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 2017.01 rev. 0       20141219_Hela_01        06/05/2017, 04:34:13 PM 18mix_reverseSGD.fasta
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
1    2       1308.585447       1308.586732        3.16E-06  2.1508  0.6785    238.7     9             22          MDSTANEVEAVK     K.M[15.9949]DSTANEVEAVK.V     K        V        sp|P07237|PDIA1_HUMAN,tr|H0Y3Z3|H0Y3Z3_HUMAN,tr|H7BZ94|H7BZ94_HUMAN   3               1_V_15.994900
2    2       1308.585447       1308.587600        6.85E+00  0.6914  0.7245    29.8      3             20          DMMDPVAVCKK      K.DM[15.9949]MDPVAVCKK.V      K        V        sp|Q6NUJ1|SAPL1_HUMAN                                                 1               2_V_15.994900,9_S_57.021464
3    2       1308.585447       1308.595463        1.84E+01  0.5926  0.7527    18.6      2             18          DMAEMQRVWK       R.DM[15.9949]AEMQRVWK.E       R        E        sp|Q15058|KIF14_HUMAN                                                 1               2_V_15.994900
1    3       1775.648171       1774.634519        4.18E-03  2.4234  0.7827    305.8     13            52          DCDLQEDACYNCGR   K.DCDLQEDACYNCGR.G            K        G        sp|P62633|CNBP_HUMAN,sp|P62633-2|CNBP_HUMAN,sp|P62633-3|CNBP_HUMAN    3               2_S_57.021464,9_S_57.021464,12_S_57.021464
2    3       1775.648171       1774.655633        4.29E+02  0.5265  0.8161    5.1       2             56          EEESAMSSDRMDCGR  K.EEESAMSSDRM[15.9949]DCGR.K  K        K        sp|Q6WCQ1|MPRIP_HUMAN,tr|J3KSW8|J3KSW8_HUMAN,sp|Q6WCQ1-2|MPRIP_HUMAN  3               11_V_15.994900,13_S_57.021464
3    3       1775.648171       1774.655633        5.79E+02  0.4773  0.8161    5.1       2             56          EEESAMSSDRMDCGR  K.EEESAM[15.9949]SSDRMDCGR.K  K        K        sp|Q6WCQ1|MPRIP_HUMAN,tr|J3KSW8|J3KSW8_HUMAN,sp|Q6WCQ1-2|MPRIP_HUMAN  3               6_V_15.994900,13_S_57.021464

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
     2       1157.810000     2313.605447     2313.113325     0.1250  33.7558 4       0.7409  1       4       42      80614   MPTFSTPGAKGEGPDVHMTLPK  K.M[147]PTFSTPGAKGEGPDVHMTLPK.G 1_V_15.994900   sp|Q09666|AHNK_HUMAN    KG      9.26E+00
     2       1157.810000     2313.605447     2313.975870     0.1309  21.1120 12      0.6483  2       3       34      80614   SSAMKKIESETTFSLIFR      R.S[167]S[167]AMKKIES[167]ETTFSLIFR.L   1_V_79.966331, 2_V_79.966331, 9_V_79.966331     sp|Q8WXI7|MUC16_HUMAN   RL      2.89E+01
     2       1157.810000     2313.605447     2314.096792     0.1309  25.9061 7       0.6440  3       3       34      80614   RLLPGSSDWEQQRHQLER      K.RLLPGSS[167]DWEQQRHQLER.R     7_V_79.966331   sp|Q6ZT98|TTLL7_HUMAN   KR      3.06E+01
     2       1157.810000     2313.605447     2314.096792     0.1950  25.9061 7       0.6440  4       3       34      80614   RLLPGSSDWEQQRHQLER      K.RLLPGS[167]SDWEQQRHQLER.R     6_V_79.966331   sp|Q6ZT98|TTLL7_HUMAN   KR      3.06E+01
     2       1157.810000     2313.605447     2312.896434     0.1972  22.5144 10      0.5965  5       3       36      80614   IDESSLTGESDHVRKSADK     K.IDES[167]S[167]LTGESDHVRKS[167]ADK.D  4_V_79.966331, 5_V_79.966331, 16_V_79.966331    sp|Q16720|AT2B3_HUMAN   KD      5.48E+01
     2       1125.870000     2249.725447     2249.032520     0.0051  29.4360 4       0.5709  1       4       40      80457   TLQEPVARPSGASSSQTPNDK   R.TLQEPVARPS[167]GASSSQTPNDK.E  10_V_79.966331  sp|Q8NBA8|DTWD2_HUMAN   RE      4.50E+01
     2       1125.870000     2249.725447     2248.771604     0.0051  35.4842 1       0.5680  2       4       30      80457   VVKETSYEMMMQCVSR        K.VVKETS[167]Y[243]EMM[147]M[147]QC[160]VS[167]R.M      6_V_79.966331, 7_V_79.966331, 10_V_15.994900, 11_V_15.994900, 13_S_57.021464, 15_V_79.966331    sp|Q9NZJ7|MTCH1_HUMAN   KM      4.68E+01
     2       1125.870000     2249.725447     2248.771604     0.0080  35.4842 1       0.5680  3       4       30      80457   VVKETSYEMMMQCVSR        K.VVKET[181]SY[243]EMM[147]M[147]QC[160]VS[167]R.M      5_V_79.966331, 7_V_79.966331, 10_V_15.994900, 11_V_15.994900, 13_S_57.021464, 15_V_79.966331    sp|Q9NZJ7|MTCH1_HUMAN   KM      4.68E+01
     2       1125.870000     2249.725447     2248.771604     0.0114  35.4842 1       0.5664  4       4       30      80457   VVKETSYEMMMQCVSR        K.VVKET[181]S[167]YEMM[147]M[147]QC[160]VS[167]R.M      5_V_79.966331, 6_V_79.966331, 10_V_15.994900, 11_V_15.994900, 13_S_57.021464, 15_V_79.966331    sp|Q9NZJ7|MTCH1_HUMAN   KM      4.79E+01
     2       1125.870000     2249.725447     2249.986133     0.0114  21.0194 12      0.5644  5       3       34      80457   GARASPRTLNLSQLSFHR      R.GARASPRT[181]LNLS[167]QLS[167]FHR.V   8_V_79.966331, 12_V_79.966331, 15_V_79.966331   sp|P29597|TYK2_HUMAN    RV      4.91E+01
     2       1248.000000     2493.985447     2494.319641     0.0776  35.6025 12      0.9110  1       4       40      100697  KFSRPLLPATTTKLSQEEQLK   K.KFSRPLLPATT[181]TKLSQEEQLK.S  11_V_79.966331  sp|Q9NYI0|PSD3_HUMAN    KS      4.80E+00
     2       1248.000000     2493.985447     2494.138504     0.0776  50.6368 8       0.8403  2       5       38      100697  LVSDVSATKIPHIWLMLSTK    R.LVSDVS[167]AT[181]KIPHIWLM[147]LST[181]K.M    6_V_79.966331, 8_V_79.966331, 16_V_15.994900, 19_V_79.966331    sp|Q9BVV2|CT195_HUMAN   RM      1.07E+01
     2       1248.000000     2493.985447     2494.138504     0.0776  50.6368 8       0.8403  3       5       38      100697  LVSDVSATKIPHIWLMLSTK    R.LVSDVS[167]AT[181]KIPHIWLM[147]LS[167]TK.M    6_V_79.966331, 8_V_79.966331, 16_V_15.994900, 18_V_79.966331    sp|Q9BVV2|CT195_HUMAN   RM      1.07E+01
     2       1248.000000     2493.985447     2494.138504     0.0776  50.6368 8       0.8403  4       5       38      100697  LVSDVSATKIPHIWLMLSTK    R.LVS[167]DVSAT[181]KIPHIWLM[147]LST[181]K.M    3_V_79.966331, 8_V_79.966331, 16_V_15.994900, 19_V_79.966331    sp|Q9BVV2|CT195_HUMAN   RM      1.07E+01
     2       1248.000000     2493.985447     2494.138504     0.0776  50.6368 8       0.8403  5       5       38      100697  LVSDVSATKIPHIWLMLSTK    R.LVS[167]DVSAT[181]KIPHIWLM[147]LS[167]TK.M    3_V_79.966331, 8_V_79.966331, 16_V_15.994900, 18_V_79.966331    sp|Q9BVV2|CT195_HUMAN   RM      1.07E+01