PAMPA (Protein Analysis by Mass Spectrometry for Ancient Species) is a software suite for ZooMS (Zooarchaeology by Mass Spectrometry) and peptide markers.
PAMPA web
Species identification from MALDI-TOF or MALDI-FT ICR spectra: access here
Find peptide markers by homology: access here
Find peptide markers by in silico digestion and peak filtering: access here
Supplement peptide tables (add masses, sequences, positions...): access here
Add deamidation: access here
Filter peptide tables by peak selection: access here
Align marker sequences: access here
Documentation
Instructions and detailed tutorial can be found at https://github.com/touzet/pampa/wiki
Local installation
The source code is available on GitHub: https://github.com/touzet/pampa
COL1A1 and COL1A2 resources
Peptide marker compilation : A curated database of peptide markers (sequence and m/z) is available at
https://docs.google.com/spreadsheets/d/1nwELNshZxF0h6DkIFNAYXDJqmq4NOSUOLWQlTZIzUDQ
Collagen sequence database : Browse our collection of collagen sequences on GitHub
https://github.com/touzet/pampa_sequences
Authors
The program has been developed by Hélène Touzet (CRIStAL) in close collaboration with Fabrice Bray (Lille ZooMS platform). The web interface has been designed by Yohan Hernandez-Courbevoie (CRIStAL), Valentin Hottler (CRIStAL), Areski Flissi (CRIStAL) and Hélène Touzet.
Publication
PAMPA: A Software for Peptide Markers and Taxonomic Identification for ZooMS Samples in Archaeology and Paleontology. F. Bray and H. Touzet. Journal of Proteome Research 2025, https://doi.org/10.1021/acs.jproteome.5c00389