opentdf 1.0.0__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- opentdf-1.0.0/.github/workflows/ci.yml +42 -0
- opentdf-1.0.0/.github/workflows/publish.yml +85 -0
- opentdf-1.0.0/.gitignore +31 -0
- opentdf-1.0.0/ATTRIBUTION.md +320 -0
- opentdf-1.0.0/CHANGELOG.md +59 -0
- opentdf-1.0.0/Cargo.toml +25 -0
- opentdf-1.0.0/LICENSE +192 -0
- opentdf-1.0.0/PKG-INFO +52 -0
- opentdf-1.0.0/README.md +62 -0
- opentdf-1.0.0/docs/.gitignore +6 -0
- opentdf-1.0.0/docs/bun.lock +2805 -0
- opentdf-1.0.0/docs/docs/changelog.md +27 -0
- opentdf-1.0.0/docs/docs/format/00-overview.md +62 -0
- opentdf-1.0.0/docs/docs/format/01-tdf-sqlite-schema.md +142 -0
- opentdf-1.0.0/docs/docs/format/02-tdf-bin-block-stream.md +43 -0
- opentdf-1.0.0/docs/docs/format/03-frame-payload-encoding.md +163 -0
- opentdf-1.0.0/docs/docs/format/04-calibration.md +108 -0
- opentdf-1.0.0/docs/docs/format/05-instrument-tables.md +333 -0
- opentdf-1.0.0/docs/docs/format/06-references-and-gaps.md +83 -0
- opentdf-1.0.0/docs/docs/guide/acquisition-modes.md +59 -0
- opentdf-1.0.0/docs/docs/guide/calibration.md +30 -0
- opentdf-1.0.0/docs/docs/guide/peaks-and-codecs.md +38 -0
- opentdf-1.0.0/docs/docs/guide/reader.md +40 -0
- opentdf-1.0.0/docs/docs/install.md +70 -0
- opentdf-1.0.0/docs/docs/intro.md +42 -0
- opentdf-1.0.0/docs/docs/license.md +24 -0
- opentdf-1.0.0/docs/docs/quickstart.md +99 -0
- opentdf-1.0.0/docs/docs/reference/api.md +13 -0
- opentdf-1.0.0/docs/docs/reference/examples.md +25 -0
- opentdf-1.0.0/docs/docusaurus.config.ts +132 -0
- opentdf-1.0.0/docs/package.json +39 -0
- opentdf-1.0.0/docs/sidebars.ts +46 -0
- opentdf-1.0.0/docs/src/css/custom.css +206 -0
- opentdf-1.0.0/docs/static/.nojekyll +0 -0
- opentdf-1.0.0/docs/static/img/favicon.ico +0 -0
- opentdf-1.0.0/docs/static/img/logo.svg +38 -0
- opentdf-1.0.0/docs/tsconfig.json +8 -0
- opentdf-1.0.0/docs/wrangler.jsonc +17 -0
- opentdf-1.0.0/examples/dump.rs +135 -0
- opentdf-1.0.0/pyproject.toml +29 -0
- opentdf-1.0.0/python/.gitignore +8 -0
- opentdf-1.0.0/python/Cargo.lock +422 -0
- opentdf-1.0.0/python/Cargo.toml +22 -0
- opentdf-1.0.0/python/README.md +34 -0
- opentdf-1.0.0/python/src/lib.rs +586 -0
- opentdf-1.0.0/python/tests/test_basic.py +58 -0
- opentdf-1.0.0/src/calibration.rs +45 -0
- opentdf-1.0.0/src/codec.rs +198 -0
- opentdf-1.0.0/src/error.rs +21 -0
- opentdf-1.0.0/src/lib.rs +24 -0
- opentdf-1.0.0/src/reader.rs +524 -0
- opentdf-1.0.0/src/types.rs +112 -0
- opentdf-1.0.0/tests/roundtrip.rs +416 -0
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components: rustfmt, clippy
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tags: ["v*"]
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concurrency:
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group: publish-${{ github.ref }}
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cancel-in-progress: true
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permissions:
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contents: read
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args: --release --out dist --find-interpreter --manifest-path python/Cargo.toml
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opentdf-1.0.0/.gitignore
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# Rust build output
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/target
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target/
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Cargo.lock
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# Reverse-engineering workspace -- never tracked
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/re/
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# Corpus data (large binary bundles, not redistributed)
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/corpus/
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nohup.out
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# Python
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**/__pycache__/
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**/*.pyc
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**/*.pyo
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*.egg-info/
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.venv/
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# Editor / OS
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*.swp
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*.swo
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.idea/
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# Docusaurus
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docs/node_modules/
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docs/build/
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docs/.docusaurus/
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docs/.cache-loader/
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# Attribution
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Bruker `.d` bundles re-distributed (for research / open-parser
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development) from public ProteomeXchange repositories. Every dataset
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listed below retains its original licence — PRIDE's default is
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CC-BY 4.0, but per-dataset terms always win. If you use any of
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these data, please cite the original submitter and the ProteomeXchange
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accession; links below resolve to the project landing page.
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Manifest generated: 2026-04-22T00:10:25.830284+00:00
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Bundles: 19
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Total size: 17.01 GB
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| Accession | Repo | Instrument | Mode | Size (MB) | Title |
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|---|---|---|---|---:|---|
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| [PXD021593](https://www.ebi.ac.uk/pride/archive/projects/PXD021593) | PRIDE | maXis | ? | 32 | A proteomic-informed view of the changes induced by loss of cellular adherence: the example of mouse macrophages |
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| [PXD009101](https://www.ebi.ac.uk/pride/archive/projects/PXD009101) | PRIDE | solariX | ? | 7 | GAGfinder: glycosaminoglycan MS/MS fragment peak finding and elemental composition assignment |
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| [PXD005859](https://www.ebi.ac.uk/pride/archive/projects/PXD005859) | PRIDE | amaZon Speed ETD | ? | 364 | Glycoproteomics of Flagellin C9LY14 from Selenomonas sputigena |
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| [PXD030992](https://www.ebi.ac.uk/pride/archive/projects/PXD030992) | PRIDE | timsTOF Pro | ? | 89 | TGFB1 induced S100 family protein expression is associated with epithelial to mesenchymal transition states and poor sur |
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| [PXD025576](https://www.ebi.ac.uk/pride/archive/projects/PXD025576) | PRIDE | timsTOF Pro | DIA/diaPASEF | 1735 | Characterizing the role of OCIAD1 in the proteolytic processing of holocytochrome c1 and CIII2 assembly |
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| [PXD031833](https://www.ebi.ac.uk/pride/archive/projects/PXD031833) | PRIDE | timsTOF Pro | DIA/diaPASEF | 162 | TTYH family members form tetrameric complexes at the cell membrane |
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| [PXD027359](https://www.ebi.ac.uk/pride/archive/projects/PXD027359) | PRIDE | timsTOF Pro | DIA/diaPASEF | 743 | AlphaTims: Indexing unprocessed trapped ion mobility spectrometry - time of flight data for fast and easy accession and |
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| [PXD034557](https://www.ebi.ac.uk/pride/archive/projects/PXD034557) | PRIDE | timsTOF pro 2 | DIA/diaPASEF | 1523 | Comparative Proteomic Profiling of Variants SARS-CoV-2 Virus-Like-Particles (VLPs) Incubated Cells |
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| [PXD006287](https://www.ebi.ac.uk/pride/archive/projects/PXD006287) | PRIDE | Bruker Daltonics amaZon series | ? | 63 | In culture cross-linking of bacterial cells reveals large scale dynamic protein-protein interactions at the peptide leve |
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| [PXD018980](https://www.ebi.ac.uk/pride/archive/projects/PXD018980) | PRIDE | maXis | ? | 615 | Characterisation of South American camelid fibres by proteomics |
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| [PXD036417](https://www.ebi.ac.uk/pride/archive/projects/PXD036417) | PRIDE | solariX | ? | 92 | Counterintuitive structural and functional effects due to naturally-occurring mutations targeting the active site of the |
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| [PXD022216](https://www.ebi.ac.uk/pride/archive/projects/PXD022216) | PRIDE | timsTOF Pro | DIA/diaPASEF | 3959 | The Proteome Landscape of Chronic Lymphocytic Leukemia |
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| [PXD030327](https://www.ebi.ac.uk/pride/archive/projects/PXD030327) | PRIDE | timsTOF Pro | DIA/diaPASEF | 1696 | Enhanced competition at the nano-bio interface enables comprehensive characterization of protein corona dynamics and dee |
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| [PXD018972](https://www.ebi.ac.uk/pride/archive/projects/PXD018972) | PRIDE | amaZon ETD | ? | 64 | Caspr2 interacts with type 1 inositol 1,4,5-trisphosphate receptor in the developing cerebellum and regulates Purkinje c |
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| [PXD038283](https://www.ebi.ac.uk/pride/archive/projects/PXD038283) | PRIDE | Bruker Daltonics solarix series | ? | 30 | Robust high throughput proteomics identification and deami-dation quantitation of extinct species up to Pleistocene with |
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| [PXD001592](https://www.ebi.ac.uk/pride/archive/projects/PXD001592) | PRIDE | Bruker Daltonics instrument model | ? | 3369 | The impact II, a very high resolution quadrupole time-of-flight instrument for deep shotgun proteomics |
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| [PXD035147](https://www.ebi.ac.uk/pride/archive/projects/PXD035147) | PRIDE | autoflex | ? | 235 | Integrated proteome and malonylome analyses reveal the potential meaning of TLN1 and ACTB in end-stage renal disease |
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| [PXD035173](https://www.ebi.ac.uk/pride/archive/projects/PXD035173) | PRIDE | timsTOF Pro | DIA/diaPASEF | 2225 | Proteomic profiling of carotid atherosclerotic plaques and adjacent intact arterial segments |
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## Per-bundle detail
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### PXD021593 — F031470HD.d.zip
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- Title: A proteomic-informed view of the changes induced by loss of cellular adherence: the example of mouse macrophages
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- Organisms: Mus musculus (mouse)
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- Publication date: 2021-09-09
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- Project instruments: maXis, TripleTOF 5600, Synapt MS
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- Reported instrument: None
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- Acquisition software: None
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- Schema: None None
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- Acquisition mode: None
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- Size: 32.3 MB
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- Source URL: https://ftp.pride.ebi.ac.uk/pride/data/archive/2021/09/PXD021593/F031470HD.d.zip
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- Licence (presumed): CC-BY-4.0 (PRIDE default)
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- Attribution string: PRIDE PXD021593: A proteomic-informed view of the changes induced by loss of cellular adherence: the example of mouse macrophages
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### PXD009101 — 2083-_EDD.d.zip
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- Title: GAGfinder: glycosaminoglycan MS/MS fragment peak finding and elemental composition assignment
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- Organisms: Homo sapiens (human)
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- Publication date: 2018-04-09
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- Project instruments: solariX
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- Reported instrument: None
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- Acquisition software: None
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- Schema: None None
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- Acquisition mode: None
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- Size: 6.8 MB
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- Source URL: https://ftp.pride.ebi.ac.uk/pride/data/archive/2018/04/PXD009101/2083-_EDD.d.zip
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- Licence (presumed): CC-BY-4.0 (PRIDE default)
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- Attribution string: PRIDE PXD009101: GAGfinder: glycosaminoglycan MS/MS fragment peak finding and elemental composition assignment
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### PXD005859 — SspFlag2_GC3_01_10982.d.zip
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- Title: Glycoproteomics of Flagellin C9LY14 from Selenomonas sputigena
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- Organisms: Selenomonas sputigena atcc 35185, Escherichia coli
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- Publication date: 2018-01-24
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- Project instruments: amaZon Speed ETD
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- Reported instrument: None
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- Acquisition software: None
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- Schema: None None
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- Acquisition mode: None
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77
|
+
- Size: 364.3 MB
|
|
78
|
+
- Source URL: https://ftp.pride.ebi.ac.uk/pride/data/archive/2018/01/PXD005859/SspFlag2_GC3_01_10982.d.zip
|
|
79
|
+
- Licence (presumed): CC-BY-4.0 (PRIDE default)
|
|
80
|
+
- Attribution string: PRIDE PXD005859: Glycoproteomics of Flagellin C9LY14 from Selenomonas sputigena
|
|
81
|
+
|
|
82
|
+
### PXD030992 — P3945_10_1_1_4638.d.zip
|
|
83
|
+
|
|
84
|
+
- Title: TGFB1 induced S100 family protein expression is associated with epithelial to mesenchymal transition states and poor survival in pancreatic cancer
|
|
85
|
+
- Organisms: Mus musculus (mouse)
|
|
86
|
+
- Publication date: 2023-02-24
|
|
87
|
+
- Project instruments: timsTOF Pro
|
|
88
|
+
- Reported instrument: None
|
|
89
|
+
- Acquisition software: None
|
|
90
|
+
- Schema: None None
|
|
91
|
+
- Acquisition mode: None
|
|
92
|
+
- Size: 88.9 MB
|
|
93
|
+
- Source URL: https://ftp.pride.ebi.ac.uk/pride/data/archive/2023/02/PXD030992/P3945_10_1_1_4638.d.zip
|
|
94
|
+
- Licence (presumed): CC-BY-4.0 (PRIDE default)
|
|
95
|
+
- Attribution string: PRIDE PXD030992: TGFB1 induced S100 family protein expression is associated with epithelial to mesenchymal transition states and poor survival in pancreatic cancer
|
|
96
|
+
|
|
97
|
+
### PXD025576 — 191118_DIAMAX_G10_Slot1-62_1_459.d.zip
|
|
98
|
+
|
|
99
|
+
- Title: Characterizing the role of OCIAD1 in the proteolytic processing of holocytochrome c1 and CIII2 assembly
|
|
100
|
+
- Organisms: Homo sapiens (human)
|
|
101
|
+
- Publication date: 2021-05-18
|
|
102
|
+
- Project instruments: timsTOF Pro
|
|
103
|
+
- Reported instrument: timsTOF Pro
|
|
104
|
+
- Acquisition software: Bruker otofControl 6.0.115.261-15059-vc141
|
|
105
|
+
- Schema: TDF 3.1
|
|
106
|
+
- Acquisition mode: DIA/diaPASEF
|
|
107
|
+
- Size: 1735.3 MB
|
|
108
|
+
- Source URL: https://ftp.pride.ebi.ac.uk/pride/data/archive/2021/05/PXD025576/191118_DIAMAX_G10_Slot1-62_1_459.d.zip
|
|
109
|
+
- Licence (presumed): CC-BY-4.0 (PRIDE default)
|
|
110
|
+
- Attribution string: PRIDE PXD025576: Characterizing the role of OCIAD1 in the proteolytic processing of holocytochrome c1 and CIII2 assembly
|
|
111
|
+
|
|
112
|
+
### PXD031833 — mTTYH1-D_coi-N2-P-200-20C_U-T_3366.d.zip
|
|
113
|
+
|
|
114
|
+
- Title: TTYH family members form tetrameric complexes at the cell membrane
|
|
115
|
+
- Organisms: Mus musculus (mouse)
|
|
116
|
+
- Publication date: 2022-08-31
|
|
117
|
+
- Project instruments: timsTOF Pro, Bruker Daltonics solarix series
|
|
118
|
+
- Reported instrument: timsTOF Pro
|
|
119
|
+
- Acquisition software: Bruker otofControl 6.2.201.416-16523-vc141
|
|
120
|
+
- Schema: TDF 3.3
|
|
121
|
+
- Acquisition mode: DIA/diaPASEF
|
|
122
|
+
- Size: 161.7 MB
|
|
123
|
+
- Source URL: https://ftp.pride.ebi.ac.uk/pride/data/archive/2022/08/PXD031833/mTTYH1-D_coi-N2-P-200-20C_U-T_3366.d.zip
|
|
124
|
+
- Licence (presumed): CC-BY-4.0 (PRIDE default)
|
|
125
|
+
- Attribution string: PRIDE PXD031833: TTYH family members form tetrameric complexes at the cell membrane
|
|
126
|
+
|
|
127
|
+
### PXD027359 — 20201207_tims03_Evo03_PS_SA_HeLa_200ng_EvoSep_prot_DDA_21min_8cm_S1-C10_1_22476.d.zip
|
|
128
|
+
|
|
129
|
+
- Title: AlphaTims: Indexing unprocessed trapped ion mobility spectrometry - time of flight data for fast and easy accession and visualization
|
|
130
|
+
- Organisms: Homo sapiens (human)
|
|
131
|
+
- Publication date: 2021-07-30
|
|
132
|
+
- Project instruments: timsTOF Pro
|
|
133
|
+
- Reported instrument: timsTOF Pro
|
|
134
|
+
- Acquisition software: timsTOF 2.0.40
|
|
135
|
+
- Schema: TDF 3.5
|
|
136
|
+
- Acquisition mode: DIA/diaPASEF
|
|
137
|
+
- Size: 743.5 MB
|
|
138
|
+
- Source URL: https://ftp.pride.ebi.ac.uk/pride/data/archive/2021/07/PXD027359/20201207_tims03_Evo03_PS_SA_HeLa_200ng_EvoSep_prot_DDA_21min_8cm_S1-C10_1_22476.d.zip
|
|
139
|
+
- Licence (presumed): CC-BY-4.0 (PRIDE default)
|
|
140
|
+
- Attribution string: PRIDE PXD027359: AlphaTims: Indexing unprocessed trapped ion mobility spectrometry - time of flight data for fast and easy accession and visualization
|
|
141
|
+
|
|
142
|
+
### PXD034557 — C1DIA_Slot1-1_1_3174.d.zip
|
|
143
|
+
|
|
144
|
+
- Title: Comparative Proteomic Profiling of Variants SARS-CoV-2 Virus-Like-Particles (VLPs) Incubated Cells
|
|
145
|
+
- Organisms: Homo sapiens (human)
|
|
146
|
+
- Publication date: 2023-04-15
|
|
147
|
+
- Project instruments: timsTOF Pro 2
|
|
148
|
+
- Reported instrument: timsTOF pro 2
|
|
149
|
+
- Acquisition software: timsTOF 3.0.22
|
|
150
|
+
- Schema: TDF 3.6
|
|
151
|
+
- Acquisition mode: DIA/diaPASEF
|
|
152
|
+
- Size: 1523.4 MB
|
|
153
|
+
- Source URL: https://ftp.pride.ebi.ac.uk/pride/data/archive/2023/04/PXD034557/C1DIA_Slot1-1_1_3174.d.zip
|
|
154
|
+
- Licence (presumed): CC-BY-4.0 (PRIDE default)
|
|
155
|
+
- Attribution string: PRIDE PXD034557: Comparative Proteomic Profiling of Variants SARS-CoV-2 Virus-Like-Particles (VLPs) Incubated Cells
|
|
156
|
+
|
|
157
|
+
### PXD006287 — XL2349_fr9_B2_01_1701.d.zip
|
|
158
|
+
|
|
159
|
+
- Title: In culture cross-linking of bacterial cells reveals large scale dynamic protein-protein interactions at the peptide level.
|
|
160
|
+
- Organisms: Bacillus subtilis subsp. subtilis str. 168
|
|
161
|
+
- Publication date: 2017-05-23
|
|
162
|
+
- Project instruments: Bruker Daltonics amaZon series
|
|
163
|
+
- Reported instrument: None
|
|
164
|
+
- Acquisition software: None
|
|
165
|
+
- Schema: None None
|
|
166
|
+
- Acquisition mode: None
|
|
167
|
+
- Size: 62.5 MB
|
|
168
|
+
- Source URL: https://ftp.pride.ebi.ac.uk/pride/data/archive/2017/05/PXD006287/XL2349_fr9_B2_01_1701.d.zip
|
|
169
|
+
- Licence (presumed): CC-BY-4.0 (PRIDE default)
|
|
170
|
+
- Attribution string: PRIDE PXD006287: In culture cross-linking of bacterial cells reveals large scale dynamic protein-protein interactions at the peptide level.
|
|
171
|
+
|
|
172
|
+
### PXD009101 — 2064-_NETD.d.zip
|
|
173
|
+
|
|
174
|
+
- Title: GAGfinder: glycosaminoglycan MS/MS fragment peak finding and elemental composition assignment
|
|
175
|
+
- Organisms: Homo sapiens (human)
|
|
176
|
+
- Publication date: 2018-04-09
|
|
177
|
+
- Project instruments: solariX
|
|
178
|
+
- Reported instrument: None
|
|
179
|
+
- Acquisition software: None
|
|
180
|
+
- Schema: None None
|
|
181
|
+
- Acquisition mode: None
|
|
182
|
+
- Size: 6.9 MB
|
|
183
|
+
- Source URL: https://ftp.pride.ebi.ac.uk/pride/data/archive/2018/04/PXD009101/2064-_NETD.d.zip
|
|
184
|
+
- Licence (presumed): CC-BY-4.0 (PRIDE default)
|
|
185
|
+
- Attribution string: PRIDE PXD009101: GAGfinder: glycosaminoglycan MS/MS fragment peak finding and elemental composition assignment
|
|
186
|
+
|
|
187
|
+
### PXD018980 — 20170224_122_Gua_ZB4359_BB2_01_383.d.zip
|
|
188
|
+
|
|
189
|
+
- Title: Characterisation of South American camelid fibres by proteomics
|
|
190
|
+
- Organisms: Camelidae
|
|
191
|
+
- Publication date: 2020-11-09
|
|
192
|
+
- Project instruments: maXis
|
|
193
|
+
- Reported instrument: None
|
|
194
|
+
- Acquisition software: None
|
|
195
|
+
- Schema: None None
|
|
196
|
+
- Acquisition mode: None
|
|
197
|
+
- Size: 614.7 MB
|
|
198
|
+
- Source URL: https://ftp.pride.ebi.ac.uk/pride/data/archive/2020/11/PXD018980/20170224_122_Gua_ZB4359_BB2_01_383.d.zip
|
|
199
|
+
- Licence (presumed): CC-BY-4.0 (PRIDE default)
|
|
200
|
+
- Attribution string: PRIDE PXD018980: Characterisation of South American camelid fibres by proteomics
|
|
201
|
+
|
|
202
|
+
### PXD036417 — NQO1-F107C_coi-N2-P_200-0C_3996.d.zip
|
|
203
|
+
|
|
204
|
+
- Title: Counterintuitive structural and functional effects due to naturally-occurring mutations targeting the active site of the disease-associated NQO1 enzyme
|
|
205
|
+
- Organisms: Homo sapiens (human)
|
|
206
|
+
- Publication date: 2022-11-23
|
|
207
|
+
- Project instruments: solariX
|
|
208
|
+
- Reported instrument: None
|
|
209
|
+
- Acquisition software: None
|
|
210
|
+
- Schema: None None
|
|
211
|
+
- Acquisition mode: None
|
|
212
|
+
- Size: 91.7 MB
|
|
213
|
+
- Source URL: https://ftp.pride.ebi.ac.uk/pride/data/archive/2022/11/PXD036417/NQO1-F107C_coi-N2-P_200-0C_3996.d.zip
|
|
214
|
+
- Licence (presumed): CC-BY-4.0 (PRIDE default)
|
|
215
|
+
- Attribution string: PRIDE PXD036417: Counterintuitive structural and functional effects due to naturally-occurring mutations targeting the active site of the disease-associated NQO1 enzyme
|
|
216
|
+
|
|
217
|
+
### PXD022216 — fmeierab_T190525_CLL_diaPASEF_02_1977.d.zip
|
|
218
|
+
|
|
219
|
+
- Title: The Proteome Landscape of Chronic Lymphocytic Leukemia
|
|
220
|
+
- Organisms: Homo sapiens (human)
|
|
221
|
+
- Publication date: 2021-09-27
|
|
222
|
+
- Project instruments: timsTOF Pro
|
|
223
|
+
- Reported instrument: timsTOF Pro
|
|
224
|
+
- Acquisition software: Bruker otofControl 5.1.81.714-13047-vc110
|
|
225
|
+
- Schema: TDF 3.1
|
|
226
|
+
- Acquisition mode: DIA/diaPASEF
|
|
227
|
+
- Size: 3958.8 MB
|
|
228
|
+
- Source URL: https://ftp.pride.ebi.ac.uk/pride/data/archive/2021/09/PXD022216/fmeierab_T190525_CLL_diaPASEF_02_1977.d.zip
|
|
229
|
+
- Licence (presumed): CC-BY-4.0 (PRIDE default)
|
|
230
|
+
- Attribution string: PRIDE PXD022216: The Proteome Landscape of Chronic Lymphocytic Leukemia
|
|
231
|
+
|
|
232
|
+
### PXD030327 — EXP21053_2021ms0297X10_A_BB2_1_1884.d.zip
|
|
233
|
+
|
|
234
|
+
- Title: Enhanced competition at the nano-bio interface enables comprehensive characterization of protein corona dynamics and deep coverage of proteomes
|
|
235
|
+
- Organisms: Homo sapiens (human)
|
|
236
|
+
- Publication date: 2022-09-02
|
|
237
|
+
- Project instruments: timsTOF Pro 2
|
|
238
|
+
- Reported instrument: timsTOF Pro
|
|
239
|
+
- Acquisition software: timsTOF 2.0.53.0
|
|
240
|
+
- Schema: TDF 3.5
|
|
241
|
+
- Acquisition mode: DIA/diaPASEF
|
|
242
|
+
- Size: 1696.2 MB
|
|
243
|
+
- Source URL: https://ftp.pride.ebi.ac.uk/pride/data/archive/2022/09/PXD030327/EXP21053_2021ms0297X10_A_BB2_1_1884.d.zip
|
|
244
|
+
- Licence (presumed): CC-BY-4.0 (PRIDE default)
|
|
245
|
+
- Attribution string: PRIDE PXD030327: Enhanced competition at the nano-bio interface enables comprehensive characterization of protein corona dynamics and deep coverage of proteomes
|
|
246
|
+
|
|
247
|
+
### PXD018972 — LA_CS-F_24May16_BE4_01_30183.d.zip
|
|
248
|
+
|
|
249
|
+
- Title: Caspr2 interacts with type 1 inositol 1,4,5-trisphosphate receptor in the developing cerebellum and regulates Purkinje cell morphology
|
|
250
|
+
- Organisms: Mus musculus (mouse)
|
|
251
|
+
- Publication date: 2020-07-13
|
|
252
|
+
- Project instruments: amaZon ETD
|
|
253
|
+
- Reported instrument: None
|
|
254
|
+
- Acquisition software: None
|
|
255
|
+
- Schema: None None
|
|
256
|
+
- Acquisition mode: None
|
|
257
|
+
- Size: 64.2 MB
|
|
258
|
+
- Source URL: https://ftp.pride.ebi.ac.uk/pride/data/archive/2020/07/PXD018972/LA_CS-F_24May16_BE4_01_30183.d.zip
|
|
259
|
+
- Licence (presumed): CC-BY-4.0 (PRIDE default)
|
|
260
|
+
- Attribution string: PRIDE PXD018972: Caspr2 interacts with type 1 inositol 1,4,5-trisphosphate receptor in the developing cerebellum and regulates Purkinje cell morphology
|
|
261
|
+
|
|
262
|
+
### PXD038283 — Ca1.d.zip
|
|
263
|
+
|
|
264
|
+
- Title: Robust high throughput proteomics identification and deami-dation quantitation of extinct species up to Pleistocene with Ultrahigh Resolution MALDI-FTICR Mass Spectrometry
|
|
265
|
+
- Organisms: Homo sapiens (human), Bos taurus (bovine), Rhinoceros, Castor fiber (eurasian beaver), Cervus, Equus caballus (horse)
|
|
266
|
+
- Publication date: 2023-04-28
|
|
267
|
+
- Project instruments: Bruker Daltonics solarix series, Q Exactive Plus
|
|
268
|
+
- Reported instrument: None
|
|
269
|
+
- Acquisition software: None
|
|
270
|
+
- Schema: None None
|
|
271
|
+
- Acquisition mode: None
|
|
272
|
+
- Size: 29.8 MB
|
|
273
|
+
- Source URL: https://ftp.pride.ebi.ac.uk/pride/data/archive/2023/04/PXD038283/Ca1.d.zip
|
|
274
|
+
- Licence (presumed): CC-BY-4.0 (PRIDE default)
|
|
275
|
+
- Attribution string: PRIDE PXD038283: Robust high throughput proteomics identification and deami-dation quantitation of extinct species up to Pleistocene with Ultrahigh Resolution MALDI-FTICR Mass Spectrometry
|
|
276
|
+
|
|
277
|
+
### PXD001592 — 025pmolUPS2_500ngY_90min1Hz1pr_BC1_01_338.d.zip
|
|
278
|
+
|
|
279
|
+
- Title: The impact II, a very high resolution quadrupole time-of-flight instrument for deep shotgun proteomics
|
|
280
|
+
- Organisms: Homo sapiens (human), Mus musculus (mouse), Saccharomyces cerevisiae (baker's yeast)
|
|
281
|
+
- Publication date: 2015-05-26
|
|
282
|
+
- Project instruments: Bruker Daltonics instrument model
|
|
283
|
+
- Reported instrument: None
|
|
284
|
+
- Acquisition software: None
|
|
285
|
+
- Schema: None None
|
|
286
|
+
- Acquisition mode: None
|
|
287
|
+
- Size: 3368.9 MB
|
|
288
|
+
- Source URL: https://ftp.pride.ebi.ac.uk/pride/data/archive/2015/05/PXD001592/025pmolUPS2_500ngY_90min1Hz1pr_BC1_01_338.d.zip
|
|
289
|
+
- Licence (presumed): CC-BY-4.0 (PRIDE default)
|
|
290
|
+
- Attribution string: PRIDE PXD001592: The impact II, a very high resolution quadrupole time-of-flight instrument for deep shotgun proteomics
|
|
291
|
+
|
|
292
|
+
### PXD035147 — JD019LPMa_HC_1_Slot1-45_1_10163.d.zip
|
|
293
|
+
|
|
294
|
+
- Title: Integrated proteome and malonylome analyses reveal the potential meaning of TLN1 and ACTB in end-stage renal disease
|
|
295
|
+
- Organisms: Homo sapiens (human)
|
|
296
|
+
- Publication date: 2023-10-24
|
|
297
|
+
- Project instruments: autoflex
|
|
298
|
+
- Reported instrument: None
|
|
299
|
+
- Acquisition software: None
|
|
300
|
+
- Schema: None None
|
|
301
|
+
- Acquisition mode: None
|
|
302
|
+
- Size: 235.3 MB
|
|
303
|
+
- Source URL: https://ftp.pride.ebi.ac.uk/pride/data/archive/2023/10/PXD035147/JD019LPMa_HC_1_Slot1-45_1_10163.d.zip
|
|
304
|
+
- Licence (presumed): CC-BY-4.0 (PRIDE default)
|
|
305
|
+
- Attribution string: PRIDE PXD035147: Integrated proteome and malonylome analyses reveal the potential meaning of TLN1 and ACTB in end-stage renal disease
|
|
306
|
+
|
|
307
|
+
### PXD035173 — 62_Slot1-54_1_2674.d.zip
|
|
308
|
+
|
|
309
|
+
- Title: Proteomic profiling of carotid atherosclerotic plaques and adjacent intact arterial segments
|
|
310
|
+
- Organisms: Homo sapiens (human)
|
|
311
|
+
- Publication date: 2025-06-05
|
|
312
|
+
- Project instruments: timsTOF Pro
|
|
313
|
+
- Reported instrument: timsTOF Pro
|
|
314
|
+
- Acquisition software: timsTOF 2.0.18.0
|
|
315
|
+
- Schema: TDF 3.5
|
|
316
|
+
- Acquisition mode: DIA/diaPASEF
|
|
317
|
+
- Size: 2225.2 MB
|
|
318
|
+
- Source URL: https://ftp.pride.ebi.ac.uk/pride/data/archive/2025/06/PXD035173/62_Slot1-54_1_2674.d.zip
|
|
319
|
+
- Licence (presumed): CC-BY-4.0 (PRIDE default)
|
|
320
|
+
- Attribution string: PRIDE PXD035173: Proteomic profiling of carotid atherosclerotic plaques and adjacent intact arterial segments
|
|
@@ -0,0 +1,59 @@
|
|
|
1
|
+
# Changelog
|
|
2
|
+
|
|
3
|
+
All notable changes to this project will be documented in this file.
|
|
4
|
+
The format follows [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
|
|
5
|
+
This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
|
|
6
|
+
|
|
7
|
+
## [1.0.0] - 2026-05-17
|
|
8
|
+
|
|
9
|
+
First stable release. The public API of `opentdf` is now considered stable
|
|
10
|
+
and will follow semantic versioning. The schema-version compatibility set
|
|
11
|
+
(TDF 3.1, 3.3, 3.5, 3.6, 3.7) is unchanged from 0.1.1.
|
|
12
|
+
|
|
13
|
+
### Added
|
|
14
|
+
|
|
15
|
+
- `publish.yml` GitHub Actions workflow: publishes the `opentdf` crate to
|
|
16
|
+
crates.io and the Python wheel to PyPI via OIDC Trusted Publishing on
|
|
17
|
+
every `v*` tag push.
|
|
18
|
+
|
|
19
|
+
### Fixed
|
|
20
|
+
|
|
21
|
+
- Removed needless borrows in `Reader::open()` calls in integration tests
|
|
22
|
+
(resolves `clippy::needless_borrows_for_generic_args`).
|
|
23
|
+
|
|
24
|
+
### Changed
|
|
25
|
+
|
|
26
|
+
- CI migrated from WarpBuild runners to standard GitHub-hosted
|
|
27
|
+
(`ubuntu-latest`, `macos-latest`, `windows-latest`).
|
|
28
|
+
|
|
29
|
+
## [0.1.1] - 2026-05-16
|
|
30
|
+
|
|
31
|
+
Initial public release.
|
|
32
|
+
|
|
33
|
+
### Added
|
|
34
|
+
|
|
35
|
+
- Rust reader for timsTOF `.d/` (TDF) bundles.
|
|
36
|
+
- SQLite metadata access via bundled `rusqlite`: `GlobalMetadata`,
|
|
37
|
+
`Frames`, mode-specific index tables, and calibration tables.
|
|
38
|
+
- Binary frame decoder supporting both compression codecs:
|
|
39
|
+
- Codec 2 (`TimsCompressionType = 2`): zstd + byte-transpose + delta.
|
|
40
|
+
- Codec 1 (`TimsCompressionType = 1`): per-scan LZF blobs with
|
|
41
|
+
signed-delta TOF stream (Rust LZF decoder; no `liblzf` dependency).
|
|
42
|
+
- TOF -> m/z and scan -> 1/K0 calibration via the
|
|
43
|
+
linear-in-sqrt(m/z) model.
|
|
44
|
+
- Acquisition-mode metadata:
|
|
45
|
+
- diaPASEF windows (`DiaFrameMsMsInfo` + `DiaFrameMsMsWindows`)
|
|
46
|
+
- PASEF DDA precursors + per-frame MS/MS info
|
|
47
|
+
- prm-PASEF targets + per-frame MS/MS info
|
|
48
|
+
- Schema-version compatibility: 3.1, 3.3, 3.5, 3.6, 3.7 verified.
|
|
49
|
+
- `examples/dump.rs`: minimal frame-peak dumper for CLI inspection.
|
|
50
|
+
- 9 integration tests, of which 8 run against a small committed probe
|
|
51
|
+
corpus and 1 (PRM) is conditional on the optional PRIDE PXD028279
|
|
52
|
+
probe being present.
|
|
53
|
+
|
|
54
|
+
### Out of scope
|
|
55
|
+
|
|
56
|
+
- `analysis.tsf` (MALDI / non-TIMS bundles).
|
|
57
|
+
- Tune-method XML blocks under `*.m/`.
|
|
58
|
+
- Proprietary polynomial calibration models (the linear model is
|
|
59
|
+
used; see `docs/format/04-tof-to-mz-calibration.md`).
|
opentdf-1.0.0/Cargo.toml
ADDED
|
@@ -0,0 +1,25 @@
|
|
|
1
|
+
[package]
|
|
2
|
+
name = "opentdf"
|
|
3
|
+
version = "1.0.0"
|
|
4
|
+
edition = "2021"
|
|
5
|
+
rust-version = "1.75"
|
|
6
|
+
description = "Rust reader for timsTOF .d/ (TDF) mass spectrometry bundles."
|
|
7
|
+
authors = ["Nathan Riley <git@nathanriley.com>"]
|
|
8
|
+
license = "Apache-2.0"
|
|
9
|
+
repository = "https://github.com/Sigilweaver/OpenTDF"
|
|
10
|
+
homepage = "https://github.com/Sigilweaver/OpenTDF"
|
|
11
|
+
readme = "README.md"
|
|
12
|
+
keywords = ["mass-spectrometry", "bruker", "timstof", "tdf", "proteomics"]
|
|
13
|
+
categories = ["parser-implementations", "science"]
|
|
14
|
+
|
|
15
|
+
[lints.rust]
|
|
16
|
+
unsafe_code = "forbid"
|
|
17
|
+
|
|
18
|
+
[dependencies]
|
|
19
|
+
thiserror = "2"
|
|
20
|
+
rusqlite = { version = "0.31", features = ["bundled"] }
|
|
21
|
+
zstd = "0.13"
|
|
22
|
+
|
|
23
|
+
[[example]]
|
|
24
|
+
name = "dump"
|
|
25
|
+
path = "examples/dump.rs"
|