About ProteomeScout
ProteomeScout is a resource for exploring proteins and post-translational modifications. This minimal build keeps the flat-file protein viewer and KSTAR tools workflows available without the legacy database-backed stack.
Included tools
Protein Search: search the TSV-backed protein dataset and open the interactive viewer.
KSTAR Tools: open plotting and dataset-prep workflows for KSTAR analyses.
KSTAR Galaxy: launch the Galaxy-hosted KSTAR calculate workflow.
ProteomeScoutAPI: API client code and usage examples.
Viewer Documentation: feature notes and usage guidance for the protein viewer.
How to Cite
- ProteomeScout: Matlock MK, Holehouse AS, Naegle KM. ProteomeScout: a repository and analysis resource for post-translational modifications and proteins. Nucleic Acids Res. 2015;43(Database issue):D521-D530. doi: 10.1093/nar/gku1154. PubMed
- ProteomeScoutAPI: Holehouse AS, Naegle KM. Reproducible Analysis of Post-Translational Modifications in Proteomes--Application to Human Mutations. PLoS One. 2015;10(12):e0144692. doi: 10.1371/journal.pone.0144692. PubMed
- KSTAR: Crowl S, Jordan BT, Ahmed H, Ma CX, Naegle KM. KSTAR: An algorithm to predict patient-specific kinase activities from phosphoproteomic data. Nat Commun. 2022;13(1):4283. doi: 10.1038/s41467-022-32017-5. PubMed
- SpY-C: Kandoor A, Silva Oliveira AC, Machida K, Blagoev BA, Naegle KM. SpY-C: Supervised Learning of Phosphopeptide Sequence Constraints Enables Global Prediction of SH2 Domain Binding 2026 doi: 10.64898/2026.08.18.744962 BioRxiv
Methods Details
Use these version details and templates to document reproducible ProteomeScout workflows.
- proteomescout-v4 version: v4
- ProteomeScoutAPI version: 3.1.1
- ProteomeScout_Dataset version: 9
Methods Boilerplate Templates
- Protein Viewer Methods: The ProteomeScout resource was used to generate the protein viewer on <date>, using the ProteomeScout web version v4, with ProteomeScout data version 9, and using built-in functions for filtering, customization, viewing, and scalar vector graphic export.
- Dataset Annotation Methods: The dataset was annotated on <date>, using the ProteomeScout web version v4, coupled with ProteomeScoutAPI version 3.1.1, with ProteomeScout data version 9.
- Dataset Preparation and Annotation Methods: The dataset was prepared on <date>, formatting peptides and unifying UniProt identifiers, and annotated using the ProteomeScout web version v4, coupled with ProteomeScoutAPI version 3.1.1, with ProteomeScout data version 9.
Version History
| ProteomeScout_Dataset | Data Update Notes | ProteomeScoutAPI | API Update Notes | ProteomeScout-v4 (web) | Web Update Notes |
|---|---|---|---|---|---|
| N/A | — | v2.0.4 | Last API version before ProteomeScout v4 update | N/A | — |
| v1 (2026-01-23) | Major update to 1/18/2026 | v3.0.0 | Automatic fetch of ProteomeScout data from Figshare; Dataset annotation class was added; Update to match new ProteomeScout data file | — | — |
| v2 = v3 (2026-04-27) | Added exons | — | — | — | — |
| v4 = v5 = v6 (2026-05-15) | Added kinase activation loops | v3.1.0 | Added kinase activation loops and exons in parsing and annotation | v4.1.0 | Adds activation loops |
| v7 (2026-06-18) | Integrated dbPTM 2025 data | — | — | — | — |
| v8 (2026-06-29) | v8 added SpY-C beta data v0.1 configuration | v3.1.1 | SpY-C parsing and bug fix: API now does not pass through PTMs connected to deprecated datasets (this can be overridden). | v4.2.1 | Adds SpY-C as feature to tracks, also updated PTM information on web selection for all available tracks. |
| v9 (2026-08-17) | SpY-C v1.0 final data replaced beta data | — | — | — | — |