####Synopsis This program takes as input a pair of files, one HCD file and one ETD file. The files are assumed to correlate meaning the Percursor of HCD scan X is the same precursor in ETD scan X+1. The correlated scans are stored as a pair then the HCD scan is filtered for the presence of ALL the desired ions, if present the scan pair is kept if absent the scan pair is removed. After filtering the remaining ETD scans are written out to either STDOUT or the file name provided.
####Examples
Filter the file HCDFile.txt for the presence of 366.14
with 0.1 m/z tolerance and output the corresponding ETD
spectra from ETDfile.txt to the file ETDout.txt.
> katikruncher --hcd HCDfile.txt --etd ETDfile.txt --mz 366.14 --mzTol 0.1 --output ETDout.txt
Other examples: Filter for the presence of both 366.14 AND 407.16 with 0.1 m/z tolerance. > katikruncher --hcd HCDfile.txt --etd ETDfile.txt --mz 366.14,407.16 --mzTol 0.1 --output ETDout.txt
Filter for the presence of both 366.14 AND 407.16 with 200 ppm tolerance.
> katikruncher --hcd HCDfile.txt --etd ETDfile.txt --mz 366.14,407.16 --mzTol 0.1 --output ETDout.txt
Usage:
katikruncher --option Value
Options --hcd, --etd, --mz and either --mzTol or --ppmTol are required
Flags:
--hcd HCDFILENAME The HCD file to filter for the
perscibed m/z values.
--etd ETDFILENAME The corrolated ETD file.
--mz F1,F2,F3 The fragments to test for in the
HCD file (All must be present).
--mzTol DELTAMZ The tolerance to allow for the m/z
values from --mz above.
--ppmTol [PPM] The tolerance in Parts Per Million for
the m/z values entered.
--keepN NUM [optional] The fragment to match must be on
of the NUM most abundant.
--out FILENAME Write the scans to FILENAME.
Write to terminal otherwise.
-h, --help This help page.
#####Author Jamie Sherman
#####Copyright Copyright (c) 2011 UCSF. Licensed under the MIT License: http://www.opensource.org/licenses/mit-license.php