion with measured m/z and known molecular formula (from SMILES or direct formula input), (2) an adduct type ([M+H]+, [M+Na]+, etc.), (3) a list of fragment ions with observed m/z values, and (4) a need to distinguish chemically valid.

- Skill: `holobiomicslab/fragment-ion-mass-matching-with-tolerance` (Agent Skill)
- Install (CLI): `npx skillmds@latest add holobiomicslab/fragment-ion-mass-matching-with-tolerance`
- Raw SKILL.md: https://api.skillmd.com/api/skills/holobiomicslab/fragment-ion-mass-matching-with-tolerance/raw
- Safety review: PASS (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- License: CC-BY-4.0
- Author: HolobiomicsLab (https://skillmd.com/u/holobiomicslab)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/holobiomicslab/fragment-ion-mass-matching-with-tolerance

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# fragment-ion-mass-matching-with-tolerance

## Summary

Match observed fragment ions in MS/MS spectra against expected subformula losses from a master molecular formula, within a dynamically adjusted mass tolerance window. This skill identifies chemically plausible fragment ions by evaluating whether each observed m/z could result from loss of a valid subformula, enabling discrimination of true fragments from chemical noise.

## When to use

Apply this skill when denoising MS/MS spectra and you have: (1) a precursor ion with measured m/z and known molecular formula (from SMILES or direct formula input), (2) an adduct type ([M+H]+, [M+Na]+, etc.), (3) a list of fragment ions with observed m/z values, and (4) a need to distinguish chemically valid fragments from noise ions. Use it especially when the measured precursor mass error exceeds the initial mass tolerance threshold, triggering an adaptive tolerance adjustment.

## When NOT to use

- When the precursor ion m/z is not accurately measured or adduct type is unknown — the tolerance adjustment depends on knowing the true precursor mass error.
- When molecular formula or SMILES information is unavailable — subformula generation requires a valid master formula as input.
- When performing electronic noise removal only — this skill addresses chemical noise via formula plausibility, not instrumental artifacts like baseline noise or isolated spikes.

## Inputs

- observed fragment ion m/z array (float32 or float64, typically paired with intensity values)
- precursor m/z (float, measured from spectrum)
- master molecular formula (string, e.g., 'C5H4N4O')
- SMILES string (string, e.g., 'O=c1nc[nH]c2nc[nH]c12') or molecular formula
- adduct type (string, e.g., '[M+H]+', '[M+Na]+', '[M-H]-')
- initial mass tolerance threshold (float, in ppm or Da)

## Outputs

- boolean tag array matching input fragment ions (True=chemically valid, False=noise)
- filtered fragment ion m/z array (only True-tagged ions retained)
- filtered intensity array (paired with filtered m/z)
- updated mass tolerance threshold (float, if precursor error triggered adjustment)

## How to apply

First, call `get_pmz_statistics()` on the precursor ion to extract the real precursor m/z and compare against the theoretical mass; if the measured error exceeds the initial tolerance, update the tolerance threshold accordingly. Second, call `get_all_subformulas()` to populate all possible subformulas derivable from the master formula (prepared via `prep_formula()` to account for SMILES-based modifications and adduct-specific atom additions). Third, for each observed fragment ion, invoke `check_candidates()` to search within the updated tolerance window for a subformula loss that would yield that fragment's m/z. Fourth, use `get_denoise_tag()` to assign True (chemically valid) or False (noise) tags based on whether a plausible subformula loss was found. The tolerance window is the critical decision point: it dynamically adjusts if precursor mass error is large, preventing over-filtering or under-filtering of candidate fragments. Retain only True-tagged ions in the final denoised spectrum.

## Related tools

- **prep_formula** (Modifies the master molecular formula based on SMILES and adduct information, adding atoms for rare adducts and benzene substructures before subformula generation) — https://github.com/FanzhouKong/spectral_denoising
- **get_pmz_statistics** (Extracts precursor ion m/z and updates mass tolerance threshold if measured mass error exceeds initial tolerance) — https://github.com/FanzhouKong/spectral_denoising
- **get_all_subformulas** (Populates all possible subformulas derivable from the master formula, sorted by mass, for use in candidate matching) — https://github.com/FanzhouKong/spectral_denoising
- **check_candidates** (For each observed fragment ion, searches for a plausible subformula loss within the tolerance window that could form that ion's m/z) — https://github.com/FanzhouKong/spectral_denoising
- **get_denoise_tag** (Assigns True/False tags to fragment ions based on whether a plausible subformula loss was found by check_candidates) — https://github.com/FanzhouKong/spectral_denoising
- **RDkit** (Molecular structure parsing and SMILES canonicalization to derive chemical information for formula modification)
- **molmass** (Precise calculation of molecular masses for subformulas and precursor ions)
- **chemparse** (Chemical formula parsing and validation)

## Examples

```
peak_denoised = sd.spectral_denoising(peak_with_noise, 'O=c1nc[nH]c2nc[nH]c12', '[M+H]+')
```

## Evaluation signals

- Verify that the number of True-tagged ions is chemically reasonable (typically 5–30 fragments for small metabolites) — too many or too few suggests tolerance is miscalibrated.
- Compare entropy similarity of the denoised spectrum (True-tagged ions only) against a reference spectrum before and after filtering; improvement > 0.1–0.2 in entropy_similarity indicates successful noise removal.
- Check that no chemically impossible subformula losses are retained (e.g., loss of negative mass or atoms absent from the master formula); validate via mass balance (precursor mass = fragment mass + loss mass).
- Confirm that the precursor ion and major known diagnostic fragments remain tagged as True; loss of these indicates over-filtering or tolerance set too conservatively.
- Audit a sample of False-tagged ions to verify they lack a match within the tolerance window — inspect the closest subformula loss candidate and its mass error to confirm it exceeds the threshold.

## Limitations

- Assumes the input SMILES string or molecular formula is correct; errors in chemical structure will propagate through subformula generation and produce incorrect tags.
- Mass tolerance window adjustment relies on accurate precursor m/z measurement; poor-quality precursor peaks or systematic instrument miscalibration can lead to inappropriate thresholds.
- Does not account for isotope patterns or high-resolution artefacts (e.g., 13C satellites); these may be tagged as noise if they fall outside the tolerance window.
- Limited to detecting losses corresponding to valid subformulas; rearrangements, radical migrations, or other complex fragmentation pathways not representable as simple formula losses will be incorrectly flagged as noise.
- Performance degrades for very large molecules (>~1000 Da) where the number of possible subformulas becomes computationally expensive; see original paper for empirical mass limits on the NIST23 database.

## Evidence

- [other] For each fragment ion, the algorithm will try to find a plausible subformula loss that could form this ion (function ``check_cnadidates``): "For any given fragment ion, the algorithm will try to find a plausible subformula loss that could form this ion (function ``check_cnadidates``)"
- [other] The formula_denoising function removes chemical noise ions in MS/MS spectra by evaluating if it could be formed from a chemically plausible subformula loss: "The ``formula_denoising`` function removes chemical noise ions in MS/MS spectra by evaluating if it could be formed from a chemically plausible subformula loss"
- [other] Get precursor ion infrmation and update the mass tolerance threshold if the measured mass error exceeds the initial tolerance: "Step 1: Get precursor ion infrmation"
- [methods] Step 2: Populate all possible subformulas from master formula, generating candidate fragments sorted by mass: "Populate all possible subformulas from the master formula using get_all_subformulas, generating candidate fragments sorted by mass."
- [methods] Modifying the master formula based on SMILES and adduct information using prep_formula, adding atoms for rare adducts and benzene substructures: "Prepare the master molecular formula by modifying it based on SMILES and adduct information using prep_formula, adding atoms for rare adducts and benzene substructures."
- [methods] Generate denoising tags for each ion using get_denoise_tag, marking ions as True (chemically valid) or False (noise): "Generate denoising tags for each ion using get_denoise_tag, marking ions as True (chemically valid) or False (noise)."