Description: Search a spectrum library for matches to query spectra.
BlibSearch [options] <query filename> <library filename> <output filename>
- <query filename> - the MS2 file containing the query spectra.
- <library filename> - the library to be searched for matches to the query. To search more than one library, provide the name of a file containing a list of libraries. Pre-built libraries are available for download or see BlibBuild for constructing libraries.
- <output filename> - the name for the SQT file with the search results. See Output section.
Output: An SQT file of the five best matches to each query. An optional report file may also be produced. See Additional Options,
--report. An MS2 file containing only those query spectra that did NOT have positive library identifications is also produced. See Additional Options,
--thresholdfor defining a positive match.
- -p, --params <file> - Specify additional options (listed below) in a parameter file. File must begin with the word 'params' and separate each option and its argument with whitespace (space, tab, new-line).
- -c, --compare <xcor | dotp> - Specify the comparison function used to asses similarity between query and library spectra. Cross correlation (xcor) and dot product (dotp) are currently available. The dot product is the default.
- -v, --verbose <0|1|2|3> - Set the verbosity level of output to stderr. The default level is 3. Level 0 is silent, 1 reports completion of the major milestones in execution, 2 additionally reports the minor milestones in execution, and 3 reports milestones as well as a running count of each spectrum as it is searched.
- -h, --help - Print a list of options available for the params file. Help for the command-line options is displayed when the program is run with no arguments.
Additional Options (for parameter file):
-b n, --bin n- Override the default peak normalization (the square root of the intensity times the square of the m/z) and instead adjust peak intensities as follows. Separate peaks in to n bins, each 1/nth of the spectrum's total m/z range. Divide each peak's intensity by the maximum intensity within its bin. Error to specify both
-z, --charge- Turns off the charge similarity requirement so that query spectra are compared to library spectra regardless of charge. In the default state, query are only compared to library spectra of the same charge (or for ambiguous multiply charged query, they are compared to both +2 and +3 library spectra).
-p, --clearPrecursor- Do not delete peaks in a 20 to +5 m/z window around precursor ion.
-x, --libpp- Turn off pre-processing of library spectra.
-s n, --minScore n- Report only those results that have a score of at least n.
-l, ---noiselast- Reverse the order of peak pre-processing steps: remove noise peaks after the intensities have been normalized. Default is to remove noise peaks first.
-M, ---no-filter-ms2- Do not print an MS2 file containing unidentified spec.
-t n, --numPeaks n- Specify the number of highest-intensity peaks to be retained after noise-peak removal. Default is 100.
-f n, --percentCurrent n- Override the
-numPeaksmethod of distinguishing signal from noise and instead retain those highest intensity peaks whose intensities sum to n times the total ion current. Requires 0 < n <= 1.
-e, --querypp- Turn off pre-processing of query spectra.
-r <filename>, --report-name <filename>- Print a report file with the same match results as the SQT file plus additional information.
-R, --report-default - Same as --report-name but the name of the report file is taken from the name of the sqt file.
-q, --sqrt- When normalizing peak intensities, do not weight each peak's intensity by the square if its m/z. Use the square root of the peak intensity. Error if both
-m n, --topMatches n- Specify how many matches are printed in both the SQT and (optional) report files. Default is to print matches with the top five scores. Use n = -1 to print all matches.
-S n, --threshold n- Use n as the minimum score to be considered a correct match. The default is 0.5.
-w n, --window n- Set the magnitude of the m/z search window (centered around the query spectrum precursor m/z). The default is n = 6 (precursor m/z +/- 3).