anesvi
commented
5 years ago Dear Bart
This is strange because everything looks totally fine in the log file.
Something breaks philosopher report generation function. I suspect the database formatting issue.
I think this needs to go to Felipe (Philosopher). However, he is away from office now. If you need it resolved very soon, can you please share your sequence database and one of the mzML files with me?
Best Alexey
From: Bart Cuypers [mailto:notifications@github.com] Sent: Friday, September 13, 2019 6:31 AM To: Nesvilab/FragPipe FragPipe@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [Nesvilab/FragPipe] 'Mapped Proteins' column incorrect => Final output containing lots of rev_ proteins. (#137)
External Email - Use Caution Describe the problem
I almost get equal numbers of 'real' (1509) and 'rev' (1651) proteins in the final output file. This seems to be traced back to the 'Mapped Proteins' column in the 'peptide.tsv' being wrong. rev matches are reported there, while these peptides are not part of the _rev sequences at all. What could be the problem here?
· I'm submitting a:
* [ ] problem running the software
* [ x] bug report
* [ ] feature request
* [ ] question· My MSFragger use case:
* [ ] Closed search (standard small precursor mass tolerance)
* [ x] Open search (large precursor mass tolerance)System info
You can find that printed on the Config tab.
- OS and version: your response here Windows 10, AMD64
- Java version: your response here 1.8.0_211
Describe your experiment Genral proteomics experiment description
e.g. Shotgun proteomics, Q-Exactive ...
Input data files
2 conditions, 12 samples per condition => 24 samples total
Sequence database your response here, preferably a link or at least name, organism etc. Leishmania Size of the either in proteins or in megabytes 33Mb, 8000 proteins Attach fragger.params file
database_name = C:\LeishPTM\20190910_LeishPTManalysis\2019-09-11-td-LdPBQ7G3I2I8_2018.protein.fa num_threads = 8 # 0=poll CPU to set num threads; else specify num threads directly (max 64)
precursor_mass_lower = -150 precursor_mass_upper = 500 precursor_mass_units = 0 # 0=Daltons, 1=ppm precursor_true_tolerance = 20 precursor_true_units = 1 # 0=Daltons, 1=ppm fragment_mass_tolerance = 20 fragment_mass_units = 1 # 0=Daltons, 1=ppm calibrate_mass = 2 # 0=Off, 1=On, 2=On and find optimal parameters decoyprefix = rev
isotope_error = 0 # 0=off, -1/0/1/2/3 (standard C13 error) mass_offsets = 0 # allow for additional precursor mass window shifts. Multiplexed with isotope_error. mass_offsets = 0/79.966 can be used as a restricted ‘open’ search that looks for unmodified and phosphorylated peptides (on any residue) precursor_mass_mode = selected
remove_precursor_peak = 0 # 0 = not remove, 1 = only remove the peak with the precursor charge, 2 = remove all peaks with all charge states. Default: 0 remove_precursor_range = -1.50,1.50 # Unit: Da. Default: -1.5,1.5 intensity_transform = 0 # 0 = none, 1 = sqrt root. Default: 0
localize_delta_mass = 1 delta_mass_exclude_ranges = (-1.5,3.5) fragment_ion_series = b,y
search_enzyme_name = Trypsin search_enzyme_cutafter = KR search_enzyme_butnotafter = P
num_enzyme_termini = 2 # 2 for enzymatic, 1 for semi-enzymatic, 0 for nonspecific digestion allowed_missed_cleavage = 1 # maximum value is 5
clip_nTerm_M = 1
maximum of 7 mods - amino acid codes, * for any amino acid, [ and ] specifies protein termini, n and c specifies peptide termini
variable_mod_01 = 15.99490 M variable_mod_02 = 42.01060 [^
variable_mod_03 = 79.96633 STY variable_mod_04 = -17.02650 nQnC variable_mod_05 = -18.01060 nE variable_mod_06 = 0.00000 site_06 variable_mod_07 = 0.00000 site_07
allow_multiple_variable_mods_on_residue = 1 # static mods are not considered max_variable_mods_per_mod = 3 # maximum of 5 max_variable_mods_combinations = 5000 # maximum of 65534, limits number of modified peptides generated from sequence
output_file_extension = pepXML output_format = pepXML output_report_topN = 1 output_max_expect = 50 report_alternative_proteins = 1 # 0=no, 1=yes
precursor_charge = 1 4 # precursor charge range to analyze; does not override any existing charge; 0 as 1st entry ignores parameter override_charge = 0 # 0=no, 1=yes to override existing precursor charge states with precursor_charge parameter
digest_min_length = 7 digest_max_length = 50 digest_mass_range = 500.0 5000.0 # MH+ peptide mass range to analyze max_fragment_charge = 2 # set maximum fragment charge state to analyze (allowed max 5)
open search parameters
track_zero_topN = 0 # in addition to topN results, keep track of top results in zero bin zero_bin_accept_expect = 0.00 # boost top zero bin entry to top if it has expect under 0.01 - set to 0 to disable zero_bin_mult_expect = 1.00 # disabled if above passes - multiply expect of zero bin for ordering purposes (does not affect reported expect) add_topN_complementary = 0
spectral processing
minimum_peaks = 15 # required minimum number of peaks in spectrum to search (default 10) use_topN_peaks = 100 min_fragments_modelling = 3 min_matched_fragments = 5 minimum_ratio = 0.01 # filter peaks below this fraction of strongest peak clear_mz_range = 0.0 0.0 # for iTRAQ/TMT type data; will clear out all peaks in the specified m/z range
additional modifications
add_Cterm_peptide = 0.000000 add_Nterm_peptide = 0.000000 add_Cterm_protein = 0.000000 add_Nterm_protein = 0.000000
add_G_glycine = 0.000000 add_A_alanine = 0.000000 add_S_serine = 0.000000 add_P_proline = 0.000000 add_V_valine = 0.000000 add_T_threonine = 0.000000 add_C_cysteine = 57.021464 add_L_leucine = 0.000000 add_I_isoleucine = 0.000000 add_N_asparagine = 0.000000 add_D_aspartic_acid = 0.000000 add_Q_glutamine = 0.000000 add_K_lysine = 0.000000 add_E_glutamic_acid = 0.000000 add_M_methionine = 0.000000 add_H_histidine = 0.000000 add_F_phenylalanine = 0.000000 add_R_arginine = 0.000000 add_Y_tyrosine = 0.000000 add_W_tryptophan = 0.000000 add_B_user_amino_acid = 0.000000 add_J_user_amino_acid = 0.000000 add_O_user_amino_acid = 0.000000 add_U_user_amino_acid = 0.000000 add_X_user_amino_acid = 0.000000 add_Z_user_amino_acid = 0.000000
Run log output
System info:
System OS: Windows 10, Architecture: AMD64
Java Info: 1.8.0_211, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
Version info:
FragPipe version 10.1
MSFragger version 2.1
Philosopher version 1.5.1 (build 1566924968)
LCMS files:
Experiment/Group: LOG
-
C:\LeishPTM\LOG\14_173LOGBR2.mzML
-
C:\LeishPTM\LOG\15_173LOGBR1.mzML
-
C:\LeishPTM\LOG\16_178LOGBR1.mzML
-
C:\LeishPTM\LOG\18_275LOGBR2.mzML
-
C:\LeishPTM\LOG\1_275LOGBR1.mzML
-
C:\LeishPTM\LOG\20_178LOGBR2.mzML
-
C:\LeishPTM\LOG\48_178BR2.mzML
-
C:\LeishPTM\LOG\49_275BR1.mzML
-
C:\LeishPTM\LOG\53_173BR2.mzML
-
C:\LeishPTM\LOG\55_178BR1.mzML
-
C:\LeishPTM\LOG\59_173BR1.mzML
-
C:\LeishPTM\LOG\61_275BR2.mzML
Experiment/Group: STAT
-
C:\LeishPTM\STAT\10_178STATBR3.mzML
-
C:\LeishPTM\STAT\11_275STATBR2.mzML
-
C:\LeishPTM\STAT\12_178STATBR1.mzML
-
C:\LeishPTM\STAT\17_275STATBR1.mzML
-
C:\LeishPTM\STAT\2_173STATBR2.mzML
-
C:\LeishPTM\STAT\3_173STATBR4.mzML
-
C:\LeishPTM\STAT\4_173STATBR1.mzML
-
C:\LeishPTM\STAT\5_178STATBR2.mzML
-
C:\LeishPTM\STAT\6_173STATBR3.mzML
-
C:\LeishPTM\STAT\7_178STATBR4.mzML
-
C:\LeishPTM\STAT\8_275STATBR3.mzML
-
C:\LeishPTM\STAT\9_275STATBR4.mzML
71 commands to execute:
Workspace [Work dir: C:\LeishPTM\20190910_LeishPTManalysis\LOG]
C:\LeishPTM\philosopher_v1.5.1_windows_amd64\philosopher.exe workspace --clean
Workspace [Work dir: C:\LeishPTM\20190910_LeishPTManalysis\LOG]
C:\LeishPTM\philosopher_v1.5.1_windows_amd64\philosopher.exe workspace --init
Workspace [Work dir: C:\LeishPTM\20190910_LeishPTManalysis\STAT]
C:\LeishPTM\philosopher_v1.5.1_windows_amd64\philosopher.exe workspace --clean
Workspace [Work dir: C:\LeishPTM\20190910_LeishPTManalysis\STAT]
C:\LeishPTM\philosopher_v1.5.1_windows_amd64\philosopher.exe workspace --init
Workspace [Work dir: C:\LeishPTM\20190910_LeishPTManalysis]
C:\LeishPTM\philosopher_v1.5.1_windows_amd64\philosopher.exe workspace --clean
Workspace [Work dir: C:\LeishPTM\20190910_LeishPTManalysis]
C:\LeishPTM\philosopher_v1.5.1_windows_amd64\philosopher.exe workspace --init
MsFragger [Work dir: C:\LeishPTM\20190910_LeishPTManalysis]
java -jar -Dfile.encoding=UTF-8 -Xmx10G C:\LeishPTM\MSFragger-2.1.jar C:\LeishPTM\20190910_LeishPTManalysis\fragger.params C:\LeishPTM\LOG\14_173LOGBR2.mzML C:\LeishPTM\LOG\15_173LOGBR1.mzML C:\LeishPTM\LOG\16_178LOGBR1.mzML C:\LeishPTM\LOG\18_275LOGBR2.mzML C:\LeishPTM\LOG\1_275LOGBR1.mzML C:\LeishPTM\LOG\20_178LOGBR2.mzML C:\LeishPTM\LOG\48_178BR2.mzML C:\LeishPTM\LOG\49_275BR1.mzML C:\LeishPTM\LOG\53_173BR2.mzML C:\LeishPTM\LOG\55_178BR1.mzML C:\LeishPTM\LOG\59_173BR1.mzML C:\LeishPTM\LOG\61_275BR2.mzML C:\LeishPTM\STAT\10_178STATBR3.mzML C:\LeishPTM\STAT\11_275STATBR2.mzML C:\LeishPTM\STAT\12_178STATBR1.mzML C:\LeishPTM\STAT\17_275STATBR1.mzML C:\LeishPTM\STAT\2_173STATBR2.mzML C:\LeishPTM\STAT\3_173STATBR4.mzML C:\LeishPTM\STAT\4_173STATBR1.mzML C:\LeishPTM\STAT\5_178STATBR2.mzML C:\LeishPTM\STAT\6_173STATBR3.mzML C:\LeishPTM\STAT\7_178STATBR4.mzML C:\LeishPTM\STAT\8_275STATBR3.mzML C:\LeishPTM\STAT\9_275STATBR4.mzML
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove C:\LeishPTM\LOG\14_173LOGBR2.pepXML C:\LeishPTM\20190910_LeishPTManalysis\LOG\14_173LOGBR2.pepXML
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove --no-err C:\LeishPTM\LOG\14_173LOGBR2.tsv C:\LeishPTM\20190910_LeishPTManalysis\LOG\14_173LOGBR2.tsv
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove C:\LeishPTM\LOG\15_173LOGBR1.pepXML C:\LeishPTM\20190910_LeishPTManalysis\LOG\15_173LOGBR1.pepXML
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove --no-err C:\LeishPTM\LOG\15_173LOGBR1.tsv C:\LeishPTM\20190910_LeishPTManalysis\LOG\15_173LOGBR1.tsv
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove C:\LeishPTM\LOG\16_178LOGBR1.pepXML C:\LeishPTM\20190910_LeishPTManalysis\LOG\16_178LOGBR1.pepXML
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove --no-err C:\LeishPTM\LOG\16_178LOGBR1.tsv C:\LeishPTM\20190910_LeishPTManalysis\LOG\16_178LOGBR1.tsv
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove C:\LeishPTM\LOG\18_275LOGBR2.pepXML C:\LeishPTM\20190910_LeishPTManalysis\LOG\18_275LOGBR2.pepXML
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove --no-err C:\LeishPTM\LOG\18_275LOGBR2.tsv C:\LeishPTM\20190910_LeishPTManalysis\LOG\18_275LOGBR2.tsv
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove C:\LeishPTM\LOG\1_275LOGBR1.pepXML C:\LeishPTM\20190910_LeishPTManalysis\LOG\1_275LOGBR1.pepXML
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove --no-err C:\LeishPTM\LOG\1_275LOGBR1.tsv C:\LeishPTM\20190910_LeishPTManalysis\LOG\1_275LOGBR1.tsv
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove C:\LeishPTM\LOG\20_178LOGBR2.pepXML C:\LeishPTM\20190910_LeishPTManalysis\LOG\20_178LOGBR2.pepXML
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove --no-err C:\LeishPTM\LOG\20_178LOGBR2.tsv C:\LeishPTM\20190910_LeishPTManalysis\LOG\20_178LOGBR2.tsv
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove C:\LeishPTM\LOG\48_178BR2.pepXML C:\LeishPTM\20190910_LeishPTManalysis\LOG\48_178BR2.pepXML
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove --no-err C:\LeishPTM\LOG\48_178BR2.tsv C:\LeishPTM\20190910_LeishPTManalysis\LOG\48_178BR2.tsv
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove C:\LeishPTM\LOG\49_275BR1.pepXML C:\LeishPTM\20190910_LeishPTManalysis\LOG\49_275BR1.pepXML
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove --no-err C:\LeishPTM\LOG\49_275BR1.tsv C:\LeishPTM\20190910_LeishPTManalysis\LOG\49_275BR1.tsv
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove C:\LeishPTM\LOG\53_173BR2.pepXML C:\LeishPTM\20190910_LeishPTManalysis\LOG\53_173BR2.pepXML
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove --no-err C:\LeishPTM\LOG\53_173BR2.tsv C:\LeishPTM\20190910_LeishPTManalysis\LOG\53_173BR2.tsv
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove C:\LeishPTM\LOG\55_178BR1.pepXML C:\LeishPTM\20190910_LeishPTManalysis\LOG\55_178BR1.pepXML
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove --no-err C:\LeishPTM\LOG\55_178BR1.tsv C:\LeishPTM\20190910_LeishPTManalysis\LOG\55_178BR1.tsv
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove C:\LeishPTM\LOG\59_173BR1.pepXML C:\LeishPTM\20190910_LeishPTManalysis\LOG\59_173BR1.pepXML
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove --no-err C:\LeishPTM\LOG\59_173BR1.tsv C:\LeishPTM\20190910_LeishPTManalysis\LOG\59_173BR1.tsv
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove C:\LeishPTM\LOG\61_275BR2.pepXML C:\LeishPTM\20190910_LeishPTManalysis\LOG\61_275BR2.pepXML
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove --no-err C:\LeishPTM\LOG\61_275BR2.tsv C:\LeishPTM\20190910_LeishPTManalysis\LOG\61_275BR2.tsv
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove C:\LeishPTM\STAT\10_178STATBR3.pepXML C:\LeishPTM\20190910_LeishPTManalysis\STAT\10_178STATBR3.pepXML
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove --no-err C:\LeishPTM\STAT\10_178STATBR3.tsv C:\LeishPTM\20190910_LeishPTManalysis\STAT\10_178STATBR3.tsv
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove C:\LeishPTM\STAT\11_275STATBR2.pepXML C:\LeishPTM\20190910_LeishPTManalysis\STAT\11_275STATBR2.pepXML
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove --no-err C:\LeishPTM\STAT\11_275STATBR2.tsv C:\LeishPTM\20190910_LeishPTManalysis\STAT\11_275STATBR2.tsv
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove C:\LeishPTM\STAT\12_178STATBR1.pepXML C:\LeishPTM\20190910_LeishPTManalysis\STAT\12_178STATBR1.pepXML
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove --no-err C:\LeishPTM\STAT\12_178STATBR1.tsv C:\LeishPTM\20190910_LeishPTManalysis\STAT\12_178STATBR1.tsv
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove C:\LeishPTM\STAT\17_275STATBR1.pepXML C:\LeishPTM\20190910_LeishPTManalysis\STAT\17_275STATBR1.pepXML
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove --no-err C:\LeishPTM\STAT\17_275STATBR1.tsv C:\LeishPTM\20190910_LeishPTManalysis\STAT\17_275STATBR1.tsv
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove C:\LeishPTM\STAT\2_173STATBR2.pepXML C:\LeishPTM\20190910_LeishPTManalysis\STAT\2_173STATBR2.pepXML
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove --no-err C:\LeishPTM\STAT\2_173STATBR2.tsv C:\LeishPTM\20190910_LeishPTManalysis\STAT\2_173STATBR2.tsv
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove C:\LeishPTM\STAT\3_173STATBR4.pepXML C:\LeishPTM\20190910_LeishPTManalysis\STAT\3_173STATBR4.pepXML
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove --no-err C:\LeishPTM\STAT\3_173STATBR4.tsv C:\LeishPTM\20190910_LeishPTManalysis\STAT\3_173STATBR4.tsv
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove C:\LeishPTM\STAT\4_173STATBR1.pepXML C:\LeishPTM\20190910_LeishPTManalysis\STAT\4_173STATBR1.pepXML
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove --no-err C:\LeishPTM\STAT\4_173STATBR1.tsv C:\LeishPTM\20190910_LeishPTManalysis\STAT\4_173STATBR1.tsv
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove C:\LeishPTM\STAT\5_178STATBR2.pepXML C:\LeishPTM\20190910_LeishPTManalysis\STAT\5_178STATBR2.pepXML
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove --no-err C:\LeishPTM\STAT\5_178STATBR2.tsv C:\LeishPTM\20190910_LeishPTManalysis\STAT\5_178STATBR2.tsv
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove C:\LeishPTM\STAT\6_173STATBR3.pepXML C:\LeishPTM\20190910_LeishPTManalysis\STAT\6_173STATBR3.pepXML
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove --no-err C:\LeishPTM\STAT\6_173STATBR3.tsv C:\LeishPTM\20190910_LeishPTManalysis\STAT\6_173STATBR3.tsv
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove C:\LeishPTM\STAT\7_178STATBR4.pepXML C:\LeishPTM\20190910_LeishPTManalysis\STAT\7_178STATBR4.pepXML
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove --no-err C:\LeishPTM\STAT\7_178STATBR4.tsv C:\LeishPTM\20190910_LeishPTManalysis\STAT\7_178STATBR4.tsv
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove C:\LeishPTM\STAT\8_275STATBR3.pepXML C:\LeishPTM\20190910_LeishPTManalysis\STAT\8_275STATBR3.pepXML
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove --no-err C:\LeishPTM\STAT\8_275STATBR3.tsv C:\LeishPTM\20190910_LeishPTManalysis\STAT\8_275STATBR3.tsv
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove C:\LeishPTM\STAT\9_275STATBR4.pepXML C:\LeishPTM\20190910_LeishPTManalysis\STAT\9_275STATBR4.pepXML
MsFragger
java -cp C:\LeishPTM\FragPipe.exe umich.msfragger.util.FileMove --no-err C:\LeishPTM\STAT\9_275STATBR4.tsv C:\LeishPTM\20190910_LeishPTManalysis\STAT\9_275STATBR4.tsv
ReportDbAnnotate [Work dir: C:\LeishPTM\20190910_LeishPTManalysis\LOG]
C:\LeishPTM\philosopher_v1.5.1_windows_amd64\philosopher.exe database --annotate C:\LeishPTM\20190910_LeishPTManalysis\2019-09-11-td-LdPBQ7G3I2I82018.protein.fa --prefix rev
ReportDbAnnotate [Work dir: C:\LeishPTM\20190910_LeishPTManalysis\STAT]
C:\LeishPTM\philosopher_v1.5.1_windows_amd64\philosopher.exe database --annotate C:\LeishPTM\20190910_LeishPTManalysis\2019-09-11-td-LdPBQ7G3I2I82018.protein.fa --prefix rev
ReportDbAnnotate [Work dir: C:\LeishPTM\20190910_LeishPTManalysis]
C:\LeishPTM\philosopher_v1.5.1_windows_amd64\philosopher.exe database --annotate C:\LeishPTM\20190910_LeishPTManalysis\2019-09-11-td-LdPBQ7G3I2I82018.protein.fa --prefix rev
PeptideProphet [Work dir: C:\LeishPTM\20190910_LeishPTManalysis\STAT]
C:\LeishPTM\philosopher_v1.5.1_windowsamd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --minprob 0.95 --decoy rev --database C:\LeishPTM\20190910_LeishPTManalysis\2019-09-11-td-LdPBQ7G3I2I8_2018.protein.fa --combine 10_178STATBR3.pepXML 11_275STATBR2.pepXML 12_178STATBR1.pepXML 6_173STATBR3.pepXML 5_178STATBR2.pepXML 17_275STATBR1.pepXML 2_173STATBR2.pepXML 3_173STATBR4.pepXML 9_275STATBR4.pepXML 4_173STATBR1.pepXML 8_275STATBR3.pepXML 7_178STATBR4.pepXML
PeptideProphet [Work dir: C:\LeishPTM\20190910_LeishPTManalysis\LOG]
C:\LeishPTM\philosopher_v1.5.1_windowsamd64\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --minprob 0.95 --decoy rev --database C:\LeishPTM\20190910_LeishPTManalysis\2019-09-11-td-LdPBQ7G3I2I8_2018.protein.fa --combine 61_275BR2.pepXML 49_275BR1.pepXML 18_275LOGBR2.pepXML 20_178LOGBR2.pepXML 16_178LOGBR1.pepXML 1_275LOGBR1.pepXML 59_173BR1.pepXML 53_173BR2.pepXML 15_173LOGBR1.pepXML 55_178BR1.pepXML 14_173LOGBR2.pepXML 48_178BR2.pepXML
ProteinProphet [Work dir: C:\LeishPTM\20190910_LeishPTManalysis]
C:\LeishPTM\philosopher_v1.5.1_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined C:\LeishPTM\20190910_LeishPTManalysis\STAT\interact.pep.xml C:\LeishPTM\20190910_LeishPTManalysis\LOG\interact.pep.xml
ReportFilter [Work dir: C:\LeishPTM\20190910_LeishPTManalysis\LOG]
C:\LeishPTM\philosopher_v1.5.1_windowsamd64\philosopher.exe filter --sequential --razor --mapmods --prot 0.01 --tag rev --pepxml C:\LeishPTM\20190910_LeishPTManalysis\LOG --protxml C:\LeishPTM\20190910_LeishPTManalysis\combined.prot.xml
ReportFilter [Work dir: C:\LeishPTM\20190910_LeishPTManalysis\STAT]
C:\LeishPTM\philosopher_v1.5.1_windowsamd64\philosopher.exe filter --sequential --razor --mapmods --prot 0.01 --tag rev --pepxml C:\LeishPTM\20190910_LeishPTManalysis\STAT --protxml C:\LeishPTM\20190910_LeishPTManalysis\combined.prot.xml
Freequant [Work dir: C:\LeishPTM\20190910_LeishPTManalysis\LOG]
C:\LeishPTM\philosopher_v1.5.1_windows_amd64\philosopher.exe freequant --ptw 0.4 --tol 10 --isolated --dir C:\LeishPTM\LOG
Freequant [Work dir: C:\LeishPTM\20190910_LeishPTManalysis\STAT]
C:\LeishPTM\philosopher_v1.5.1_windows_amd64\philosopher.exe freequant --ptw 0.4 --tol 10 --isolated --dir C:\LeishPTM\STAT
ReportReport [Work dir: C:\LeishPTM\20190910_LeishPTManalysis\LOG]
C:\LeishPTM\philosopher_v1.5.1_windows_amd64\philosopher.exe report
ReportReport [Work dir: C:\LeishPTM\20190910_LeishPTManalysis\STAT]
C:\LeishPTM\philosopher_v1.5.1_windows_amd64\philosopher.exe report
PTMShepherd [Work dir: C:\LeishPTM\20190910_LeishPTManalysis]
java -Xmx10G -Xmx10G -cp "C:\Users\cuype\AppData\Local\Temp\fragpipe\batmass-io-1.16.1.jar;C:\Users\cuype\AppData\Local\Temp\fragpipe\commons-math3-3.6.1.jar;C:\Users\cuype\AppData\Local\Temp\fragpipe\ptmshepherd-0.2.2.jar" edu.umich.andykong.ptmshepherd.PTMShepherd C:\LeishPTM\20190910_LeishPTManalysis\shepherd.config
Workspace [Work dir: C:\LeishPTM\20190910_LeishPTManalysis\LOG]
C:\LeishPTM\philosopher_v1.5.1_windows_amd64\philosopher.exe workspace --clean
Workspace [Work dir: C:\LeishPTM\20190910_LeishPTManalysis\STAT]
C:\LeishPTM\philosopher_v1.5.1_windows_amd64\philosopher.exe workspace --clean
Workspace [Work dir: C:\LeishPTM\20190910_LeishPTManalysis]
C:\LeishPTM\philosopher_v1.5.1_windows_amd64\philosopher.exe workspace --clean
~~~~~~~~~ fragpipe.config ~~~~~~~~~
#FragPipe (10.1) runtime properties
#Wed Sep 11 00:05:57 CEST 2019
override_charge=false
ui.name.report.check.genspeclib=false
calibrate_mass=On and find optimal parameters
search_enzyme_butnotafter=P
max_variable_mods_per_mod=3
delta_mass_exclude_ranges=(-1.5,3.5)
output_report_topN=1
misc.fragger.remove-precursor-range-hi=1.5
misc.slice-db=1
output_format=PEP_XML
ui.name.downstream.check.run-pep-proph=true
histo_smoothbins=3
peakpicking_width=0.002
ui.name.report.check.dontuseprotprophfile=false
misc.fragger.precursor-charge-hi=4
ui.name.report.check.multiexp=false
misc.fragger.digest-mass-lo=500
min_fragments_modelling=3
ui.name.report.check.printdecoys=false
allowed_missed_cleavage=1
search_enzyme_cutafter=KR
precursor_mass_lower=-150
misc.fragger.clear-mz-hi=0
peakpicking_promRatio=0.3
misc.fragger.remove-precursor-range-lo=-1.5
fragment_mass_units=PPM
num_enzyme_termini=ENZYMATIC
ui.name.report.text.filter=--sequential --razor --mapmods --prot 0.01
ui.name.report.check.labelfree=true
min_matched_fragments=5
max_fragment_charge=2
misc.fragger.precursor-charge-lo=1
ui.name.downstream.text.pep-proph-cmd=--nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --minprob 0.95
ui.name.downstream.check.separate-protxml=false
intensity_transform=None
add_topN_complementary=0
num_threads=8
output_max_expect=50
use_topN_peaks=100
remove_precursor_peak=Do not remove
zero_bin_mult_expect=1.00
allow_multiple_variable_mods_on_residue=true
precursor_mass_mode=selected
ui.name.report.check.mzid=false
precursor_mass_units=ABS
mass_offsets=0
misc.ram=10
digest_min_length=7
zero_bin_accept_expect=0.00
minimum_peaks=15
digest_max_length=50
misc.fragger.clear-mz-lo=0
track_zero_topN=0
precursor_true_units=PPM
ui.name.downstream.check.combine-pepxml=true
localize_delta_mass=true
ui.name.downstream.check.run-crystalc=false
max_variable_mods_combinations=5000
ui.name.downstream.check.run-prot-proph=true
search_enzyme_name=Trypsin
clip_nTerm_M=true
ui.name.report.run-shepherd=true
ion_series_definitions=
ui.name.downstream.text.prot-proph-cmd=--maxppmdiff 2000000
fragment_ion_series=b,y
ui.name.report.text.labelfree=--ptw 0.4 --tol 10 --isolated
precursor_true_tolerance=20
precursor_mass_upper=500
report_alternative_proteins=true
isotope_error=0
misc.fragger.digest-mass-hi=5000
fragment_mass_tolerance=20
minimum_ratio=0.01
Workspace [Work dir: C:\LeishPTM\20190910_LeishPTManalysis\LOG]
C:\LeishPTM\philosopher_v1.5.1_windows_amd64\philosopher.exe workspace --clean
INFO[00:05:57] Executing Workspace v1.5.1
INFO[00:05:58] Removing workspace
INFO[00:05:58] Done
Process 'Workspace' finished, exit code: 0
Workspace [Work dir: C:\LeishPTM\20190910_LeishPTManalysis\LOG]
C:\LeishPTM\philosopher_v1.5.1_windows_amd64\philosopher.exe workspace --init
INFO[00:05:58] Executing Workspace v1.5.1
INFO[00:05:59] Creating workspace
INFO[00:05:59] Done
Process 'Workspace' finished, exit code: 0
Workspace [Work dir: C:\LeishPTM\20190910_LeishPTManalysis\STAT]
C:\LeishPTM\philosopher_v1.5.1_windows_amd64\philosopher.exe workspace --clean
INFO[00:05:59] Executing Workspace v1.5.1
INFO[00:05:59] Removing workspace
INFO[00:05:59] Done
Process 'Workspace' finished, exit code: 0
Workspace [Work dir: C:\LeishPTM\20190910_LeishPTManalysis\STAT]
C:\LeishPTM\philosopher_v1.5.1_windows_amd64\philosopher.exe workspace --init
INFO[00:06:00] Executing Workspace v1.5.1
INFO[00:06:00] Creating workspace
INFO[00:06:00] Done
Process 'Workspace' finished, exit code: 0
Workspace [Work dir: C:\LeishPTM\20190910_LeishPTManalysis]
C:\LeishPTM\philosopher_v1.5.1_windows_amd64\philosopher.exe workspace --clean
INFO[00:06:01] Executing Workspace v1.5.1
INFO[00:06:01] Removing workspace
INFO[00:06:01] Done
Process 'Workspace' finished, exit code: 0
Workspace [Work dir: C:\LeishPTM\20190910_LeishPTManalysis]
C:\LeishPTM\philosopher_v1.5.1_windows_amd64\philosopher.exe workspace --init
INFO[00:06:02] Executing Workspace v1.5.1
INFO[00:06:02] Creating workspace
INFO[00:06:02] Done
Process 'Workspace' finished, exit code: 0
MsFragger [Work dir: C:\LeishPTM\20190910_LeishPTManalysis]
java -jar -Dfile.encoding=UTF-8 -Xmx10G C:\LeishPTM\MSFragger-2.1.jar C:\LeishPTM\20190910_LeishPTManalysis\fragger.params C:\LeishPTM\LOG\14_173LOGBR2.mzML C:\LeishPTM\LOG\15_173LOGBR1.mzML C:\LeishPTM\LOG\16_178LOGBR1.mzML C:\LeishPTM\LOG\18_275LOGBR2.mzML C:\LeishPTM\LOG\1_275LOGBR1.mzML C:\LeishPTM\LOG\20_178LOGBR2.mzML C:\LeishPTM\LOG\48_178BR2.mzML C:\LeishPTM\LOG\49_275BR1.mzML C:\LeishPTM\LOG\53_173BR2.mzML C:\LeishPTM\LOG\55_178BR1.mzML C:\LeishPTM\LOG\59_173BR1.mzML C:\LeishPTM\LOG\61_275BR2.mzML C:\LeishPTM\STAT\10_178STATBR3.mzML C:\LeishPTM\STAT\11_275STATBR2.mzML C:\LeishPTM\STAT\12_178STATBR1.mzML C:\LeishPTM\STAT\17_275STATBR1.mzML C:\LeishPTM\STAT\2_173STATBR2.mzML C:\LeishPTM\STAT\3_173STATBR4.mzML C:\LeishPTM\STAT\4_173STATBR1.mzML C:\LeishPTM\STAT\5_178STATBR2.mzML C:\LeishPTM\STAT\6_173STATBR3.mzML C:\LeishPTM\STAT\7_178STATBR4.mzML C:\LeishPTM\STAT\8_275STATBR3.mzML C:\LeishPTM\STAT\9_275STATBR4.mzML
MSFragger version MSFragger-2.1
Batmass-IO version 1.16.1
(c) University of Michigan
RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved.
System OS: Windows 10, Architecture: AMD64
Java Info: 1.8.0_211, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
JVM started with 9102 MB memory
***FIRST SEARCH****
Parameters:
num_threads = 8
database_name = C:\LeishPTM\20190910_LeishPTManalysis\2019-09-11-td-LdPBQ7G3I2I8_2018.protein.fa
decoyprefix = rev
precursor_mass_lower = -20.0
precursor_mass_upper = 20.0
precursor_mass_units = 1
precursor_true_tolerance = 20.0
precursor_true_units = 1
fragment_mass_tolerance = 20.0
fragment_mass_units = 1
calibrate_mass = 2
evaluate_mass_calibration = false
isotope_error = 0/1
mass_offsets = 0
precursor_mass_mode = SELECTED
localize_delta_mass = false
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
search_enzyme_name = Trypsin
search_enzyme_cutafter = KR
search_enzyme_butnotafter = P
num_enzyme_termini = 2
allowed_missed_cleavage = 1
clip_nTerm_M = true
allow_multiple_variable_mods_on_residue = false
max_variable_mods_per_mod = 3
max_variable_mods_combinations = 5000
output_file_extension = pepXML
output_format = pepXML
output_report_topN = 1
output_max_expect = 50.0
report_alternative_proteins = false
override_charge = false
precursor_charge_low = 1
precursor_charge_high = 4
digest_min_length = 7
digest_max_length = 50
digest_mass_range_low = 500.0
digest_mass_range_high = 5000.0
max_fragment_charge = 2
track_zero_topN = 0
zero_bin_accept_expect = 0.0
zero_bin_mult_expect = 1.0
add_topN_complementary = 0
minimum_peaks = 15
use_topN_peaks = 100
minIonsScoring = 3
min_matched_fragments = 5
minimum_ratio = 0.01
intensity_transform = 0
remove_precursor_peak = 0
remove_precursor_range = -1.50,1.50
clear_mz_range_low = 0.0
clear_mz_range_high = 0.0
excluded_scan_list_file =
variable_mod_01 = 15.99490 M
variable_mod_02 = 42.01060 [^
Selected fragment tolerance 0.10 Da and maximum fragment slice size of 6.29 GB.
79893140 fragments to be searched in 1 slices (1.19 GB total)
Operating on slice 1 of 1:
001. 14_173LOGBR2.mzML 10.9 s
001. 14_173LOGBR2.mzML 10.9 s [progress: 34706/34706 (100.00%) - 8698.25 spectra/s] - completed 4.0 s
002. 15_173LOGBR1.mzML 8.3 s
002. 15_173LOGBR1.mzML 8.3 s [progress: 34957/34957 (100.00%) - 10802.53 spectra/s] - completed 3.2 s
003. 16_178LOGBR1.mzML 8.3 s
003. 16_178LOGBR1.mzML 8.3 s [progress: 36774/36774 (100.00%) - 8417.03 spectra/s] - completed 4.4 s
004. 18_275LOGBR2.mzML 6.9 s
004. 18_275LOGBR2.mzML 6.9 s [progress: 34164/34164 (100.00%) - 10415.85 spectra/s] - completed 3.3 s
005. 1_275LOGBR1.mzML 9.3 s
005. 1_275LOGBR1.mzML 9.3 s [progress: 35329/37227 (94.90%) - 7018.08 spectra/s]
005. 1_275LOGBR1.mzML 9.3 s [progress: 37227/37227 (100.00%) - 7086.81 spectra/s] - completed 5.3 s
006. 20_178LOGBR2.mzML 7.9 s
006. 20_178LOGBR2.mzML 7.9 s [progress: 35059/35059 (100.00%) - 7606.64 spectra/s] - completed 4.6 s
007. 48_178BR2.mzML 8.4 s
007. 48_178BR2.mzML 8.4 s [progress: 34249/34249 (100.00%) - 8238.87 spectra/s] - completed 4.2 s
008. 49_275BR1.mzML 8.0 s
008. 49_275BR1.mzML 8.0 s [progress: 33583/33583 (100.00%) - 9430.78 spectra/s] - completed 3.6 s
009. 53_173BR2.mzML 8.2 s
009. 53_173BR2.mzML 8.2 s [progress: 32117/32117 (100.00%) - 6699.42 spectra/s] - completed 4.8 s
010. 55_178BR1.mzML 7.6 s
010. 55_178BR1.mzML 7.6 s [progress: 31561/31561 (100.00%) - 7858.81 spectra/s] - completed 4.0 s
011. 59_173BR1.mzML 9.4 s
011. 59_173BR1.mzML 9.4 s [progress: 34480/34480 (100.00%) - 7018.12 spectra/s] - completed 4.9 s
012. 61_275BR2.mzML 9.5 s
012. 61_275BR2.mzML 9.5 s [progress: 33540/33540 (100.00%) - 7666.29 spectra/s] - completed 4.4 s
013. 10_178STATBR3.mzML 7.2 s
013. 10_178STATBR3.mzML 7.2 s [progress: 31987/31987 (100.00%) - 11904.35 spectra/s] - completed 2.7 s
014. 11_275STATBR2.mzML 9.3 s
014. 11_275STATBR2.mzML 9.3 s [progress: 34238/36940 (92.69%) - 6844.86 spectra/s]
014. 11_275STATBR2.mzML 9.3 s [progress: 36940/36940 (100.00%) - 7075.27 spectra/s] - completed 5.2 s
015. 12_178STATBR1.mzML 8.2 s
015. 12_178STATBR1.mzML 8.2 s [progress: 34744/34744 (100.00%) - 8424.83 spectra/s] - completed 4.1 s
016. 17_275STATBR1.mzML 6.9 s
016. 17_275STATBR1.mzML 6.9 s [progress: 31167/31167 (100.00%) - 11056.05 spectra/s] - completed 2.8 s
017. 2_173STATBR2.mzML 7.5 s
017. 2_173STATBR2.mzML 7.5 s [progress: 35496/35496 (100.00%) - 9821.80 spectra/s] - completed 3.6 s
018. 3_173STATBR4.mzML 8.2 s
018. 3_173STATBR4.mzML 8.2 s [progress: 36127/36127 (100.00%) - 8880.78 spectra/s] - completed 4.1 s
019. 4_173STATBR1.mzML 7.5 s
019. 4_173STATBR1.mzML 7.5 s [progress: 40199/40199 (100.00%) - 8995.08 spectra/s] - completed 4.5 s
020. 5_178STATBR2.mzML 7.4 s
020. 5_178STATBR2.mzML 7.4 s [progress: 33832/33832 (100.00%) - 9766.74 spectra/s] - completed 3.5 s
021. 6_173STATBR3.mzML 9.2 s
021. 6_173STATBR3.mzML 9.2 s [progress: 24108/36598 (65.87%) - 4777.65 spectra/s]
021. 6_173STATBR3.mzML 9.2 s [progress: 36598/36598 (100.00%) - 6315.44 spectra/s] - completed 5.8 s
022. 7_178STATBR4.mzML 8.3 s
022. 7_178STATBR4.mzML 8.3 s [progress: 35608/35608 (100.00%) - 8897.55 spectra/s] - completed 4.0 s
023. 8_275STATBR3.mzML 8.8 s
023. 8_275STATBR3.mzML 8.8 s [progress: 30628/38496 (79.56%) - 5975.03 spectra/s]
023. 8_275STATBR3.mzML 8.8 s [progress: 38496/38496 (100.00%) - 6747.77 spectra/s] - completed 5.7 s
024. 9_275STATBR4.mzML 8.6 s
024. 9_275STATBR4.mzML 8.6 s [progress: 34662/34662 (100.00%) - 8338.22 spectra/s] - completed 4.2 s***FIRST SEARCH DONE IN 5.071 MIN**
*****MASS CALIBRATION**
-----|---------------|---------------|---------------|---------------
| MS1 (Old) | MS1 (New) | MS2 (Old) | MS2 (New)-----|---------------|---------------|---------------|---------------
Run | Median MAD | Median MAD | Median MAD | Median MAD
001 | -0.18 1.38 | 0.07 1.21 | -0.12 4.89 | -0.04 4.79
002 | -0.15 1.17 | -0.06 1.12 | -0.29 4.84 | -0.24 4.83
003 | -0.13 1.32 | 0.10 1.28 | -0.82 4.90 | -0.73 4.81
004 | -0.14 1.21 | -0.00 1.20 | 0.49 5.02 | 0.33 4.98
005 | -0.06 1.28 | 0.03 1.25 | -0.08 4.99 | -0.03 4.91
006 | -0.12 1.16 | -0.08 1.20 | -0.55 4.85 | -0.35 4.83
007 | -0.11 1.16 | -0.02 1.19 | 0.54 5.11 | 0.38 5.13
008 | -0.15 1.16 | -0.01 1.16 | 0.27 4.88 | 0.17 4.86
009 | -0.19 1.27 | -0.02 1.22 | -1.25 5.25 | -0.85 5.24
010 | -0.27 1.22 | -0.05 1.19 | 0.49 4.78 | 0.32 4.78
011 | -0.13 1.22 | 0.04 1.21 | -0.56 4.79 | -0.41 4.79
012 | -0.18 1.29 | -0.01 1.15 | 0.49 4.80 | 0.33 4.78
013 | -0.17 1.38 | 0.03 1.26 | -0.12 4.84 | -0.08 4.91
014 | -0.04 1.49 | -0.13 1.21 | -0.67 5.26 | -0.47 5.13
015 | -0.18 1.28 | 0.01 1.22 | -0.74 4.86 | -0.55 4.90
016 | -0.14 1.18 | -0.03 1.19 | -0.25 4.77 | -0.14 4.81
017 | -0.21 1.36 | 0.10 1.25 | 0.42 4.77 | 0.32 4.77
018 | -0.15 1.23 | -0.09 1.23 | -1.39 5.03 | -0.97 4.97
019 | -0.05 1.16 | -0.02 1.27 | -0.97 5.26 | -0.69 5.19
020 | -0.14 1.32 | 0.06 1.21 | -0.21 4.93 | -0.15 4.95
021 | -0.08 1.37 | 0.13 1.30 | -1.42 5.28 | -1.18 5.14
022 | -0.18 1.35 | -0.03 1.26 | -0.12 5.15 | -0.03 5.15
023 | -0.15 1.45 | -0.08 1.24 | -1.01 5.91 | -0.76 5.73
024 | -0.23 1.28 | -0.03 1.20 | 0.30 4.58 | 0.17 4.58
-----|---------------|---------------|---------------|---------------
Finding the optimal parameters:
-------|-------|-------|-------|-------|-------|-------
MS2 | 7 | 10 | 15 | 20 | 25 | 30
-------|-------|-------|-------|-------|-------|-------
Count | 156786| 190045| 201712| 197418| 188864| 128582
-------|-------|-------|-------|-------|-------|-------
-------|-------|-------|-------|-------|-------
Peaks | 100_1 | 125_1 | 150_1 | 175_0 | 200_0
-------|-------|-------|-------|-------|-------
Count | 201712| 206033| 210196| 213959| 216666
-------|-------|-------|-------|-------|-------
New precursor_true_tolerance = 8.000000 PPM
New fragment_mass_tolerance = 15 PPM
New use_topN_peaks = 200
New minimum_ratio = 0.000000
**MASS CALIBRATION DONE IN 54.689 MIN***
****MAIN SEARCH****
Parameters:
num_threads = 8
database_name = C:\LeishPTM\20190910_LeishPTManalysis\2019-09-11-td-LdPBQ7G3I2I8_2018.protein.fa
decoyprefix = rev
precursor_mass_lower = -150.0
precursor_mass_upper = 500.0
precursor_mass_units = 0
precursor_true_tolerance = 8.0
precursor_true_units = 1
fragment_mass_tolerance = 15.0
fragment_mass_units = 1
calibrate_mass = 2
evaluate_mass_calibration = false
isotope_error = 0
mass_offsets = 0
precursor_mass_mode = SELECTED
localize_delta_mass = true
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
search_enzyme_name = Trypsin
search_enzyme_cutafter = KR
search_enzyme_butnotafter = P
num_enzyme_termini = 2
allowed_missed_cleavage = 1
clip_nTerm_M = true
allow_multiple_variable_mods_on_residue = true
max_variable_mods_per_mod = 3
max_variable_mods_combinations = 5000
output_file_extension = pepXML
output_format = pepXML
output_report_topN = 1
output_max_expect = 50.0
report_alternative_proteins = true
override_charge = false
precursor_charge_low = 1
precursor_charge_high = 4
digest_min_length = 7
digest_max_length = 50
digest_mass_range_low = 500.0
digest_mass_range_high = 5000.0
max_fragment_charge = 2
track_zero_topN = 0
zero_bin_accept_expect = 0.0
zero_bin_mult_expect = 1.0
add_topN_complementary = 0
minimum_peaks = 15
use_topN_peaks = 200
minIonsScoring = 3
min_matched_fragments = 5
minimum_ratio = 0.0
intensity_transform = 0
remove_precursor_peak = 0
remove_precursor_range = -1.50,1.50
clear_mz_range_low = 0.0
clear_mz_range_high = 0.0
excluded_scan_list_file =
variable_mod_01 = 15.99490 M
variable_mod_02 = 42.01060 [^
Number of unique peptides
of length 7: 94961
of length 8: 88223
of length 9: 80988
of length 10: 75255
of length 11: 71776
of length 12: 66203
of length 13: 60785
of length 14: 56922
of length 15: 52735
of length 16: 49724
of length 17: 46342
of length 18: 42893
of length 19: 40025
of length 20: 37860
of length 21: 35186
of length 22: 33166
of length 23: 30602
of length 24: 28780
of length 25: 26812
of length 26: 24823
of length 27: 22895
of length 28: 21644
of length 29: 20345
of length 30: 18880
of length 31: 17446
of length 32: 16216
of length 33: 14907
of length 34: 13902
of length 35: 13009
of length 36: 12200
of length 37: 11341
of length 38: 9914
of length 39: 9649
of length 40: 8822
of length 41: 8210
of length 42: 7473
of length 43: 6979
of length 44: 6303
of length 45: 5159
of length 46: 4218
of length 47: 3130
of length 48: 2278
of length 49: 1537
of length 50: 965In total 1301483 peptides.
Generated 2066017 modified peptides.
Selected fragment tolerance 0.01 Da and maximum fragment slice size of 7.05 GB.
160986052 fragments to be searched in 1 slices (2.40 GB total)
Operating on slice 1 of 1:
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 138/34667 (0.40%) - 27.10 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 830/34667 (2.39%) - 82.12 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 1958/34667 (5.65%) - 129.22 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 2941/34667 (8.48%) - 145.16 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 3816/34667 (11.01%) - 150.42 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 4461/34667 (12.87%) - 146.52 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 5100/34667 (14.71%) - 143.76 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 5754/34667 (16.60%) - 141.84 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 6422/34667 (18.52%) - 140.79 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 7174/34667 (20.69%) - 141.70 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 7977/34667 (23.01%) - 143.08 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 8789/34667 (25.35%) - 144.45 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 9575/34667 (27.62%) - 145.11 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 10347/34667 (29.85%) - 145.67 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 11119/34667 (32.07%) - 146.07 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 11882/34667 (34.27%) - 146.30 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 12632/34667 (36.44%) - 146.39 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 13377/34667 (38.59%) - 146.51 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 14128/34667 (40.75%) - 146.58 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 14856/34667 (42.85%) - 146.45 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 15566/34667 (44.90%) - 146.09 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 16338/34667 (47.13%) - 146.40 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 17174/34667 (49.54%) - 147.26 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 18089/34667 (52.18%) - 148.67 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 19016/34667 (54.85%) - 150.01 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 19932/34667 (57.50%) - 151.15 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 20884/34667 (60.24%) - 152.44 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 21839/34667 (63.00%) - 153.73 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 22840/34667 (65.88%) - 155.17 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 23899/34667 (68.94%) - 156.91 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 24725/34667 (71.32%) - 157.05 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 25706/34667 (74.15%) - 158.18 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 26885/34667 (77.55%) - 160.37 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 29547/34667 (85.23%) - 171.08 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 34639/34667 (99.92%) - 194.80 spectra/s]
001. 14_173LOGBR2.mzBIN_calibrated 5.9 s [progress: 34667/34667 (100.00%) - 194.84 spectra/s] - completed 177.9 s
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 1692/34910 (4.85%) - 330.21 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 2705/34910 (7.75%) - 264.37 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 3633/34910 (10.41%) - 237.56 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 4576/34910 (13.11%) - 224.64 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 5471/34910 (15.67%) - 215.12 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 6368/34910 (18.24%) - 208.51 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 7233/34910 (20.72%) - 203.26 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 8094/34910 (23.19%) - 198.90 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 9064/34910 (25.96%) - 198.30 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 10023/34910 (28.71%) - 197.42 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 10977/34910 (31.44%) - 196.56 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 11953/34910 (34.24%) - 196.35 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 12968/34910 (37.15%) - 196.48 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 13949/34910 (39.96%) - 196.42 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 14939/34910 (42.79%) - 196.25 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 15832/34910 (45.35%) - 195.09 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 16638/34910 (47.66%) - 193.05 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 17403/34910 (49.85%) - 190.67 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 18195/34910 (52.12%) - 188.93 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 18962/34910 (54.32%) - 187.15 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 19751/34910 (56.58%) - 185.63 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 20504/34910 (58.73%) - 184.04 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 21289/34910 (60.98%) - 182.85 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 22083/34910 (63.26%) - 181.84 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 22891/34910 (65.57%) - 180.93 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 23689/34910 (67.86%) - 180.08 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 24558/34910 (70.35%) - 179.77 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 25475/34910 (72.97%) - 179.88 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 26393/34910 (75.60%) - 179.93 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 27499/34910 (78.77%) - 181.16 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 29845/34910 (85.49%) - 190.27 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 33957/34910 (97.27%) - 209.78 spectra/s]
002. 15_173LOGBR1.mzBIN_calibrated 5.8 s [progress: 34910/34910 (100.00%) - 213.79 spectra/s] - completed 163.3 s
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 1663/36732 (4.53%) - 327.56 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 2741/36732 (7.46%) - 269.52 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 3827/36732 (10.42%) - 251.26 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 4890/36732 (13.31%) - 240.24 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 5925/36732 (16.13%) - 232.41 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 6945/36732 (18.91%) - 227.29 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 7922/36732 (21.57%) - 222.04 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 8722/36732 (23.74%) - 213.76 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 9541/36732 (25.97%) - 207.88 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 10324/36732 (28.11%) - 202.79 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 11118/36732 (30.27%) - 198.58 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 11903/36732 (32.40%) - 194.98 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 12674/36732 (34.50%) - 191.85 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 13427/36732 (36.55%) - 188.58 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 14187/36732 (38.62%) - 185.87 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 14937/36732 (40.66%) - 183.56 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 15706/36732 (42.76%) - 181.71 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 16478/36732 (44.86%) - 180.16 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 17248/36732 (46.96%) - 178.69 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 17984/36732 (48.96%) - 176.98 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 18770/36732 (51.10%) - 175.85 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 19539/36732 (53.19%) - 174.72 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 20325/36732 (55.33%) - 173.90 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 21102/36732 (57.45%) - 173.10 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 21908/36732 (59.64%) - 172.46 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 22683/36732 (61.75%) - 171.78 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 23527/36732 (64.05%) - 171.54 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 24369/36732 (66.34%) - 171.39 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 25285/36732 (68.84%) - 171.75 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 26253/36732 (71.47%) - 172.44 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 27214/36732 (74.09%) - 173.05 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 28366/36732 (77.22%) - 174.67 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 31897/36732 (86.84%) - 190.40 spectra/s]
003. 16_178LOGBR1.mzBIN_calibrated 6.6 s [progress: 36732/36732 (100.00%) - 213.10 spectra/s] - completed 172.4 s
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 1755/34115 (5.14%) - 341.44 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 2887/34115 (8.46%) - 283.87 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 3924/34115 (11.50%) - 257.36 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 4916/34115 (14.41%) - 242.26 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 5916/34115 (17.34%) - 233.05 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 6793/34115 (19.91%) - 223.12 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 7681/34115 (22.52%) - 216.41 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 8562/34115 (25.10%) - 211.21 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 9386/34115 (27.51%) - 205.63 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 10225/34115 (29.97%) - 201.53 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 11046/34115 (32.38%) - 198.12 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 11877/34115 (34.81%) - 195.20 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 12699/34115 (37.22%) - 192.77 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 13501/34115 (39.57%) - 190.37 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 14311/34115 (41.95%) - 188.46 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 15155/34115 (44.42%) - 187.00 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 15996/34115 (46.89%) - 185.67 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 16797/34115 (49.24%) - 184.18 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 17615/34115 (51.63%) - 183.00 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 18422/34115 (54.00%) - 181.88 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 19281/34115 (56.52%) - 181.27 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 20137/34115 (59.03%) - 180.74 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 21031/34115 (61.65%) - 180.49 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 21857/34115 (64.07%) - 179.75 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 22771/34115 (66.75%) - 179.78 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 23681/34115 (69.42%) - 179.83 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 24602/34115 (72.11%) - 179.80 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 25597/34115 (75.03%) - 180.38 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 26771/34115 (78.47%) - 182.18 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 28450/34115 (83.39%) - 187.08 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 30826/34115 (90.36%) - 196.23 spectra/s]
004. 18_275LOGBR2.mzBIN_calibrated 5.2 s [progress: 34115/34115 (100.00%) - 212.85 spectra/s] - completed 160.3 s
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 1445/37183 (3.89%) - 285.52 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 2372/37183 (6.38%) - 233.26 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 3200/37183 (8.61%) - 209.89 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 3998/37183 (10.75%) - 196.72 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 4842/37183 (13.02%) - 190.86 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 5670/37183 (15.25%) - 186.62 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 6541/37183 (17.59%) - 184.46 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 7441/37183 (20.01%) - 183.28 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 8324/37183 (22.39%) - 182.42 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 9196/37183 (24.73%) - 181.58 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 10117/37183 (27.21%) - 181.57 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 11000/37183 (29.58%) - 180.93 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 11882/37183 (31.96%) - 180.29 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 12752/37183 (34.30%) - 179.81 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 13595/37183 (36.56%) - 178.78 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 14479/37183 (38.94%) - 178.45 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 15342/37183 (41.26%) - 178.08 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 16201/37183 (43.57%) - 177.53 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 17040/37183 (45.83%) - 176.91 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 17821/37183 (47.93%) - 175.70 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 18551/37183 (49.89%) - 174.18 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 19291/37183 (51.88%) - 172.81 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 20003/37183 (53.80%) - 171.49 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 20682/37183 (55.62%) - 169.94 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 21375/37183 (57.49%) - 168.60 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 22105/37183 (59.45%) - 167.58 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 22822/37183 (61.38%) - 166.55 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 23518/37183 (63.25%) - 165.55 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 24254/37183 (65.23%) - 164.86 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 25060/37183 (67.40%) - 164.70 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 25864/37183 (69.56%) - 164.45 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 26636/37183 (71.63%) - 164.11 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 27527/37183 (74.03%) - 164.50 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 28495/37183 (76.63%) - 165.23 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 30595/37183 (82.28%) - 172.29 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 34901/37183 (93.86%) - 191.06 spectra/s]
005. 1_275LOGBR1.mzBIN_calibrated 7.0 s [progress: 37183/37183 (100.00%) - 199.51 spectra/s] - completed 186.4 s
006. 20_178LOGBR2.mzBIN_calibrated 5.9 s
006. 20_178LOGBR2.mzBIN_calibrated 5.9 s [progress: 1720/35020 (4.91%) - 337.72 spectra/s]
006. 20_178LOGBR2.mzBIN_calibrated 5.9 s [progress: 2804/35020 (8.01%) - 276.56 spectra/s]
006. 20_178LOGBR2.mzBIN_calibrated 5.9 s [progress: 3833/35020 (10.95%) - 252.17 spectra/s]
006. 20_178LOGBR2.mzBIN_calibrated 5.9 s [progress: 4893/35020 (13.97%) - 240.75 spectra/s]
006. 20_178LOGBR2.mzBIN_calibrated 5.9 s [progress: 5905/35020 (16.86%) - 232.62 spectra/s]
006. 20_178LOGBR2.mzBIN_calibrated 5.9 s [progress: 6937/35020 (19.81%) - 227.85 spectra/s]
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006. 20_178LOGBR2.mzBIN_calibrated 5.9 s [progress: 35020/35020 (100.00%) - 221.87 spectra/s] - completed 157.8 s
007. 48_178BR2.mzBIN_calibrated 5.5 s
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007. 48_178BR2.mzBIN_calibrated 5.
CuypersBart
sarah-haynes
prvst
chhh
Describe the problem
I almost get equal numbers of 'real' (1509) and 'rev' (1651) proteins in the final output file. This seems to be traced back to the 'Mapped Proteins' column in the 'peptide.tsv' being wrong. rev matches are reported there, while these peptides are not part of the _rev sequences at all. What could be the problem here?
System info
You can find that printed on the Config tab.
Java version: your response here 1.8.0_211
Describe your experiment
Genral proteomics experiment description
e.g. Shotgun proteomics, Q-Exactive ...
Input data files
2 conditions, 12 samples per condition => 24 samples total
Sequence database
Leishmania 33Mb, 8000 proteins
Attach fragger.params file
Run log output