Comet parameter: output_txtfile

Controls whether to output search results into a tab-delimited text file (.txt).
Valid values are 0 (do not output) or 1 (output).
The default value is “0” if this parameter is missing.
“peff_modified_peptide” column is present only if a PEFF search is performed. PEFF modifications will contain bracketed OBO identifiers for each PEFF modification. User specified static and variable modifications will still be reported as bracketed mass differences. For example: K.n[144.1000]RT[MOD:00047]EAR.S
The “modifications” column reports a comma separated list of modifications in the format “position_code_massdiff”, e.g. “3_V_15.9949”. The “position” field is the position of the peptide residue where position 1 is the first residue. A position of “0” denotes the previous flanking amino acid and a position of 1 greater than the peptide length denotes the following flanking amino acid; these are relevant for PEFF substitutions. The “code” field can be “S” for a static modification, “V” for a variable modification, “P” for a PEFF modification, and “p” for a PEFF substitution. In the case of a PEFF substitution, the original amino acid is listed in the “massdiff” field, e.g. “2_p_L” indicates the 2nd residue was originally a leucine before the PEFF substitution.
The “modifications” string can be appended with:
- “_N” to denote a N-term protein modification, e.g. “1_S_-17.0265_N”
- “_n” to denote a N-term peptide modification, e.g. “1_A_42.0146_n”
- “_C” to denote a C-term protein modification, e.g. “9_R_356.1882_C”
- “_c” to denote a C-term peptide modification, e.g. “12_K_42.0106_c”

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.

CometVersion 2022.01 rev. 0   20170103_HelaQC_01   01/13/2023, 03:07:37 PM human.small
scan  num   charge   exp_neutral_mass  calc_neutral_mass e-value  xcorr delta_cn sp_score ions_matched   ions_total  plain_peptide  modified_peptide  prev_aa  next_aa  protein  protein_count  modifications  retention_time_sec   sp_rank
4  3  1593.645971 1591.615160 8.24E+00 0.9960   0.0658   22.7  5  48 DYDSNLNASRDDK  K.DYDS[79.9663]NLNASRDDK.K K  K  sp|Q14573|ITPR3_HUMAN   1  4_V_79.966331  1241.7   15
5  3  1593.645971 1592.668956 1.47E+01 0.9305   0.0041   38.0  6  52 KDADVEDEDTEEAK R.KDADVEDEDTEEAK.T   R  T  sp|O60306|AQR_HUMAN  1  -  1241.7   3
1  2  1198.478447 1195.478399 1.20E+01 0.6363   0.2096   46.8  4  16 MNCLDCLDR   R.MNCLDCLDR.T  R  T  sp|O15056|SYNJ2_HUMAN   1  3_S_57.021464,6_S_57.021464   1241.8   1
2  2  1198.478447 1198.494758 4.07E+01 0.5030   0.0399   41.7  3  16 YEVSSPYFK   R.YEVS[79.9663]SPYFK.V  R  V  sp|P55290|CAD13_HUMAN   1  4_V_79.966331  1241.8   2
3  2  1198.478447 1198.494758 4.07E+01 0.5028   0.0396   41.7  3  16 YEVSSPYFK   R.YEVSS[79.9663]PYFK.V  R  V  sp|P55290|CAD13_HUMAN   1  5_V_79.966331  1241.8   2
4  2  1198.478447 1196.471916 4.89E+01 0.4829   0.0384   32.7  3  16 TYKMSMANR   K.TYKM[15.9949]S[79.9663]MANR.G  K  G  sp|P31327|CPSM_HUMAN 1  4_V_15.994900,5_V_79.966331   1241.8   3
5  2  1198.478447 1196.471916 5.12E+01 0.4779   0.0284   32.7  3  16 TYKMSMANR   K.TYKMS[79.9663]M[15.9949]ANR.G  K  G  sp|P31327|CPSM_HUMAN 1  5_V_79.966331,6_V_15.994900   1241.8   3

Sample output for a PEFF search; note the two amino acid substitutions encoded in the modifications column.

CometVersion 2017.01 rev. 0       20141219_Hela_01        06/05/2017, 04:08:04 PM nextprot_all.peff
scan   num  charge  exp_neutral_mass  calc_neutral_mass  e-value   xcorr   delta_cn  sp_score  ions_matched  ions_total  plain_peptide        modified_peptide                           peff_modified_peptide                          prev_aa next_aa protein                          protein_count   modifications
1    2       2115.965447       2114.972957        1.00E-03  1.7280  0.4856    52.4      7             36          TTHFVEGGDAGNREDQINR  K.TTHFVEGGDAGNREDQINR.L                    K.TTHFVEGGDAGNREDQINR.L                        K       L       nxp:NX_P18124-1                  1
2    2       2115.965447       2115.969012        1.90E+00  0.8888  0.5306    10.3      4             36          VVSPAAVHCALRSPPPEAR  R.VVS[79.9663]PAAVHCALRS[79.9663]PPPEAR.A  R.VVS[MOD:00046]PAAVHCALRS[MOD:00046]PPPEAR.A  R       A       nxp:NX_O43488-1                  1               3_P_79.966331,13_P_79.966331,4_p_R
3    2       2115.965447       2115.978285        3.83E+00  0.8111  0.5925    6.6       3             34          ILDLTECSAVQFDYSQER   R.ILDLTECSAVQFDYSQER.V                     R.ILDLTECSAVQFDYSQER.V                         R       V       nxp:NX_Q9UN19-1,nxp:NX_Q9UN19-2  2
1    2       1388.661763       1388.661917        1.03E-04  2.0068  0.6812    351.0     10            20          QAHLTNQYMQR          R.QAHLTNQYMQR.M                            R.QAHLTNQYMQR.M                                R       M       nxp:NX_P11940-1,nxp:NX_P11940-2  2
2    2       1388.661763       1388.654524        1.91E+01  0.6397  0.6921    15.2      3             26          AGAGSGASGERWQR       R.AGAGSGASGERWQR.V                         R.AGAGSGASGERWQR.V                             R       V       nxp:NX_Q13424-1,nxp:NX_Q13424-2  2               8_p_G
3    2       1388.661763       1388.670096        2.32E+01  0.6179  0.6931    17.0      3             22          TPTTPLPQTPTR         K.TPTTPLPQT[79.9663]PTR.R                  K.TPTTPLPQT[MOD:00047]PTR.R                    K       R       nxp:NX_Q8WU20-1                  1               9_P_79.966331

Note that there is a different text output if Comet is compiled with the Crux flag (i.e. add -DCRUX to the CXXFLAGS in the Makefiles under Linux or #define CRUX in Common.h). Here’s the Crux-specific text output where the files have a “.target.txt” or “.decoy.txt” extensions.

scan  charge   spectrum precursor m/z  spectrum neutral mass   peptide mass   delta_cn sp score sp rank  xcorr score xcorr rank  b/y ions matched  b/y ions total total matches/spectrum  sequence modified sequence modifications  protein id  flanking aa e-value
3  532.222600  1593.645971 1592.643804 0.5933   382.0618 1  2.6817   1  14 52 849   RAAEDDEDDDVDTK K.RAAEDDEDDDVDTK.K   -  sp|P06454|PTMA_HUMAN KK 2.73E-06
3  532.222600  1593.645971 1591.647706 0.6174   44.5599  2  1.0906   2  7  52 849   YDMGILDLGSGDEK R.YDMGILDLGS[79.9663]GDEK.V   10_V_79.966331 sp|A3KN83|SBNO1_HUMAN   RV 3.57E+00
3  532.222600  1593.645971 1591.637795 0.6286   13.5461  40 1.0261   3  4  48 849   TYYLMDPSGNAHK  R.TYYLM[15.9949]DPS[79.9663]GNAHK.W 5_V_15.994900,8_V_79.966331   sp|O15530|PDPK1_HUMAN   RW 6.31E+00
3  532.222600  1593.645971 1591.615160 0.6530   22.6996  15 0.9960   4  5  48 849   DYDSNLNASRDDK  K.DYDS[79.9663]NLNASRDDK.K 4_V_79.966331  sp|Q14573|ITPR3_HUMAN   KK 8.24E+00
3  532.222600  1593.645971 1592.668956 0.6544   38.0146  3  0.9305   5  6  52 849   KDADVEDEDTEEAK R.KDADVEDEDTEEAK.T   -  sp|O60306|AQR_HUMAN  RT 1.47E+01
2  600.246500  1198.478447 1195.478399 0.2096   46.8252  1  0.6363   1  4  16 427   MNCLDCLDR   R.MNCLDCLDR.T  3_S_57.021464,6_S_57.021464   sp|O15056|SYNJ2_HUMAN   RT 1.20E+01
2  600.246500  1198.478447 1198.494758 0.2098   41.7443  2  0.5030   2  3  16 427   YEVSSPYFK   R.YEVS[79.9663]SPYFK.V  4_V_79.966331  sp|P55290|CAD13_HUMAN   RV 4.07E+01
2  600.246500  1198.478447 1198.494758 0.2411   41.7443  2  0.5028   3  3  16 427   YEVSSPYFK   R.YEVSS[79.9663]PYFK.V  5_V_79.966331  sp|P55290|CAD13_HUMAN   RV 4.07E+01
2  600.246500  1198.478447 1196.471916 0.2490   32.7316  3  0.4829   4  3  16 427   TYKMSMANR   K.TYKM[15.9949]S[79.9663]MANR.G  4_V_15.994900,5_V_79.966331   sp|P31327|CPSM_HUMAN KG 4.89E+01
2  600.246500  1198.478447 1196.471916 0.2703   32.7316  3  0.4779   5  3  16 427   TYKMSMANR   K.TYKMS[79.9663]M[15.9949]ANR.G  5_V_79.966331,6_V_15.994900   sp|P31327|CPSM_HUMAN KG 5.12E+01
3  416.869700  1247.587271 1245.604642 0.0096   31.5543  8  1.1721   1  5  36 784   YLAVESPFLK  K.YLAVES[79.9663]PFLK.E 6_V_79.966331  sp|P50416|CPT1A_HUMAN   KE 2.53E+00
3  416.869700  1247.587271 1244.552944 0.1794   61.5555  1  1.1609   2  6  40 784   MVEGHDEVMAK K.MVEGHDEVMAK.S   -  sp|A6NNT2|CP096_HUMAN   KS 2.78E+00
3  416.869700  1247.587271 1247.600697 0.1922   51.6947  2  0.9618   3  6  48 784   SHHANSPTAGAAK  K.SHHANSPTAGAAK.S -  sp|Q15555|MARE2_HUMAN   KS 1.48E+01
3  416.869700  1247.587271 1246.574739 0.2308   24.9601  19 0.9468   4  4  36 784   AFVWSSTLTR  K.AFVWS[79.9663]STLTR.H 5_V_79.966331  sp|A6NNF4|ZN726_HUMAN   KH 1.68E+01
3  416.869700  1247.587271 1244.560792 0.2511   41.4564  5  0.9015   5  5  32 784   HMQEWLETR   R.HM[15.9949]QEWLETR.G  2_V_15.994900  sp|P07311|ACYP1_HUMAN   RG 2.46E+01
3  432.885100  1295.633471 1295.658212 0.4386   429.6465 1  2.2225   1  19 40 917   LGIHEDSQNRK K.LGIHEDSQNRK.K   -  sp|P07900|HS90A_HUMAN   KK 1.29E-02
3  432.885100  1295.633471 1295.623480 0.5113   200.3429 2  1.2476   2  13 36 917   RQITVDSEIR  K.RQITVDS[79.9663]EIR.K 7_V_79.966331  sp|P11532|DMD_HUMAN  KK 4.97E+00
3  432.885100  1295.633471 1295.656026 0.5308   77.2904  30 1.0861   3  9  40 917   VALDSLVLQMK R.VALDS[79.9663]LVLQMK.S   5_V_79.966331  sp|Q14147|DHX34_HUMAN   RS 1.33E+01
3  432.885100  1295.633471 1292.616604 0.5450   84.5115  24 1.0427   4  11 40 917   ALKSSQAFFSK K.ALKSSQAFFS[79.9663]K.L   10_V_79.966331 sp|O00566|MPP10_HUMAN   KL 1.74E+01
3  432.885100  1295.633471 1294.628231 0.5551   70.6711  42 1.0112   5  11 40 917   QALEEKASALR R.QALEEKAS[79.9663]ALR.T   8_V_79.966331  sp|A0A096LP49|CC187_HUMAN  RT 2.11E+01