Tools
This section covers the executable tools that are distributed as part of HiCOPS. The provided tools aid in peptide database processing, MS/MS data conversions, and runtime support. The subsequent sections provide an overview of the listed tools.
Runtime
The following tools help generate input parameters and run HiCOPS.
hicops_config
hicops_config generates a compact params file, called uparams.txt from a user-friendly parameters/setting file. The generated uparams.txt is used with HiCOPS as arguments. A template of user-friendly parameters file can also be generated. More details here.
hicops_comet
hicops_comet serves as the main utility for running HiCOPS on XSEDE Comet using a user-friendly parameters file. A template parameters file can also be generated. More details here.
Database Preprocessing
The following tools help prepare the peptide sequence database for HiCOPS.
db_prep
db_prep prepares coarse-grained peptide sequence clusters from a peptide sequence database (in FASTA format). The generated files are used as input database to HiCOPS. More details here.
MS Data Processing
The following tools help prepare the experimental MS/MS data for HiCOPS.
raw2ms2
raw2ms2 is a wrapper for the ProteoWizard’s msconvert tool on Linux systems. This tools requires docker to be installed on the system. Alternatively, the users may directly use msconvert tool for MS/MS data conversion to MS2 format. More details here.
extractms2
extractms2 extracts a range of MS/MS spectra from an MS2 file and writes them to a new file. This tools may be used in debugging purposes or data sampling. More details here.