Skip to content

PAMPA CRAFT: Selection

Jump to bottom
touzet edited this page Jan 8, 2025 · 1 revision

The selection module takes as input a peptide table and a collection of MS spectra from the same species, and selects peptide markers from the table that correspond to peaks in the spectra.

This module can be used independently or in combination with any of the four other modules: allpeptides, homology, fillin, and deamidation. See the documentation for each of these modules for more details.

Usage

python3 pampa_craft.py --selection -p table_A.tsv -s SPECTRA -e ERROR -o new_table.tsv

This command filters peptides markers from table_A based on peaks identified within the set of MS mass spectra in the SPECTRA folder. It selects peptides whose masses are present in at least half of the mass spectra. The chosen peptides are then compiled into a new table, new_table.tsv.

Peptide table (-p)

This table contains the list of peptide markers that will be filtered out. The format of this table is described in Peptide tables.

Mass spectra (-s)

The program processes a batch of mass spectra simultaneously. All mass spectra files are contained within the same folder, with one of the following extensions: .csv or .txt (in CSV format), .mgf (in MGF format), or .mzML (in mzML format). Any other files present will be disregarded. See Mass spectra for more information about the format and the requirements.

Error margin tolerance (-e)

The error margin is related to the resolution of the mass spectrometer, that is its ability to distinguish closely spaced peaks. We employ it to set an upper bound on the deviation between a peak and the theoretical mass of the marker peptide. This option can be expressed in Daltons or in ppm.

  • If the value is smaller than 1, it is assumed to be in Da (Daltons). In this case, recommended values are 0.1 for maldi TOF, and 0.01 for maldi FT.
  • If the value is larger than 1, it is assumed to be in ppm (parts per million). In this case, recommended values are 50 for maldi TOF, and 5 for maldi FTICR.

Output files (-o)

This option enables you to specify the name of the main output file, in TSV format. You can include the desired path to the directory where the file should be created. If the specified directory does not exist, it will be created automatically.

Clone this wiki locally