Percolator

PIN and POUT file formats

Since version 1.15, Percolator has its own input format called PIN (for Percolator-IN). PIN files are XML files whose structure is defined by the schema percolator_in.xml, (currently at its 1.1 version).

Similarly, Percolator’s output (called PUT for Percolator-OUT) is defined by the schema percolator_out.xml, (also at its 1.1 version).

Supposing pin.xml is a valid XML file in PIN format, Percolator can be run using the following options:

$ percolator [options] -E pin.xml -X output.xml

After a successful termination, output.xml will contain Percolator’s output formatted in POUT format; the file will be overwritten, or created if not already existing.

SQT file format

Percolator 1.14 and below accepted SQT files in input; SQT files are the default output of Crux software toolkit. Although SQT files are not supported directly any more, Percolator is now shipped with a converter program called Sqt2pin available from the downloads section. Supposing target.sqt and decoy.sqt are two valid SQT files, they can be (merged and) converted into a PIN file by invoking sqt2pin with the following options:

$ sqt2pin [options] -o output.xml target.sqt decoy.sqt

After a successful termination, output.xml will contain Sqt2pin’s output formatted in PIN format; the file will be overwritten, or created if not already existing.

Percolator does not support SRF files, which are Bioworks Sequest output files, but those can be converted to SQT files using John Prince’s Srf2sqt; it is available at github. Alternativelyit can be obtained by running gem

$ gem install ms-sequest

Tab-delimited file format

Percolator accepts input in a simple Tab-delimited format where each row contains a per PSM:

id <tab> label <tab> feature1 <tab> ... <tab> featureN <tab> peptide <tab> proteinId1 <tab> .. <tab> proteinIdM 

label is a flag set to 1 for target PSMs, and -1 for decoys. If Percolator is run with --doc option the first and second feature (third and fourth column) should contain the retention time and difference between observed and calculated mass/charge. Example files may be downloaded here

To run Percolator on a Tab-delimited input, use the following optins:

$ percolator -j tab-delimited -X output.xml

where tab-delimited is a valid Tab-delimited file.

Supposing pin.xml is a valid XML file in PIN format, it is possible to use Percolator as a converter and generate Tab-delimited files from PIN files by using the following options:

$ percolator -E pin.xml -J tab-delimited

After a successful termination, tab-delimited will contain a valid Tab-delimited file that can be fed to Percolator through the -j described above; the file will be overwritten, or created if not already existing.

Mascot

Mascot users might be interested in the Mascot file parser for Percolator: mascot-percolator written by Markus Brosch at Sanger institute.

Percolator is provided as a part of Mascot Server version 2.3.