crux make-pin [options] <target input>


Make-pin is a utility program that combines a collection of target and decoy peptide-spectrum matches (PSMs) into a single file in pin format, according to this format. The resulting file can be provided as input to crux percolator.

make-pin requires as input two sets of PSMs, one set derived from matching observed spectra against real ("target") peptides and a second set derived from matching the same spectra against "decoy" peptides. The output file contains, for each PSM, a set of features for use by the Percolator algorithm. These features are summarized here.

Note that, in the stand-alone version of Percolator, the functionality provided by crux make-pin is incorporated into a program called sqt2pin. However, a significant difference between crux percolator and the stand-alone version of the program is that crux percolator does not require an explicit call to crux make-pin: if input is provided to crux percolator in a non-pin format, then the input will be automatically converted to pin format.



The program writes files to the folder crux-output by default. The name of the output folder can be set by the user using the --output-dir option. The following files will be created: