Limiting searches

Both PAMPA CLASSIFY and PAMPA CRAFT make it possible to filter markers from the peptide tables or FASTA sequences to narrow down the search according to various criteria such as organism, gene name, sequence identifier, PTMs, etc. This is done by creating a limit file that contains a list of constraints. The limit file is then invoked with option -l (see PAMPA CLASSIFY and PAMPA CRAFT documentation).

General principle and syntax of a limit file

If you want to create a limit file, you should follow these guidelines:

• Create a text file.

• Each line in the file should comprise one or several of these fields :

  • "OS=" for authorized taxon names
  • "OX=" for authorized taxids
  • "GN=" for authorized gene names
  • "SeqID=" for authorized sequence identifiers
  • "PTM=" for authorized PTMs
  • "Status=" will use only peptide markers with specified status
  • "Deamidation=" for selection of marker names for which deamidation will be applied

• Separate multiple elements for a field with commas.

The limit file can comprise an arbitrary number of lines, with each line representing a distinct constraint. The resulting selection is determined by the union of all these constraints.

In the presence of a taxonomy (as is the case with the pre-computed model --mammals), the OS and OX fields become applicable to clades at any taxonomic rank (e.g. genus, family, order). In such instances, the constraint will choose all descendants accordingly.

Examples for FASTA sequences

If you want to limit your search to a specific set of organisms from a FASTA file or a set of FASTA files, the limit file might look like this:

OS= Diceros bicornis, Cervus elaphus, Bos taurus, Equus caballus   

You can combine constraints. For instance, limiting the search to markers coming from COL1A2 gives:

OS=Diceros bicornis, Cervus elaphus, Bos taurus, Equus caballus GN=COL1A2

This means that the search will focus on markers from COL1A2 within the specified organisms.

In the presence of a taxonomy, the OS and OX fields become applicable to clades at any taxonomic rank (e.g. genus, family, order). In such instances, the constraint will choose all descendants accordingly.

OS=Pecora GN=COL1A1

This will select all COL1A1 markers for species from the Pecora infraorder. Equivalently, you might have used the taxID of Pecora, with the OX field.

OX=35500 GN=COL1A1

Examples for peptide tables

The same logic applies to select peptide markers in a peptide tables. Besides OS, OX, and GN token, the constraints can also apply to PTM and Status token.

OS=Pecora GN=COL1A1 PTM=H 

The constraint "PTM=H" (H is for hydroxylation) excludes markers with deamidations.

If you want to further refine this selection and use only peptide markers whose status is MS or MS/MS, you should type:

OS=Pecora GN=COL1A1 PTM=H Status=MS, MS/MS

Example for deamidation

The deamidation token comes with the --deamidation option of PAMPA CRAFT and PAMPA CLASSIFY. It allows to specify the list of markers for which deamidation can be applied.

Deamidation= COL1A2-978/A, COL1A1-586/F

If no limit file is provided, or if the limit file does not contain this token, all markers will be eligible to deamidation.