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chem-msms-predict

Predict LC-MS/MS (MS2, tandem mass spectra) from SMILES via ICEBERG, a two-stage deep neural network. Outputs predicted m/z vs intensity spectrum, fragment ion SMILES, and a spectrum plot.

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価格未確認★ 161 GitHub スター登録情報の更新日 · 2026年9月6日agent-skill

概要

Predict LC-MS/MS (MS2, tandem mass spectra) from SMILES via ICEBERG, a two-stage deep neural network. Outputs predicted m/z vs intensity spectrum, fragment ion SMILES, and a spectrum plot.

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LC-MS/MS Spectrum Prediction

Goal

Predict the LC-MS/MS (tandem mass) spectrum of a molecule given its SMILES string using ICEBERG — a two-stage GNN that first generates a fragmentation DAG (fragment ions) and then predicts their intensities. Output is a predicted spectrum (m/z, intensity) with optional fragment SMILES assignments per peak.

When to Use This Skill

  • A SMILES string is known and a predicted LC-MS/MS spectrum (m/z vs intensity) is needed.
  • Fragment ion assignments (SMILES per peak) are required.
  • No reference spectrum exists, or comparison to a predicted spectrum is desired.
  • Companion skill chem-spectrum-matcher can compare predicted vs experimental spectra.

When NOT to Use This Skill

  • Experimental spectrum already available — use it directly; no prediction needed.
  • Only compound name known — first resolve to SMILES via drug-db-pubchem, then call this skill.
  • GC-MS or other MS types — ICEBERG is trained on LC-MS/MS only; flag a warning before proceeding.
  • Organometallics or MW > 1000 — predictions may be unreliable or fail due to unsupported element types.

Prerequisites

1. Download ICEBERG checkpoints

Download from coleygroup/ms-pred releases and place in downloads/:

downloads/
├── iceberg_dag_gen_msg_best.ckpt     # generator (stage 1)
└── iceberg_dag_inten_msg_best.ckpt   # intensity predictor (stage 2)

Flag error and stop if either checkpoint is missing.

2. Set up the conda environment
bash conda-envs/msms-agent/install.sh

The ms_pred Python package is installed from GitHub automatically by the install script.

Instructions

Step 1 — Run inference and generate spectrum
# Env: ms-gen
python .agents/skills/chem-msms-predict/scripts/predict_msms.py \
    --smiles "c1ccccc1C(=O)OCCN" \
    --gen_ckpt downloads/iceberg_dag_gen_msg_best.ckpt \
    --inten_ckpt downloads/iceberg_dag_inten_msg_best.ckpt \
    --collision_energies 20 40 \
    --adduct "[M+H]+" \
    --instrument "Orbitrap" \
    --output_dir results/msms_prediction

Key parameters:

  • --smiles — input molecule as SMILES string
  • --gen_ckpt / --inten_ckpt — paths to ICEBERG checkpoints
  • --collision_energies — one or more collision energies in eV (e.g. 20 40 60); model was trained on absolute eV values
  • --adduct — supported adducts: [M+H]+, [M-H]-, [M+Na]+, [M+NH4]+, and others from ms_pred.common.ion2mass
  • --instrument — instrument type for intensity prediction (e.g. "Orbitrap", "QTOF")
  • --threshold — confidence cutoff for DAG fragment generator (default 0.1; lower = more fragments)
  • --sparse_k — maximum number of peaks returned (default 100)
  • --cuda_devices — GPU device IDs (e.g. "0" or "0,1"); omit or set to None for CPU

Outputs written to --output_dir:

FileDescription
spectrum.pngStem plot of predicted spectrum, one panel per collision energy
fragments.jsonJSON list per CE: {mz, intensity, fragment_smiles} sorted by intensity
input_configs.yamlAll run parameters for reproducibility
Step 2 — Inspect fragment assignments (optional)

fragments.json maps each predicted peak to the fragment ion SMILES responsible for it:

{
  "20": [
    {"mz": 122.0600, "intensity": 1.0, "fragment_smiles": "c1ccccc1C=O"},
    ...
  ]
}

Use this to rationalize which bonds fragment at which energy.

Step 3 — Compare with experimental spectrum (optional)

If an experimental spectrum is available, use the companion skill:

→ chem-spectrum-matcher

Examples

2-Aminoethyl benzoate (c1ccccc1C(=O)OCCN)
# Env: ms-gen
python .agents/skills/chem-msms-predict/examples/predict_smiles.py \
    --gen_ckpt downloads/iceberg_dag_gen_msg_best.ckpt \
    --inten_ckpt downloads/iceberg_dag_inten_msg_best.ckpt \
    --output_dir .agents/test/msms_example

Expected output:

  • spectrum.png — two-panel spectrum (20 eV + 40 eV)
  • fragments.json — fragment assignments for both energies
  • Precursor [M+H]+ ≈ 166.087 Da

Constraints

  • Environment: All scripts require the ms-gen conda environment. ms_pred is installed automatically from GitHub by conda-envs/msms-agent/install.sh.
  • Checkpoints required: Script raises FileNotFoundError if --gen_ckpt or --inten_ckpt are missing.
  • Collision energy units: Use absolute eV values. To convert NCE → eV, set nce=True in iceberg_prediction() directly.
  • Non-binned output only: This skill uses binned_out=False (high-precision m/z). Binned output disables fragment assignment.
  • Single-compound inference: Provide one SMILES per call. For batch prediction, loop over SMILES and use separate output dirs.
  • Unsupported elements: Molecules containing metals, lanthanides, or rare main-group elements may fail or produce low-quality predictions.
  • MW limit: ICEBERG is unreliable for MW > 1000 Da.

References


Author: Magdalena Lederbauer Contact: GitHub @mlederbauer

ファイルのメタデータ
name: chem-msms-predict
description: Predict LC-MS/MS (MS2, tandem mass spectra) from SMILES via ICEBERG, a two-stage deep neural network. Outputs predicted m/z vs intensity spectrum, fragment ion SMILES, and a spectrum plot.
category: [chemistry, drug-discovery]
元のテキストを表示
---
name: chem-msms-predict
description: Predict LC-MS/MS (MS2, tandem mass spectra) from SMILES via ICEBERG, a two-stage deep neural network. Outputs predicted m/z vs intensity spectrum, fragment ion SMILES, and a spectrum plot.
category: [chemistry, drug-discovery]
---

# LC-MS/MS Spectrum Prediction

## Goal

Predict the LC-MS/MS (tandem mass) spectrum of a molecule given its SMILES string using ICEBERG — a two-stage GNN that first generates a fragmentation DAG (fragment ions) and then predicts their intensities. Output is a predicted spectrum (m/z, intensity) with optional fragment SMILES assignments per peak.

## When to Use This Skill

- A SMILES string is known and a predicted LC-MS/MS spectrum (m/z vs intensity) is needed.
- Fragment ion assignments (SMILES per peak) are required.
- No reference spectrum exists, or comparison to a predicted spectrum is desired.
- Companion skill `chem-spectrum-matcher` can compare predicted vs experimental spectra.

## When NOT to Use This Skill

- **Experimental spectrum already available** — use it directly; no prediction needed.
- **Only compound name known** — first resolve to SMILES via `drug-db-pubchem`, then call this skill.
- **GC-MS or other MS types** — ICEBERG is trained on LC-MS/MS only; flag a warning before proceeding.
- **Organometallics or MW > 1000** — predictions may be unreliable or fail due to unsupported element types.

## Prerequisites

### 1. Download ICEBERG checkpoints

Download from [coleygroup/ms-pred releases](https://github.com/coleygroup/ms-pred) and place in `downloads/`:

```
downloads/
├── iceberg_dag_gen_msg_best.ckpt     # generator (stage 1)
└── iceberg_dag_inten_msg_best.ckpt   # intensity predictor (stage 2)
```

**Flag error and stop** if either checkpoint is missing.

### 2. Set up the conda environment

```bash
bash conda-envs/msms-agent/install.sh
```

The `ms_pred` Python package is installed from GitHub automatically by the install script.

## Instructions

### Step 1 — Run inference and generate spectrum

```bash
# Env: ms-gen
python .agents/skills/chem-msms-predict/scripts/predict_msms.py \
    --smiles "c1ccccc1C(=O)OCCN" \
    --gen_ckpt downloads/iceberg_dag_gen_msg_best.ckpt \
    --inten_ckpt downloads/iceberg_dag_inten_msg_best.ckpt \
    --collision_energies 20 40 \
    --adduct "[M+H]+" \
    --instrument "Orbitrap" \
    --output_dir results/msms_prediction
```

**Key parameters:**
- `--smiles` — input molecule as SMILES string
- `--gen_ckpt` / `--inten_ckpt` — paths to ICEBERG checkpoints
- `--collision_energies` — one or more collision energies in eV (e.g. `20 40 60`); model was trained on absolute eV values
- `--adduct` — supported adducts: `[M+H]+`, `[M-H]-`, `[M+Na]+`, `[M+NH4]+`, and others from `ms_pred.common.ion2mass`
- `--instrument` — instrument type for intensity prediction (e.g. `"Orbitrap"`, `"QTOF"`)
- `--threshold` — confidence cutoff for DAG fragment generator (default `0.1`; lower = more fragments)
- `--sparse_k` — maximum number of peaks returned (default `100`)
- `--cuda_devices` — GPU device IDs (e.g. `"0"` or `"0,1"`); omit or set to `None` for CPU

**Outputs written to `--output_dir`:**
| File | Description |
|------|-------------|
| `spectrum.png` | Stem plot of predicted spectrum, one panel per collision energy |
| `fragments.json` | JSON list per CE: `{mz, intensity, fragment_smiles}` sorted by intensity |
| `input_configs.yaml` | All run parameters for reproducibility |

### Step 2 — Inspect fragment assignments (optional)

`fragments.json` maps each predicted peak to the fragment ion SMILES responsible for it:

```json
{
  "20": [
    {"mz": 122.0600, "intensity": 1.0, "fragment_smiles": "c1ccccc1C=O"},
    ...
  ]
}
```

Use this to rationalize which bonds fragment at which energy.

### Step 3 — Compare with experimental spectrum (optional)

If an experimental spectrum is available, use the companion skill:

→ [`chem-spectrum-matcher`](../chem-spectrum-matcher/SKILL.md)

## Examples

### 2-Aminoethyl benzoate (`c1ccccc1C(=O)OCCN`)

```bash
# Env: ms-gen
python .agents/skills/chem-msms-predict/examples/predict_smiles.py \
    --gen_ckpt downloads/iceberg_dag_gen_msg_best.ckpt \
    --inten_ckpt downloads/iceberg_dag_inten_msg_best.ckpt \
    --output_dir .agents/test/msms_example
```

Expected output:
- `spectrum.png` — two-panel spectrum (20 eV + 40 eV)
- `fragments.json` — fragment assignments for both energies
- Precursor `[M+H]+` ≈ 166.087 Da

## Constraints

- **Environment**: All scripts require the `ms-gen` conda environment. `ms_pred` is installed automatically from GitHub by `conda-envs/msms-agent/install.sh`.
- **Checkpoints required**: Script raises `FileNotFoundError` if `--gen_ckpt` or `--inten_ckpt` are missing.
- **Collision energy units**: Use absolute eV values. To convert NCE → eV, set `nce=True` in `iceberg_prediction()` directly.
- **Non-binned output only**: This skill uses `binned_out=False` (high-precision m/z). Binned output disables fragment assignment.
- **Single-compound inference**: Provide one SMILES per call. For batch prediction, loop over SMILES and use separate output dirs.
- **Unsupported elements**: Molecules containing metals, lanthanides, or rare main-group elements may fail or produce low-quality predictions.
- **MW limit**: ICEBERG is unreliable for MW > 1000 Da.

## References

- Alberts, M. et al., "Artificial intelligence for context-aware mass spectrometry", *Nature Methods*, 2025. [DOI:10.1038/s41592-025-02658-z](https://doi.org/10.1038/s41592-025-02658-z)
- ICEBERG source code: [github.com/coleygroup/ms-pred](https://github.com/coleygroup/ms-pred)

---

**Author:** Magdalena Lederbauer
**Contact:** [GitHub @mlederbauer](https://github.com/mlederbauer)

ソースを確認

価格と実行コスト

Skill の入手
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ライセンス
MIT
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無料で入手できても実行が無料とは限りません。価格は安全評価ではありません。 価格情報を送る →

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手順のパスを記録しています。実行テスト、安全保証、互換性認証ではありません。

インストール前にレビュー: 自動インストールを避ける

ライセンス: MIT

  • Dependency or permission surface needs review
  • Permission surface may require sandboxing
  • The skill requires manual download of ICEBERG checkpoints from an external GitHub release, which introduces a supply-chain dependency that is not automated or verified.
  • The SKILL.md excerpt is truncated at the end ('Si'), but the full file likely contains complete constraints; no critical information appears missing.
  • Quality score needs review
  • Permission surface needs review: secrets or environment access, shell or command execution
  • Stars/forks activity: 161 stars, 24 forks; issue activity unavailable in current metadata
  • Dependency/runtime risk: command execution surface, credential or environment access
  • Permission surface: secrets or environment access, shell or command execution
完全な監査を開く

ツール一覧はメタデータであり、互換性のテスト結果ではありません。プロンプトは提案です。

小さなタスクから始める

  1. 1ソースを読み、入力、出力、依存関係、権限を確認します。
  2. 2Agent に計画を求め、設定と費用を承認してから隔離環境でテストします。
  3. 3出力と変更ファイルを確認し、実行した結果だけを報告します。再現用にソースの版を保存します。

依存関係、API キー、外部サービスの料金をソースで確認してください。公開リポジトリでも全サービスが無料とは限りません。

出典と利用上の注意

登録済み

メタデータと審査情報は参考です。人気、ソースの発見、実行成功は別の事実です。

ソースリポジトリ
learningmatter-mit/AtomisticSkills
ライセンス
MIT
バージョン
1.0.0
最終 GitHub プッシュ
2026年9月3日
登録情報の更新日
2026年9月6日

登録されたバージョンです。ソースのリリース情報を確認してください。

品質

66/100

有望

信頼

57/100

Do not auto-install

監査

73/100

要レビュー

  • Dependency or permission surface needs review
  • Permission surface may require sandboxing
  • The skill requires manual download of ICEBERG checkpoints from an external GitHub release, which introduces a supply-chain dependency that is not automated or verified.
  • The SKILL.md excerpt is truncated at the end ('Si'), but the full file likely contains complete constraints; no critical information appears missing.
  • Quality score needs review
  • Permission surface needs review: secrets or environment access, shell or command execution
  • Stars/forks activity: 161 stars, 24 forks; issue activity unavailable in current metadata
  • Dependency/runtime risk: command execution surface, credential or environment access
  • Permission surface: secrets or environment access, shell or command execution
Verified installs
—
成果
—

コピーはインストールではありません。件数は成功報告に基づき、品質全体を保証しません。

Agent 接続

Registry API 経由で判断、信頼、監査、ユースケース、インストールのシグナルを提供し、UI をスクレイピングせずに Agent が順位付けできます。

詳細情報
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    "description": "Predict LC-MS/MS (MS2, tandem mass spectra) from SMILES via ICEBERG, a two-stage deep neural network. Outputs predicted m/z vs intensity spectrum, fragment ion SMILES, and a spectrum plot.",
    "category": "other",
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      "successfulOutcomes": 0,
      "failedOutcomes": 0,
      "installAttempts": 0,
      "installSuccessRate": null,
      "successRate": null,
      "recentSuccessRate": null,
      "recentFailureRate": null,
      "riskBlocked": 0,
      "setupRequired": 0,
      "notRelevant": 0,
      "avgOutputQuality": null,
      "avgTimeToUsefulMs": null,
      "productionOutcomes": 0,
      "humanReviewRequired": 0,
      "uniqueAgents": 0,
      "lastOutcomeAt": null
    },
    "signals": [],
    "penalties": [
      "No real agent outcome evidence yet"
    ]
  },
  "audit": {
    "score": 73,
    "risk_level": "needs_review",
    "risk_label": "Needs review",
    "warnings": [
      "Dependency or permission surface needs review",
      "Permission surface may require sandboxing",
      "The skill requires manual download of ICEBERG checkpoints from an external GitHub release, which introduces a supply-chain dependency that is not automated or verified.",
      "The SKILL.md excerpt is truncated at the end ('Si'), but the full file likely contains complete constraints; no critical information appears missing.",
      "Quality score needs review",
      "Permission surface needs review: secrets or environment access, shell or command execution",
      "Stars/forks activity: 161 stars, 24 forks; issue activity unavailable in current metadata",
      "Dependency/runtime risk: command execution surface, credential or environment access"
    ]
  },
  "safety_gate": {
    "tier": "blocked",
    "label": "Blocked for auto-install",
    "auto_install_policy": "block",
    "auto_install_allowed": false,
    "human_review_required": true,
    "blocked": true,
    "recommended_action": "Do not auto-install. Inspect the source, dependencies, and permission surface first."
  },
  "quality": {
    "score": 66,
    "label": "Promising"
  },
  "supply": {
    "track": "Coding and developer agents",
    "scenario": "Coding",
    "maintenance": "1mo since push",
    "risk": "Needs review"
  },
  "alternative_skills": [],
  "do_not_use_when": [
    "teams that need a vendor-supported SLA",
    "production agents without a repository review",
    "The skill requires manual download of ICEBERG checkpoints from an external GitHub release, which introduces a supply-chain dependency that is not automated or verified.",
    "High-risk permission hints: Shell or command execution, Secrets or environment access",
    "Dependency or permission surface needs review",
    "Permission surface may require sandboxing",
    "The SKILL.md excerpt is truncated at the end ('Si'), but the full file likely contains complete constraints; no critical information appears missing.",
    "Quality score needs review"
  ],
  "agent_contract": {
    "task_input": "Use chem-msms-predict in an agent workflow",
    "recommended_action": "Do not auto-install. Inspect the source, dependencies, and permission surface first.",
    "install_policy": "block",
    "minimum_review_before_use": [
      "Trust: 65/100 Manual review",
      "Audit: 73/100 Needs review",
      "Safety: 33/100 Avoid automatic install",
      "Review repository, license, install command, and permission surface before production use."
    ],
    "expected_agent_output": {
      "selected_skill": "learningmatter-mit-chem-msms-predict (chem-msms-predict)",
      "install_command": "npx skills add learningmatter-mit/AtomisticSkills --skill chem-msms-predict",
      "risk_summary": "Needs review; Blocked for auto-install; Review before production",
      "verification_result": "Report the smallest successful task, files touched, warnings, and any missing setup."
    }
  },
  "outcome_feedback": {
    "endpoint": "https://www.openagentskill.com/api/agent/outcome",
    "method": "POST",
    "requires_resolve_event_id": true,
    "event_id_source": "Use install_receipt.outcome_feedback.event_id or feedback.event_id returned by /api/agent/resolve for the current task.",
    "expected_outcomes": [
      "success",
      "failed",
      "not_relevant",
      "blocked_by_risk",
      "setup_required"
    ],
    "payload_template": {
      "event_id": "<install_receipt.outcome_feedback.event_id or feedback.event_id from /api/agent/resolve>",
      "skill_slug": "learningmatter-mit-chem-msms-predict",
      "task": "Use chem-msms-predict in an agent workflow",
      "agent": "codex",
      "outcome": "success",
      "install_used": true,
      "risk_blocked": false,
      "setup_required": false,
      "task_success": true,
      "output_quality": 4,
      "error_type": null,
      "human_review_required": false,
      "workspace": "sandbox",
      "time_to_useful_ms": 120000,
      "notes": "Report the smallest successful task, setup friction, files touched, and risk notes."
    }
  },
  "endpoints": {
    "web": "https://www.openagentskill.com/skills/learningmatter-mit-chem-msms-predict",
    "api": "https://www.openagentskill.com/api/agent/skills/learningmatter-mit-chem-msms-predict",
    "audit": "https://www.openagentskill.com/skills/learningmatter-mit-chem-msms-predict/audit",
    "eval": "https://www.openagentskill.com/api/agent/evals?slug=learningmatter-mit-chem-msms-predict&task=Use%20chem-msms-predict%20in%20an%20agent%20workflow&max_risk=medium",
    "resolve": "https://www.openagentskill.com/api/agent/resolve?task=Use%20chem-msms-predict%20in%20an%20agent%20workflow&agent=codex&max_risk=medium",
    "receipt": "https://www.openagentskill.com/api/agent/receipt?task=Use%20chem-msms-predict%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text",
    "install": "https://www.openagentskill.com/api/skills/learningmatter-mit-chem-msms-predict/install",
    "manifest": "https://www.openagentskill.com/api/registry/manifest/learningmatter-mit-chem-msms-predict"
  }
}

クリエイター向け

掲載元

Registry により登録

申請可能

この掲載は公開ソースから登録されており、メンテナー申請が承認されるまで公式として表示されません。

インデックス作成者
OpenAgentSkill コミュニティインデックス

帰属は公開リポジトリまたは作成者プロフィールにリンクされています。作成者は掲載を申請して所有権シグナルを更新できます。

このスキルを申請

所有者の申請

このスキル掲載を申請

この Registry により登録 掲載は learningmatter-mit に帰属していますが、まだ公式として表示されていません。申請すると、確認済み所有者シグナルが追加され、今後の公開、インストール、監査更新の信頼性が高まります。

共有キット

クリエイター被リンクキット

README にエビデンスバッジを追加

開発者がリポジトリを評価する場所で、正規掲載、現在の信頼・監査シグナル、実際の Agent-Proven エビデンスを表示します。

[![Listed on OpenAgentSkill](https://www.openagentskill.com/api/badge/learningmatter-mit-chem-msms-predict?metric=listed&label=Listed)](https://www.openagentskill.com/skills/learningmatter-mit-chem-msms-predict?ref=github&utm_source=github&utm_medium=referral&utm_campaign=creator_badge)
[![OpenAgentSkill Trust](https://www.openagentskill.com/api/badge/learningmatter-mit-chem-msms-predict?metric=trust&label=Trust)](https://www.openagentskill.com/skills/learningmatter-mit-chem-msms-predict?ref=github&utm_source=github&utm_medium=referral&utm_campaign=creator_badge)
[![OpenAgentSkill Audit](https://www.openagentskill.com/api/badge/learningmatter-mit-chem-msms-predict?metric=audit&label=Audit)](https://www.openagentskill.com/skills/learningmatter-mit-chem-msms-predict/audit)
[![Agent Proven](https://www.openagentskill.com/api/badge/learningmatter-mit-chem-msms-predict?metric=proven&label=Agent%20Proven)](https://www.openagentskill.com/skills/learningmatter-mit-chem-msms-predict?ref=github&utm_source=github&utm_medium=referral&utm_campaign=creator_badge)

コミュニティシグナル

このスキルが Agent ワークフローに役立つかを共有してください。集約されたフィードバックがランキングを改善します。