Harmonized GNPS + MassSpecGym MS/MS spectra with NPClassifier and ChemOnt labels, top128 release

This dataset contains zstd-compressed MGF spectra from GNPS public libraries andMassSpecGym, harmonized with canonical SMILES, InChIKey, molecular formula,NPClassifier labels, and ChemOnt/ClassyFire labels. It is intended forbenchmarking and modelling structure-aware MS/MS classification. Labels arecomputational annotations, not experimentally curated ground truth. File `combined-gnps-mass-spec-gym-npc-faithful.harmonized-subset.top128.mgf.zst` Spectra: `443,905` Unique canonical SMILES: `45,007` Unique SPLASH identifiers: `443,905` Peaks per spectrum: `3-128` Size: `182M` SHA-256: `aee5a595960ef1284fe9977b6560a1ff771c07bb28c4a8e2e2ef47020b35724e` Sources | Source | Spectra | Unique SMILES ||---|---:|---:|| GNPS `ALL_GNPS.mgf` | `389,560` | `42,583` || MassSpecGym MGF | `54,345` | `9,120` | Source URLs: `https://external.gnps2.org/gnpslibrary/ALL_GNPS.mgf` `https://huggingface.co/datasets/roman-bushuiev/MassSpecGym/resolve/main/data/auxiliary/MassSpecGym.mgf?download=true` Annotations NPClassifier labels were predicted with NPClassifier.rs `Faithful`, CUDA f32,batch size `2048`. Coverage: NPClassifier: `7` pathways, `75` superclasses, `503` classes ChemOnt: `2` kingdoms, `20` superclasses, `303` classes, `734` subclasses, `1,580` direct parents Each MGF record includes source provenance, `SMILES`, `INCHIKEY`, `FORMULA`,`SPLASH`, NPC labels/scores, and ChemOnt labels. Processing Spectra were parsed and serialized with `mascot-rs` at commit`e9641034f75d019279a63f99d767d83a3bed55d1`. SMILES were canonicalized with`smiles-parser`; RDKit `2024.03.3` was used for tautomer-canonical SMILES andInChIKeys. Filters retained valid organic structures with non-zero precursorm/z, non-zero charge, `3-128` peaks, no post-top128 duplicate SPLASH collision,complete NPC labels, and no `(SPLASH, PEPMASS)` NPC/ChemOnt disagreement group. Difference From The Top60 Release Peak retention was increased from top `60` to top `128`. SPLASH values and collision groups were recomputed after top128 peak retention. Top128 base MGF: `567,068` mascot-valid spectra. Top128 harmonized MGF before final mascot filtering: `444,187` spectra. Final strict `mascot-rs` accept/reject pass dropped `282` records. Final file fully loads with current `mascot-rs`: `443,905` validated records. Validation Missing `CHARGE`: `0` Charge/ionmode mismatches: `0` Missing `IONMODE`: `361` Total retained peaks: `17,098,616`本数据集包含来自GNPS公共质谱库与MassSpecGym的、经Zstandard（zstd）压缩的Mascot通用格式（MGF）质谱图谱，已与规范简化分子线性输入规范（SMILES）、国际化学标识符键（InChIKey）、分子式、NPClassifier标签及ChemOnt/ClassyFire标签完成对齐标准化。本数据集旨在用于结构感知型质谱二级（MS/MS）分类的基准测试与建模。其中的标签均为计算生成的注释，而非经实验人工审核的真实基准真值。 ### 数据集文件 `combined-gnps-mass-spec-gym-npc-faithful.harmonized-subset.top128.mgf.zst` ### 基本统计 | 统计项 | 数值 | | --- | --- | | 质谱图谱总数 | 443,905 | | 唯一规范SMILES数量 | 45,007 | | 唯一SPLASH标识符数量 | 443,905 | | 单张图谱峰数范围 | 3~128 | | 文件大小 | 182 MB | | SHA-256哈希值 | aee5a595960ef1284fe9977b6560a1ff771c07bb28c4a8e2e2ef47020b35724e | ### 数据来源 | 来源 | 质谱图谱数 | 唯一SMILES数 | | --- | ---: | ---: | | GNPS `ALL_GNPS.mgf` | 389,560 | 42,583 | | MassSpecGym MGF | 54,345 | 9,120 | ### 源地址 https://external.gnps2.org/gnpslibrary/ALL_GNPS.mgf https://huggingface.co/datasets/roman-bushuiev/MassSpecGym/resolve/main/data/auxiliary/MassSpecGym.mgf?download=true ### 注释信息 NPClassifier标签通过commit为`e9641034f75d019279a63f99d767d83a3bed55d1`的`NPClassifier.rs`工具的`Faithful`模式、CUDA浮点32（f32）精度、批次大小2048进行预测。注释覆盖范围如下： - NPClassifier：7条通路、75个超类、503个类别 - ChemOnt：2个界、20个超类、303个类别、734个子类、1,580个直接父类 每条MGF记录均包含来源溯源信息、SMILES、INCHIKEY、分子式、SPLASH标识符、NPClassifier标签/得分及ChemOnt标签。 ### 数据处理流程 质谱图谱通过commit为`e9641034f75d019279a63f99d767d83a3bed55d1`的`mascot-rs`工具进行解析与序列化。SMILES通过`smiles-parser`完成规范化；使用RDKit 2024.03.3版本生成互变异构体规范化SMILES与InChIKey。 本次筛选保留符合以下全部条件的有效有机结构： 1. 前体m/z非零 2. 电荷非零 3. 峰数介于3~128之间 4. 经前128峰筛选后无重复SPLASH标识符冲突 5. 拥有完整NPClassifier标签 6. 不存在`(SPLASH, PEPMASS)`对应的NPClassifier与ChemOnt标签不一致的分组 ### 与Top60版本的差异 1. 保留的主峰数从前60峰提升至前128峰 2. 在完成前128峰筛选后，重新计算了SPLASH标识符与碰撞分组 3. 前128峰原始MGF文件：经`mascot-rs`验证的图谱共567,068张 4. 最终`mascot-rs`筛选前的对齐标准化前128峰MGF文件：共444,187张图谱 5. 经严格的`mascot-rs`接受/拒绝规则过滤后，剔除了282条记录 6. 最终文件可通过当前版本的`mascot-rs`完整加载，共443,905条经验证的记录 ### 验证结果 | 验证项 | 数值 | | --- | --- | | 缺失`CHARGE`字段 | 0 | | 电荷与离子模式不匹配 | 0 | | 缺失`IONMODE`字段 | 361 | | 总保留峰数 | 17,098,616 |