Description: Processes spectra in an MS2 file and prints resulting spectra to a new MS2 file. This provides a means of either viewing processed spectra (with a visualization tool) and a mechanism for building libraries of processed spectra.
BlibUPpMS2 [options] <input MS2> <ouput MS2>
- <input MS2> - an MS2 file containing spectra to be processed.
- <ouput MS2> - the name of the file to which results are printed.
Output: An MS2 file containing each input spectrum modified by peak binning, noise reduction, and intensity normalization.
Options: Defaults are as for BlibSearch.
-b, --bin <n>- Use n bins to normalize intensities.
-p, --clearPrecursor- Do not delete peaks in a -20 to +5 m/z window around precursor ion.
-l, --noiselast- Remove noise peaks after normalizing intensities. Default is to remove them first.
-t, --numPeaks <n>- Use the n top-ranking peaks as signal. Default is 100.
-f, --percentCurrent <n>- Use a fraction, n, of total current to determine signal/noise cut off. Requires 0 < n <= 1.
-q, --sqrt- Use sqaure root of intensties for peak normalization.
-v, --verbose <0|1|2>- Set the verbosity level of the output to stderr. Default is 2.