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PAMPA CRAFT

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touzet edited this page Dec 12, 2024 · 18 revisions

PAMPA CRAFT is for the design of custom peptide tables, that can then be utilized by PAMPA CLASSIFY.

usage: 
pampa_craft  [-h] 
   [--homology | --allpeptides | --fillin] 
   [-f FASTA | -d DIRECTORY] [-p PEPTIDE_TABLE] [-s SPECTRA PATH] [-l LIMIT] -o OUTPUT

The four options —-homology, --denovo, and --fillin represent four distinct approaches for constructing a new peptide table:

  • homology: generates new peptide markers by sequence similarity from an existing set of markers.
  • allpeptides: constructs new peptide markers by performing systematic in silico tryptic digestion on a collection of protein sequences.
  • fillin: supplements an existing peptide table by filling in missing values: masses, positions, sequences, etc.
  • deamidation

Additionnaly, the option -s enables filtering markers based on peaks identified within a set of mass spectra (see Mass spectra for the accepted formats). This option can be combined with any of the other four options.

The full usage description of each of these options is provided below.

Homology

With this option, the input consists of a set of well-defined marker peptides, and the goal is to search a set of target protein sequences for similar peptides. New peptides are discovered through sequence alignment, allowing up to 10% mismatches between peptides. The algorithm also ensures that the new peptides can undergo tryptic digestion and infers new cleavage sites when necessary. Masses are automatically computed.

 usage:
 python3 pampa_craft --homology
   -p PEPTIDE_TABLE [PEPTIDE_TABLE]
   Peptide table(s) that contain model peptide markers
   -f FASTA      Fasta file for new species
   -d DIRECTORY  Directory containing Fasta files for new species
   -l LIMIT      Limit file that applies to the Fasta sequences.
   -o OUTPUT     Path to the output file (new peptide table)

Example

python3 pampa_craft --homology - p table_A.tsv -f sequences.fasta -o table_B.tsv

This command uses peptide markers from table_A.tsv, matches them to amino-acid sequences in sequences.fasta, and generates a new peptide table, table_B, containing markers corresponding to sequences in sequences.fasta.

Peptide table (-p)

This table contains the list of peptide markers that will be used as models to find new markers in new sequences by homology. The format of this table is described Peptide tables.

Target sequences (-f, -d and -l)

[Either -f or -d is required. -l is optional] The target sequences are the amino-acids sequences in which the new markers are searched. Those sequences can be available either in a (multi-)FASTA file (-f option), or in a directory containing FASTA files (-d option). In both cases, the set of sequences can optionally be limited to a subset of organisms, molecules or sequence identifiers with -l option.

Option -f : The specified file can contain an arbitrary number of FASTA sequences, coming from various organisms. Refer to the FASTA sequences section for details on the syntax used in FASTA headings.

Option -d: The directory can contain an arbitrary number of FASTA files, following the same requirements as with '-f' option. Only files with extension .fa or .fasta will be examined.

Option -l: This option allows to filter the set of FASTA sequences to limit the selection according to the organism (OS=), the taxid (OX=), the gene name (GN=), the sequence identifier (SeqID=). The full description of the syntax is given in section Limiting searches.

Output file (-o)

This is the name of the new peptide table created by the program, that contains homologous peptide markers.

Allpeptides

This option allows to infer all tryptic peptides from a set of FASTA sequences through in silico digestion, allowing for up to one missed cleavage. Masses are then automatically computed using PTM inference (see PTMs).

usage:
pampa_craft --allpeptides
   -f FASTA      Fasta file for new species
   -d DIRECTORY  Directory containing Fasta files for new species
   -l LIMIT      Limit file that 
   -o OUTPUT     Path to the output file (new peptide table)

Target sequences (-f, -d and -l)

The target sequences consist of amino acid sequences in FASTA format that will undergo tryptic digestion. These sequences can be provided either as a (multi-)FASTA file (using the -f option) or as multiple FASTA files within a directory (using the -d option). The use of either -f or -d is required. Additionally, users have the option to selectively limit the set of sequences to a specific subset of organisms, molecules, or sequence identifiers using the -l option.

Option -f : The specified file can contain an arbitrary number of FASTA sequences, coming from various organisms. Refer to the [FASTA sequences](#FASTA sequences) section for details on the syntax used in FASTA headings.

Option -d: The directory can contain an arbitrary number of FASTA files, following the same requirements as with '-f' option. Only files with extension .fa or .fasta will be examined.

Option -l: This option allows to filter the set of FASTA sequences to limit the selection according to the organism (OS=), the taxid (OX=), the gene name (GN=), the sequence identifier (SeqID=). The full description of the syntax is given in section Limiting searches.

Output file (-o)

[Required] This is the name of the new table containing tryptic peptides created by the program.

--fillin option

This option allows to fill in missing fields in a peptide table. It can automatically compute masses for peptides that lack this information.
If Fasta sequences are provided, it can calculate peptide positions or, conversely, deduce the sequence of a peptide marker from its position in the sequence. It is of particular interest, for instance, in supplementing a manually created peptide table.

Peptide mass is computed from the peptide sequence and the PTM description. If no PTM description is provided, PTMs are determined automatically based on the rules outlined in the PTM description section.

 usage:
 python3 pampa_craft --fillin 
   -p PEPTIDE_TABLE Peptide table to supplement
   -o OUTPUT        Path to the output file (new peptide table)

Peptide table (-p)

Name of the peptide table to complete.

Output file (-o)

Name of the new table obtained by completion of the input table.

Spectra filtering: -s and -e options

This pair of option enables filtering markers based on peaks identified within a set of mass spectra. It can be applied in conjunction with --homology, --denovo, --fillin or independently.

Examples

python3 pampa_craft.py --denovo -s SPECTRA_DIR -e 0.1 -f sequences.fasta -o new_table.tsv

This command generates all tryptic peptides from the sequences of sequences.fasta, computes the theoretical masses, and select tryptic peptides that are present in at least half of the mass spectra present in SPECTRA_DIR. The chosen peptides are then compiled into a new table, new_table.tsv.

python3 pampa_craft.py --fillin -p table_A -s SPECTRA_DIR   -e 0.1 -o new_table.tsv

This command fills in missing information in table_A (like missing masses) and selects peptides whose masses are present in at least half of the mass spectra in SPECTRA_DIR. The chosen peptides are then compiled into a new table, new_table.tsv.

python3 pampa_craft.py -p table_A -s SPECTRA_DIR  -e 0.1 -o new_table.tsv

In contrast to the previous example, this command uses peptide markers from table_A as they are. So those with missing masses are ignored. The command selects peptides whose masses are present in at least half of the mass spectra in SPECTRA_DIR. The chosen peptides are then compiled into a new table, new_table.tsv.

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