Example:
output_txtfile = 0
output_txtfile = 1
Here's snippet of sample output below. The first line of the output file is a header line which contains the Comet version, search start time/date, and search database. The second line contains the column headers. Only the top hit for each search is reported in the text output; the parameter "num_output_lines" does not apply to the text output.
CometVersion 2013.02 rev. 0 100 10/04/2013, 08:37:09 AM /net/pr/vol1/ProteomicsResource/dbase/SGD/SGDyeast.fasta.20101117 scan charge exp_neutral_mass calc_neutral_mass e-value xcorr delta_cn sp_score ions_matched ions_total plain_peptide peptide prev_aa next_aa protein duplicate_protein_count 5129 1 599.9698 602.3136 1.73E+01 0.6847 0.0995 44.3 4 8 DAKNR R.DAKNR.I R I YML019W 0 5385 1 601.3290 603.3228 1.73E+01 0.5316 0.1905 70.9 3 8 NLTEK R.NLTEK.T R T YBL024W 1 5496 1 601.3358 599.3755 1.67E+01 0.4527 0.1315 6.6 2 8 VVNIR R.VVNIR.L R L YJL012C 0 5430 1 602.3329 605.2591 2.33E+01 0.4222 0.0854 73.2 4 8 DVGCR K.DVGCR.I K I YER085C 0 5829 1 616.4184 615.3414 5.26E+01 0.4321 0.0658 8.5 2 8 KPPMK -.KPPM*K.Q - Q DECOY__YBR025C 2
Comet's text output is different if Comet was compiled for Crux compatibility. Here's the example text output if you are running Comet in Crux. Note that up to 5 hits per spectrum are reported and there is just a single column header line.
scan charge spectrum precursor m/z spectrum neutral mass matches/spectrum peptide mass e-value xcorr score xcorr rank delta_cn sp score sp rank b/y ions matched b/y ions total sequence flanking aa protein id 5129 1 600.9771 599.9698 5440 602.3136 1.73E+01 0.6847 1 0.0995 44.3 19 4 8 DAKNR RI YML019W 5129 1 600.9771 599.9698 5440 602.3249 1.96E+01 0.6714 2 0.1016 46.1 17 5 10 RTGGGR RI YGR054W 5129 1 600.9771 599.9698 5440 602.3136 1.99E+01 0.6698 3 0.1131 77.6 6 5 8 NISNR KV YMR033W 5129 1 600.9771 599.9698 5440 601.2820 2.16E+01 0.6612 4 0.1240 38.6 22 4 8 EPSNR RD YPL161C 5129 1 600.9771 599.9698 5440 600.3231 0.00E+00 0.6532 5 0.1389 104.6 3 6 8 IESPR KM YLL021W 5385 1 602.3363 601.3290 6518 603.3228 1.73E+01 0.5316 1 0.1905 70.9 2 3 8 NLTEK RT YBL024W 5385 1 602.3363 601.3290 6518 600.3707 1.86E+01 0.5249 2 0.2022 31.0 8 3 8 ARNIK KT DECOY_YIL159W 5385 1 602.3363 601.3290 6518 602.3249 2.02E+01 0.5173 3 0.2134 47.4 4 3 8 ARNSR KI DECOY_YLL040C 5385 1 602.3363 601.3290 6518 601.3184 2.19E+01 0.5100 4 0.2148 7.1 19 2 10 GAVNNK KS DECOY_YMR125W 5385 1 602.3363 601.3290 6518 599.4119 0.00E+00 0.5091 5 0.2148 28.3 9 3 8 ALLKR RI YML107C