Orbithrash precursor

From Mswiki

Orbithrash_precursor is an algorithm to determine to monoisotopic m/z, monoisotopic mass, and charge state for every precursor ion selected for data-dependent MS/MS. It requires ms2 files and their corresponding ms1 files. The precursor scans must be obtained at high resolution (in the orbitrap), and must collected in centroid mode. The program also requires a orbithrash_precursor_options.txt file. A sample options file can be found in /data/6/jrjohns1/orbithrash_precursor/orbithrash_precursor_options.txt. The parameters in this file are fairly self-explanatory.

Once the monoisotopic m/z and charge state are determined, SEQUEST may be set to use a small ppm mass accuracy window for very high confidence identifications. Also, as charge states are automatically assigned, the chance of assigning spectra incorrectly is drastically reduced. Orbithrash is able to confidently assign monoisotopic m/z and charge state information for approximately 80% of data. The remaining 20% can be separated and searched with SEQUEST using different parameters.

To run the program in a directory containing ms2 and ms1 files, the command is:

/data/6/jrjohns1/orbithrash_precursor/orbithrash_precursor filename1.ms2 filename2.ms2 filename3.ms2 ...

The output will be filename.ms2.monomz files. An I line is added for each spectrum analyzed by orbithrash_precursor indicating whether the algorithm was able to confidently identify the monoisotopic m/z and charge state (THRASH_SUCCESS). In order to separate spectra that were assigned from those that were not, the GetThrashed perl script may be run as follows:

/data/6/jrjohns1/orbithrash_precursor/GetThrashed filename1.ms2.monomz filename2.ms2.monomz filename2.ms2.monomz ...

The script will create two files for each input file, one labeled filename.ms2.monomz.success and one labeled filename.ms2.monomz.fail. The .success file contains only spectra where all precursor ions had confidently assigned monoisotopic m/z and charge states, the .fail file contains those that could not be assigned. Remember to rename the files before submitting for a SEQUEST search (the SEQUEST submit scripts only recognize files ending in .ms2).