iPiG GUI

This gives an overview how to run a mapping with the iPiG GUI.
For more details about the data formats look at the corresponding wiki page: [Input Formats]

Input

• Peptide Spectrum Matches
  • Indicate the file with peptide spectrum matches (PSMs) of interest in mzIdentML or text format
• Output Path (Optional)
  • Specify an output path for the result files (execution path is used by default)

Resources

• UCSC/Ensembl Genes table file
  • Indicate a file with reference gene annotations in USCS table format (UCSC or Ensembl genes are currently supported)
• UCSC/Ensembl Amino Acid Sequences table file
  • Indicate a file with reference amino acid sequences corresponding to the gene annotations file in USCS table format
• UniProt ID-mapping file (optional but recommended)
  • Indicate the Uniprot ID-mapping file (tab-delimited table)
• Proteome fasta file (optional)
  • Indicate a Uniprot proteome in fasta format

Export Settings

• Score range & Threshold
  • For the outputs give the score range of the PSMs and define thresholds to separate PSMs in three scoring groups
• Colors
  • For the BED output give three RGB colors that indicates the scoring group of each PSM. Suitable colors (grey, orange, green) are provided by the default configuration file (ipig.conf).

Execution

• Start
  • Run the mapping by pressing the Start-button

Configuration

• Load
  • Load a configuration file to import the parameters for Resources and Export Settings
• Save
  • Save a configuration file to keep the selected Resources and Export Settings