MORPHEUS (revision 142) LOG PARAMETERS Input Data File: /home/lev/pyteomics_filtering_example/example.mzML Unknown Precursor Charge State Range: +2..+4 Absolute MS/MS Intensity Threshold: disabled Relative MS/MS Intensity Threshold: disabled Maximum Number of MS/MS Peaks: 400 Assign Charge States: true De-isotope: false Protein FASTA Database: /home/lab006/fasta/sprot_human_decoy.fasta Create Target–Decoy Database On The Fly: false Protease: trypsin (no proline rule) Maximum Missed Cleavages: 2 Initiator Methionine Behavior: variable Fixed Modifications: carbamidomethylation of C Variable Modifications: none Maximum Variable Modification Isoforms Per Peptide: 1024 Precursor Mass Tolerance: ±10 ppm (monoisotopic) Precursor Monoisotopic Peak Correction: 0..+1 Product Mass Tolerance: ±0.5 Da (monoisotopic) Maximum False Discovery Rate: 1% Consider Modified Forms as Unique Peptides: false Maximum Threads: 12 Minimize Memory Usage: false Output Folder: /home/lev/pyteomics_filtering_example RESULTS 40,494 total (20,247 target + 20,247 decoy + 0 on-the-fly decoy) proteins 7,757,214 total (3,907,752 target + 3,849,462 decoy) non-unique peptides 21,312 MS/MS spectra 758 target (7 decoy) PSMs at 0.937% PSM FDR (17.076 Morpheus score threshold) 746 unique target (7 decoy) peptides at 0.953% unique peptide FDR (17.076 Morpheus score threshold) 412 target (4 decoy) protein groups at 0.971% protein group FDR (18.074 summed Morpheus score threshold) 1.54 minutes to analyze