Comet parameter: output_txt_file

  • Controls whether to output search results into a tab-delimited text file (.txt).
  • Valid values are 0 (do not output) or 1 (output).

Example:
output_txt_file= 0
output_txt_file= 1

Here is an example output: 

##      100     CometVersion 2013.01 rev. 0     08/23/2013, 01:34:23 PM 08/23/2013, 01:34:42 PM /db/SGD/SGDyeast.fasta
5129    1       600.9771        602.3620        9.62E+00        0.7456  0.0817  77.6    5/8             LISNR   K.LISNR.E       YNL297C 0
5385    1       602.3363        604.3301        1.60E+01        0.5316  0.0424  70.9    3/8             NLTEK   R.NLTEK.T       YBL024W 1
5496    1       602.3431        600.3828        2.16E+01        0.4527  0.0234  6.6     2/8             VVNIR   R.VVNIR.L       YJL012C 0
5430    1       603.3402        604.3665        1.48E+01        0.4519  0.0658  63.0    4/10            LIGSSK  R.LIGSSK.L      YDL090C 0
5861    1       604.3820        603.2885        1.17E+01        0.4390  0.1804  152.1   4/8             KHGDF   K.KHGDF.-       YKL062W 0
5897    1       604.3834        606.3457        9.39E+00        0.5628  0.0154  59.6    5/10            ITTSGK  K.ITTSGK.H      YPL015C 0

The first line of the output file is a header line which contains the Comet version, search start and stop times/dates, and search database. Subsequent output lines contains the following columns:

  • scan number
  • precursor charge state
  • experimental peptide mass (singly protonated)
  • calculated peptide mass (singly protonated)
  • expectation-value
  • xcorr
  • dCn
  • Sp score
  • matched/total ions
  • plain peptide
  • peptide (with prev/next amino acid and mods)
  • protein
  • # duplicate proteins