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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
5160 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
5160 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
5161 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
5161 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
5161 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
5161 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
5161 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
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 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
5160 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
5160 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
5160 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
5160 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
5160 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
5161 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
5161 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
5161 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
5161 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
5161 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
5162 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
5162 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
5162 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
5162 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
5162 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
5165 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
5165 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
5165 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
5165 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
5165 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
Here’s a description of each column in the regular Comet (non-Crux) output:
- scan: The scan number of the spectrum that was searched.
- num: For each scan, the top N best scoring peptides are returned, controlled by the num_output_lines parameter. This column displays the peptide order for each scan, starting at “1” to indicate the top scoring peptide, “2” to indicate the second best scoring peptide, etc.
- charge: The precursor charge state.
- exp_neutral_mass: The experimental neutral mass of the measured precursor ion.
- calc_neutral_mass: The calculated neutral mass of the matched peptide.
- e_value: The expectation value or E-value score for the peptide. See this paper for some info on how Comet calculates E-values (although there is a correction where the log transform of the cumulative xcorr distribution is used instead of the log transform of the xcorr histogram).
- xcorr: The cross correlation score for the peptide. Here’s a very nice illustration of how this score is calculated by Will Fondrie.
- delta_cn: The deltaCn which is the difference in the normalized cross correlation score, historically between top hit and next best hit. In Comet, each deltaCn score for each row is the difference in the normalized cross correlation score between that hit and next lower peptide hit.
- sp_score: The preliminary score which is the sum of peak intensities that match the peptide and accounts for continuity of an ion series and the length of the peptide. I think of this as a quick/simple peptide match score that now exists only for backwards compatibility for post-search processing tools.
- ions_matched: Out of the total number of theoretical fragment ions being considered in the search, this is the number of those ions that were found in the experimental spectrum.
- ions_total: The total number of theoretical fragment ions for the peptide.
- plain_peptide: The raw peptide sequence.
- modified_peptide: The peptide sequence including previous and next amino acids as well as any variable modifications.
- prev_aa: In the first protein that contains this peptide, the amino acid just before or n-terminal to the peptide.
- next_aa: In the first protein that contains this peptide, the amino acid just after or c-terminal to the peptide.
- protein: A comma separated list of proteins that contain the identified peptide. The maximum number of proteins printed out is controlled by the max_duplicate_proteins parameter.
- protein_count: The total number of proteins in the database that contains the peptide.
- modifications: An encoding of static and variable modifications in the peptide as described above.
- retention_time_sec: If available from the query file, this reports the retention time in seconds of the spectrum being searched.
- sp_rank: The rank of the preliminary score (Sp). If the peptide results were ordered by the sp_score column, this column reports the rank order of this peptide when sorted by sp_score. So if this peptide had the fourth highest sp_score, this column would contain a “4”.