# ------------------------------------------------------------------
# PeptideShaker 2.0.30 Report File
#
# Originally saved by: rubenbakker @ MacBook-Pro.local
#                  on: 10 Jun 2021, 10:29
# ------------------------------------------------------------------


Thu Jun 10 10:10:56 CEST 2021        Import process for time-series

Thu Jun 10 10:10:57 CEST 2021        Importing sequences from input_fasta_file.fasta.
Thu Jun 10 10:11:37 CEST 2021        Importing gene mappings.
Thu Jun 10 10:11:41 CEST 2021        Establishing local database connection.
Thu Jun 10 10:11:41 CEST 2021        Reading identification files.
Thu Jun 10 10:11:41 CEST 2021        Parsing FKL2920-S102-A-34.msgf.mzid.gz.
Thu Jun 10 10:12:06 CEST 2021        Checking spectra for FKL2920-S102-A-34.msgf.mzid.gz.
Thu Jun 10 10:12:06 CEST 2021        Importing PSMs from FKL2920-S102-A-34.msgf.mzid.gz
Thu Jun 10 10:12:32 CEST 2021        3 identified spectra (0.0%) did not present a valid peptide.
Thu Jun 10 10:12:32 CEST 2021        110 of the best scoring peptides were excluded by the import filters:
Thu Jun 10 10:12:32 CEST 2021            - 80.9% peptide mapping to both target and decoy.
Thu Jun 10 10:12:32 CEST 2021            - 19.1% peptide presenting high mass or isotopic deviation.
Thu Jun 10 10:12:32 CEST 2021        Parsing FKL2920-S102-A-34.t.xml.gz.
Thu Jun 10 10:12:32 CEST 2021        Checking spectra for FKL2920-S102-A-34.t.xml.gz.
Thu Jun 10 10:12:32 CEST 2021        Importing PSMs from FKL2920-S102-A-34.t.xml.gz
Thu Jun 10 10:12:32 CEST 2021        56 identified spectra (25.7%) did not present a valid peptide.
Thu Jun 10 10:12:32 CEST 2021        102 of the best scoring peptides were excluded by the import filters:
Thu Jun 10 10:12:32 CEST 2021            - 45.1% peptide length less than 8 or greater than 30.
Thu Jun 10 10:12:32 CEST 2021            - 54.9% peptide presenting high mass or isotopic deviation.
Thu Jun 10 10:12:32 CEST 2021        Parsing FKL2920-S105-A-35.msgf.mzid.gz.
Thu Jun 10 10:13:05 CEST 2021        Checking spectra for FKL2920-S105-A-35.msgf.mzid.gz.
Thu Jun 10 10:13:06 CEST 2021        Importing PSMs from FKL2920-S105-A-35.msgf.mzid.gz
Thu Jun 10 10:13:27 CEST 2021        3 identified spectra (0.0%) did not present a valid peptide.
Thu Jun 10 10:13:27 CEST 2021        138 of the best scoring peptides were excluded by the import filters:
Thu Jun 10 10:13:27 CEST 2021            - 87.0% peptide mapping to both target and decoy.
Thu Jun 10 10:13:27 CEST 2021            - 13.0% peptide presenting high mass or isotopic deviation.
Thu Jun 10 10:13:27 CEST 2021        Parsing FKL2920-S105-A-35.t.xml.gz.
Thu Jun 10 10:13:27 CEST 2021        Checking spectra for FKL2920-S105-A-35.t.xml.gz.
Thu Jun 10 10:13:27 CEST 2021        Importing PSMs from FKL2920-S105-A-35.t.xml.gz
Thu Jun 10 10:13:27 CEST 2021        42 identified spectra (21.1%) did not present a valid peptide.
Thu Jun 10 10:13:27 CEST 2021        88 of the best scoring peptides were excluded by the import filters:
Thu Jun 10 10:13:27 CEST 2021            - 51.1% peptide length less than 8 or greater than 30.
Thu Jun 10 10:13:27 CEST 2021            - 47.7% peptide presenting high mass or isotopic deviation.
Thu Jun 10 10:13:27 CEST 2021            - 1.1% unrecognized modifications.
Thu Jun 10 10:13:27 CEST 2021        Parsing FKL2920-S18-A-6.msgf.mzid.gz.
Thu Jun 10 10:13:54 CEST 2021        Checking spectra for FKL2920-S18-A-6.msgf.mzid.gz.
Thu Jun 10 10:13:54 CEST 2021        Importing PSMs from FKL2920-S18-A-6.msgf.mzid.gz
Thu Jun 10 10:14:16 CEST 2021        3 identified spectra (0.0%) did not present a valid peptide.
Thu Jun 10 10:14:16 CEST 2021        140 of the best scoring peptides were excluded by the import filters:
Thu Jun 10 10:14:16 CEST 2021            - 76.4% peptide mapping to both target and decoy.
Thu Jun 10 10:14:16 CEST 2021            - 23.6% peptide presenting high mass or isotopic deviation.
Thu Jun 10 10:14:16 CEST 2021        Parsing FKL2920-S18-A-6.t.xml.gz.
Thu Jun 10 10:14:16 CEST 2021        Checking spectra for FKL2920-S18-A-6.t.xml.gz.
Thu Jun 10 10:14:16 CEST 2021        Importing PSMs from FKL2920-S18-A-6.t.xml.gz
Thu Jun 10 10:14:16 CEST 2021        70 identified spectra (19.6%) did not present a valid peptide.
Thu Jun 10 10:14:16 CEST 2021        128 of the best scoring peptides were excluded by the import filters:
Thu Jun 10 10:14:16 CEST 2021            - 43.0% peptide length less than 8 or greater than 30.
Thu Jun 10 10:14:16 CEST 2021            - 55.5% peptide presenting high mass or isotopic deviation.
Thu Jun 10 10:14:16 CEST 2021            - 1.6% unrecognized modifications.
Thu Jun 10 10:14:16 CEST 2021        Parsing FKL2920-S21-A-7.msgf.mzid.gz.
Thu Jun 10 10:14:44 CEST 2021        Checking spectra for FKL2920-S21-A-7.msgf.mzid.gz.
Thu Jun 10 10:14:44 CEST 2021        Importing PSMs from FKL2920-S21-A-7.msgf.mzid.gz
Thu Jun 10 10:15:07 CEST 2021        4 identified spectra (0.0%) did not present a valid peptide.
Thu Jun 10 10:15:07 CEST 2021        151 of the best scoring peptides were excluded by the import filters:
Thu Jun 10 10:15:07 CEST 2021            - 73.5% peptide mapping to both target and decoy.
Thu Jun 10 10:15:07 CEST 2021            - 26.5% peptide presenting high mass or isotopic deviation.
Thu Jun 10 10:15:07 CEST 2021        Parsing FKL2920-S21-A-7.t.xml.gz.
Thu Jun 10 10:15:07 CEST 2021        Checking spectra for FKL2920-S21-A-7.t.xml.gz.
Thu Jun 10 10:15:07 CEST 2021        Importing PSMs from FKL2920-S21-A-7.t.xml.gz
Thu Jun 10 10:15:07 CEST 2021        74 identified spectra (19.3%) did not present a valid peptide.
Thu Jun 10 10:15:07 CEST 2021        153 of the best scoring peptides were excluded by the import filters:
Thu Jun 10 10:15:07 CEST 2021            - 49.7% peptide length less than 8 or greater than 30.
Thu Jun 10 10:15:07 CEST 2021            - 48.4% peptide presenting high mass or isotopic deviation.
Thu Jun 10 10:15:07 CEST 2021            - 2.0% unrecognized modifications.
Thu Jun 10 10:15:07 CEST 2021        Parsing FKL2920-S30-A-10.msgf.mzid.gz.
Thu Jun 10 10:15:34 CEST 2021        Checking spectra for FKL2920-S30-A-10.msgf.mzid.gz.
Thu Jun 10 10:15:34 CEST 2021        Importing PSMs from FKL2920-S30-A-10.msgf.mzid.gz
Thu Jun 10 10:15:59 CEST 2021        4 identified spectra (0.0%) did not present a valid peptide.
Thu Jun 10 10:15:59 CEST 2021        168 of the best scoring peptides were excluded by the import filters:
Thu Jun 10 10:15:59 CEST 2021            - 73.2% peptide mapping to both target and decoy.
Thu Jun 10 10:15:59 CEST 2021            - 26.8% peptide presenting high mass or isotopic deviation.
Thu Jun 10 10:15:59 CEST 2021        Parsing FKL2920-S30-A-10.t.xml.gz.
Thu Jun 10 10:15:59 CEST 2021        Checking spectra for FKL2920-S30-A-10.t.xml.gz.
Thu Jun 10 10:15:59 CEST 2021        Importing PSMs from FKL2920-S30-A-10.t.xml.gz
Thu Jun 10 10:15:59 CEST 2021        48 identified spectra (26.7%) did not present a valid peptide.
Thu Jun 10 10:15:59 CEST 2021        102 of the best scoring peptides were excluded by the import filters:
Thu Jun 10 10:15:59 CEST 2021            - 51.0% peptide length less than 8 or greater than 30.
Thu Jun 10 10:15:59 CEST 2021            - 48.0% peptide presenting high mass or isotopic deviation.
Thu Jun 10 10:15:59 CEST 2021        File import completed. 374973 first hits imported (3281204 total) from 405528 spectra.
Thu Jun 10 10:15:59 CEST 2021        [374385 first hits passed the initial filtering]
Thu Jun 10 10:16:00 CEST 2021        Computing assumptions probabilities.
Thu Jun 10 10:16:04 CEST 2021        Saving assumptions probabilities, selecting best match, scoring modification localization.
Thu Jun 10 10:18:58 CEST 2021        Computing PSM probabilities.
Thu Jun 10 10:18:59 CEST 2021        Resolving peptide inference issues.
Thu Jun 10 10:26:46 CEST 2021        Saving probabilities, building peptides and proteins.
Thu Jun 10 10:27:11 CEST 2021        Generating peptide map.
Thu Jun 10 10:27:18 CEST 2021        Computing peptide probabilities.
Thu Jun 10 10:27:19 CEST 2021        Saving peptide probabilities.
Thu Jun 10 10:27:23 CEST 2021        Simplifying protein groups.
Thu Jun 10 10:27:24 CEST 2021        5494 unlikely protein mappings found:
Thu Jun 10 10:27:24 CEST 2021            - 1839 protein groups supported by predicted or uncertain proteins.
Thu Jun 10 10:27:24 CEST 2021            - 11 protein groups supported by low confidence peptides.
Thu Jun 10 10:27:24 CEST 2021            - 3605 protein groups explained by simpler groups.
Thu Jun 10 10:27:25 CEST 2021        Mapping shared peptides.
Thu Jun 10 10:27:30 CEST 2021        Generating protein map.
Thu Jun 10 10:27:32 CEST 2021        Selecting leading proteins, inferring peptide and protein inference status.
Thu Jun 10 10:27:38 CEST 2021        Computing protein probabilities.
Thu Jun 10 10:27:39 CEST 2021        Saving protein probabilities.
Thu Jun 10 10:27:56 CEST 2021        Validating identifications at 1% FDR, quality control of matches.
Thu Jun 10 10:28:41 CEST 2021        Scoring PTMs in peptides.
Thu Jun 10 10:28:55 CEST 2021        Estimating spectrum counting scaling values.
Thu Jun 10 10:28:58 CEST 2021        Scoring PTMs in proteins, gathering summary metrics.
Thu Jun 10 10:29:10 CEST 2021        Identification processing completed (18 minutes 14.0 seconds).