SAAPedia: An interactive local database for substituted amino acid peptide (SAAP) sequences derived using mass spectrometry proteomics-based methods.

Import a CSV, TSV, or Excel (.xlsx) file; SAAPedia de-duplicates and normalizes it, then lets you browse, filter, and sort the results, attach source-paper DOIs to datasets, and export any selection as a UniProt-style FASTA of the SAAPs.

Everyone runs their own copy locally — download the repo, start it, open a browser. The repo ships with a populated saap.db from Tsour et al., Nature 2026 and our other research at the Slavov Lab, so there's data to explore right away.

• Backend: FastAPI + SQLite
• Frontend: React
• Requirement: Python 3.9+

Find a short introduction to SAAPedia here.

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Starting the app

Download the repo (green Code ▸ Download ZIP on GitHub, or git clone), then:

macOS / Linux

cd SAAPedia
./run.sh

The first run creates a Python environment and installs dependencies (~15 s); later runs start in a second or two. When you see running at: http://127.0.0.1:8000, open that URL. Stop with Ctrl+C on Windows or Option+C on Mac.

Windows (or if run.sh won't run)

cd SAAPedia\backend
python -m venv .venv
.venv\Scripts\activate
pip install -r requirements.txt
uvicorn app.main:app

Then open http://127.0.0.1:8000.

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Using the app

• Browse — one row per unique SAAP with rollups (observations, datasets, species, best PEP, max positional probability, and more). Search, filter (dataset, digest, species, acquisition, AAS, flags, thresholds), and sort any column. Click a peptide to see every underlying observation. Select rows to export to FASTA or delete or export everything matching the current filter.
• Import — drop a CSV, TSV, or Excel file.
• Datasets — view each dataset with counts, edit Dataset to DOI mappings, open the linked paper, or clear all data.

What counts as one SAAP?

A SAAP is uniquely identified by (SAAP, BP, AAS) — the substituted peptide, its base peptide, and the amino-acid substitution. Every imported row becomes one observation linked to its SAAP. # datasets is the number of distinct (Dataset, Species) pairs the SAAP is actually observed in (any N Datasets column in the file is ignored). Re-importing the same file is safe — exact duplicate rows are detected and not double-counted.

Import rules

• A peptide is dropped if it has no UniProt accession.
• Columns are matched tolerantly (case / spacing / punctuation-insensitive). The import summary reports any unmapped columns, so nothing is silently mis-read.

Recognized columns: SAAP, BP, AAS, Dataset, TMT/Tissue, Digest, Species, Data acquisition, PEP, Positional probability, N evidence fragments, UniProt, RefProteins, Genes, missed_cleavage, AAS_at_peptide_terminus, greater_than_shared, Immunoglobulin, Trypsin. Add new header spellings in backend/app/column_map.py.

Exports

FASTA

A major utility of SAAPedia is the ability to export all or a select number of SAAP sequences into a MaxQuant, FragPipe, or other quantitative proteomics engine-compatible UniProt-style FASTA.

Options:

1. Export SAAP sequences alone as their own FASTA
2. Export SAAP sequences appended to a reference proteome (uploaded from local desktop)
3. Export SAAP sequences only with reverse decoys
4. Export an entire FASTA containing reference proteome and SAAP sequences with all reverse decoys appended

.CSV

There is also the option to export the SAAP database as a .csv file for downstream analysis.

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Where is my data?

All data lives in a single SQLite file at backend/saap.db. It stays on your machine and is per-copy — importing on your machine doesn't affect anyone else's. Delete the file (or use Datasets ▸ Clear all data) to start over.

Project layout

SAAPedia/
├── run.sh                 # one-command launcher (macOS/Linux)
└── backend/
    ├── requirements.txt
    └── app/
        ├── main.py        # FastAPI app + routes + serves the UI
        ├── database.py    # SQLite engine/session
        ├── models.py      # SAAP, Observation, DatasetInfo
        ├── column_map.py  # tolerant header → field mapping
        ├── ingest.py      # parse, de-dup, clean
        ├── crud.py        # queries + rollups
        ├── fasta.py       # variant-peptide FASTA
        └── static/        # build-free React app (index.html, app.js, styles.css, vendor/)

Interactive API docs live at http://127.0.0.1:8000/docs while the app is running.