Search a spectrum library for matches to query spectra.


BlibSearch [options] <spectrum filename> <library filename>[+]


  • <spectrum filename> – A file containing spectra to search. File formats accepted are .ms2, .cms2, .mzXML, .mzML, .MGF, and .wiff (Windows only).
  • <library name> – The library to be searched for matches to the query. Libraries may be filtered (the output of BlibFilter) or redundant (the output of BilbBuild). More than one library can be listed on the command line.


Results are printed to a report file (tab-delimited text). The file may be named with the --report-file option or by default it is named after the spectrum file with the extension replaced with .report. A seprate report file is written for any decoy spectra searched. An optional sqlite .psm file may also be produced.


  • -c [ --clear-precursor ] <true|false> – Remove the peaks in a X m/z window around the precursor from the query and library spectrum. Default true.
  • --topPeaksForSearch <num> – Use this many of the highest intensity peaks. Default 100.
  • -w [ --mz-window ] <size> – Compare query to library spectra with precursor m/z +/- size. Default 3.
  • -L [ --low-charge <charge> – ] Search only spectra with charge no less than this. Default 1.
  • -H [ --high-charge ] <charge> – Search only spectra with charge no higher than this. Default 5.
  • -m [ --report-matches ] <num> – Return this number of the best matches for each query. Use -1 to report all. Default 5.
  • --psm-result-file <name> – Return results in a .psm file of the given name. Default no .psm file.
  • -R [ --report-file ] <name> – Return results in report file of the given nam. Default is .report.
  • --preserve-order – Search spectra in the order they appear in the file. Default to search as sorted by precursor m/z.
  • -p [ --parameter-file ] <name> – File containing search parameters. Command line values override file values.
  • -v [ --verbosity ] <level> – Control the level of output to stderr. (silent, error, status, warn, debug, detail, all) Default status.
  • -h [ --help ] – Print help message.