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Peptide tables

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touzet edited this page Oct 2, 2025 · 14 revisions

In PAMPA, peptide markers are organized into peptide tables that are information-rich structures designed for collecting, storing, and exchanging data. These tables compile key details for each peptide marker, along with supplementary metadata that enhances traceability and contextual understanding. They include sequence, mass, PTMs, genetic context, analytical status, and more.

Definition and construction

A peptide table is a TSV (Tab-Separated Value) file where the first row of the file contain column headings, each other row corresponds to a peptide and each column to a field. Such type of file can be created and visualized by any spreadsheet software (such as Excel, Google Sheets, LibreOffice, Numbers).

Seventeen fields are recognized by PAMPA.

  • Rank: Taxonomic rank (e.g., Species, Family, Order)
  • TaxID: Taxonomic identifier
  • Taxon name: Scientific name
  • Common name: Common name corresponding to the scientific name
  • Sequence: Marker peptide sequence
  • PTM: Description of post-translational modifications (PTMs) applied to the peptide marker (see PTMs).
  • Marker: Marker name
  • Mass: Peptide mass
  • Gene: Gene name (e.g., COL1A1)
  • Hel: Start position of the peptide marker relatively to the helical region
  • Length: Length of the peptide marker
  • SeqID: Sequence identifier(s) of the protein sequence from which the marker peptide is derived
  • Begin: Start position of the peptide marker within the protein sequence
  • End: End position of the peptide marker within the protein sequence
  • Digestion (yes/no): the peptide is a tryptic peptide.
  • Status: Information on the peptide’s validation method (e.g., genetic, MS, or MS/MS)
  • Comment: Additional comments about the marker

Not all fields need to be initialized; you can select the relevant ones based on the context. You also have the option to include additional fields (i.e., extra columns) for your own purposes. These fields will be disregarded by PAMPA.

Where to find peptide tables, how to generate them ?

Peptide tables are designed to be in an open format, allowing anyone to create and modify them. In practice, there are several methods for obtaining peptide tables.

  • Several pre-defined tables are included with the PAMPA code, accessible in the Peptide_tables directory. You can use them, copy them and modify them. Please avoid relocating or altering the original files, as they are utilized by the program. Those peptide tables are visible at https://docs.google.com/spreadsheets/d/1nwELNshZxF0h6DkIFNAYXDJqmq4NOSUOLWQlTZIzUDQ .

  • You can manually create peptide table files using any spreadsheet software and opting for the TSV export format.

  • PAMPA CRAFT offers automated or semi-automated methods for generating peptide tables from your own data.

See next

How to utilize peptide tables to analyse MS spectra and identify associated species: PAMPA CLASSIFY

How to construct peptide tables from known markers or from FASTA sequences : PAMPA CRAFT

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