# Agent input data

输入 zip 为 disulfide_mapping_input.zip，解压后包含：
1. protein_sequence.fasta、cysteine_map.csv 和 peptide_library.csv：21 aa 肽的序列、六个半胱氨酸在蛋白和酶切肽中的位置，以及肽段中性单同位素质量。
2. candidate_disulfides.csv：三个酶切肽之间所有可能的跨肽半胱氨酸配对及理论二硫键连接质量。同一个 peptide_pair 内不同配对的连接质量相同，需用 MS/MS 诊断离子定位。
3. nonreduced_features.csv：三个批次、三个重复和每个色谱 feature_group 的两个离子通道；字段含保留时间、m/z、z、同位素间距和峰面积。两个通道分别对应质子化离子和钠加合离子，但文件不直接给出通道名称；同一 feature_group_id 的两行属于同一组。
4. nonreduced_run_metadata.csv：每个批次/重复的 run-level internal standard area；bond_response_factors.csv：六种观测连接的响应因子。
5. diagnostic_ion_library.csv 和 msms_ions.csv：每个候选连接的理论诊断离子，以及每个 feature_group 的观测 MS/MS 离子 m/z 和相对强度。
6. differential_alkylation.csv：每个批次/重复/半胱氨酸的 NEM 与 IAM 峰面积；alkylation_response_factors.csv：两种标签的响应因子。NEM 在还原前加入，IAM 在还原后加入。
7. product_specification.json：目标 native connectivity、烷基化 reference signal、诊断离子和前体质量 QC、半胱氨酸闭合及批次放行标准。
所有输入 CSV 均为 UTF-8 逗号分隔且无缺失值；数据由肽段单同位素质量、质子化/钠加合质量、二硫键脱氢、碎片质量和响应/测量波动构造，不含私密实验、患者或企业数据。

## Annotator input notes

# Differential alkylation and disulfide mapping dataset

This package contains a small, batch-style characterization dataset for a 21-residue disulfide-rich peptide (DSB-21) with six cysteines. The tryptic digest has three peptide components, each containing two cysteines. `candidate_disulfides.csv` lists every cross-peptide cysteine pairing that is chemically possible from these three digest peptides. Candidate bonds sharing a peptide pair have the same linked-peptide precursor mass, so precursor mass by itself is not a bond-localization result.

`nonreduced_features.csv` contains two ion channels for each chromatographic feature group. The channels are protonated and sodium-adduct forms, but the channel identity is intentionally not written in the file. The repeated `feature_group_id` identifies channels belonging to one chromatographic component. `nonreduced_run_metadata.csv` supplies a run-level internal standard area. `diagnostic_ion_library.csv` and `msms_ions.csv` provide theoretical and observed MS/MS masses for localizing the cysteine pair. Areas contain nonzero response and measurement variation.

In `differential_alkylation.csv`, NEM was added before reduction and IAM after reduction. Thus NEM reports pre-existing free thiol, while IAM reports cysteine sites that were disulfide-bound before reduction. The two tag response-factor columns are supplied in `alkylation_response_factors.csv`; the independent corrected-signal reference for the alkylation closure check is in `product_specification.json`. `bond_response_factors.csv` supplies response correction for each localized disulfide feature.

`product_specification.json` contains the intended native connectivity and batch acceptance criteria. These records are physics- and chemistry-based synthetic data with realistic response variation; they are not private experimental or patient data and contain no missing values.


## File inventory

| file | bytes |
|---|---:|
| `README_input.md` | 1918 |
| `alkylation_response_factors.csv` | 132 |
| `bond_response_factors.csv` | 106 |
| `candidate_disulfides.csv` | 617 |
| `cysteine_map.csv` | 145 |
| `diagnostic_ion_library.csv` | 2075 |
| `differential_alkylation.csv` | 3961 |
| `msms_ions.csv` | 18307 |
| `nonreduced_features.csv` | 12075 |
| `nonreduced_run_metadata.csv` | 303 |
| `peptide_library.csv` | 168 |
| `product_specification.json` | 485 |
| `protein_sequence.fasta` | 32 |

## Computed numeric profile

### `alkylation_response_factors.csv`

Rows: 6; columns: 3.

| column | min | max | missing |
|---|---:|---:|---:|
| `NEM_response_factor` | 0.95 | 1.08 | 0 |
| `IAM_response_factor` | 0.94 | 1.06 | 0 |

### `bond_response_factors.csv`

Rows: 6; columns: 2.

| column | min | max | missing |
|---|---:|---:|---:|
| `relative_response_factor` | 0.89 | 1.12 | 0 |

### `candidate_disulfides.csv`

Rows: 12; columns: 7.

| column | min | max | missing |
|---|---:|---:|---:|
| `theoretical_linked_neutral_mass_Da` | 1415.6029 | 1528.6077 | 0 |

### `cysteine_map.csv`

Rows: 6; columns: 5.

| column | min | max | missing |
|---|---:|---:|---:|
| `protein_position` | 2 | 19 | 0 |
| `position_in_peptide` | 2 | 5 | 0 |

### `diagnostic_ion_library.csv`

Rows: 48; columns: 4.

| column | min | max | missing |
|---|---:|---:|---:|
| `theoretical_mz` | 895.38344 | 1416.5309 | 0 |

### `differential_alkylation.csv`

Rows: 108; columns: 5.

| column | min | max | missing |
|---|---:|---:|---:|
| `replicate` | 1 | 3 | 0 |
| `area` | 12193.109 | 678653.76 | 0 |

### `msms_ions.csv`

Rows: 324; columns: 5.

| column | min | max | missing |
|---|---:|---:|---:|
| `replicate` | 1 | 3 | 0 |
| `ion_mz` | 121.65646 | 1416.5326 | 0 |
| `relative_intensity` | 0.010758795 | 0.34490617 | 0 |

### `nonreduced_features.csv`

Rows: 108; columns: 10.

| column | min | max | missing |
|---|---:|---:|---:|
| `replicate` | 1 | 3 | 0 |
| `retention_time_min` | 18.17139 | 25.517424 | 0 |
| `mz` | 472.87402 | 517.87157 | 0 |
| `charge` | 3 | 3 | 0 |
| `isotope_spacing_Da` | 0.33434494 | 0.3345607 | 0 |
| `area` | 1718.5563 | 897628.19 | 0 |

### `nonreduced_run_metadata.csv`

Rows: 9; columns: 3.

| column | min | max | missing |
|---|---:|---:|---:|
| `replicate` | 1 | 3 | 0 |
| `internal_standard_area` | 995908.22 | 1003774.6 | 0 |

### `peptide_library.csv`

Rows: 3; columns: 4.

| column | min | max | missing |
|---|---:|---:|---:|
| `neutral_monoisotopic_mass_Da` | 680.29857 | 793.30333 | 0 |