Comet

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 a "_N" to denote a N-term protein modification, "_n" to denote a N-term peptide modification, "_C" to denote a C-term protein modification, or a "_c" to denote a C-term peptide modification. For example "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
10685  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
10685  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
10685  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
14937  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
14937  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
14937  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
10007  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
10007  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
10007  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
10019  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
10019  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
10019  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 Crux flag in Common.h). ".target.txt"

scan    charge 2       2       1157.810000 2       2       1157.810000 2       2       1157.810000 2       2       1157.810000 2       2       1157.810000 3       2       1125.870000 3       2       1125.870000 3       2       1125.870000 3       2       1125.870000 3       2       1125.870000 4       2       1248.000000 4       2       1248.000000 4       2       1248.000000 4       2       1248.000000 4       2       1248.000000

a different text output if Comet is compiled with the (i.e. add -DCRUX to the CXXFLAGS in the Makefiles under Linux or #define CRUX Here's the Crux-specific text output where the files have a or ".decoy.txt" extensions. 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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

Comet

MS/MS database search

Comet parameter: output_txtfile