library K562_q3bad_PV.txt.mz_corrected Name of library file being analyzed format Peakview Library format, one of OpenSWATH, Peakview, or Spectronaut pepions 36431 Number of peptide ions (i.e. precursor, sequence + modifications + charge) fragments 218586 Number of fragment (fragment ions) in library ptp_percent 89.17 Percentage of proteotypic peptides (not shared) shared_percent 10.83 Percentage of shared peptides shared_pepions 3945 Number of shared pepions peptides 32489 Number of distinct peptide sequences mod_peps 32577 Number of distinct modified peptides (sequences + modifications) mod_percent 16.5 percentage of distinct modified peptides with a mass modification total_mods 6100 Number of mass modified amino acids chg_2 63.1 Percentage of charge 2 precursors chg_3 32.1 Percentage of charge 3 precursors precursor_min 399.5 Minimum precursor m/z (mass/charge) in library precursor_max 1248.0 Maximum precursor m/z in library fragment_min 101.0 Minimum fragment m/z in library fragment_max 1497.8 Maximum fragment m/z in library avg_len 13.8 Average peptide Length avg_num_frags 6.00 Average number of fragment per assay (precursor) avg_frag_len 0.43 Average fragment sequence length short_perc 0 Percentage of assays with 5 or fewer transitions fragment_above_precursor 0.484 Percentage of fragment m/z above precursor m/z y_perc 75.8 Percentage of y ions b_perc 24.2 Percentage of b ions t6_y_perc 75.8 Percentage of y ions considering only the top 6 fragments per assay avg_intensity 4418.4 Average Intensity rt_min 1.0 Minimum RT (retention time) in library rt_max 214.7 Maximum RT in library rt_med 98.1 Median RT in library rt_rsq 0.992 r-squared value of fit between RT of +2 and +3 charge states for the same modified peptide rt_five 99.3 Percentage of +2/+3 charge pairs of the same mod pep within 5 RT units of each other n_irt 11 Number of iRT peptides in library irt_cnt 90 Number of iRT assays (precursor + fragment) low_nr 30788 Number of fragment annotated as y1,y2,b1, or b2 db_peps 1204435 Peptides in reference library, often 7-50 AA seen_peps 22659 Number of library peptides seen mc_peps 2501 Number of Missed cleavage peptides db_prots 40936 Number of Proteins in reference library lib_prots 4528 Number of proteins with at least one assay in ion library seen_prots 4528 Number of library proteins seen ux_prots 0 Unexplained (not in reference library) proteins decoy_pct 0 Percentage of decoy (optionally includes "alternative", non-db decoys) assays mixed_pct 0 Percentage of mixed decoy/target (has both decoy and no-decoy annotations) assays fwd_pct 100.0 Percentage of target (non-decoy) assays med_ppp 4 Median number of peptides per protein mean_ppp 9.9 Mean number of peptides per protein stddev_ppp 15.8 Standard deviation of the number of peptides per protein 3_sigma_ppp 83 number of peptides per protein more than 3 standard deviations from the mean max_intensity_idx 1.0 Average index of most intense fragment precursor_ok 36431 Number of assays where precursor is within 5 PPM (parts per million m/z) of theoretical precursor_bad 0 Number of assays where fragment is more than 5 PPM from theoretical fragment_ok 218586 Number of assays where fragment is within 1 PPM of theoretical fragment_bad 0 Number of assays where precursor is more than 1 PPM from theoretical fragment_na 0 Number of assays where peak annotation not found in expected b/y series fragment_avg_mdiff 0.0000 Average m/z difference between reported and theoretical fragment swa_defined 36431 Number of peptide ions that fall into a defined SWATH bin swa_missing 0 Number of peptide ions that fail to fall into a defined SWATH bin ( Pepions - swa_defined) swa_conflict 5 Number of fragment_ions that fall into same SWATH(s) as precursor swa_ok 255523 Number of fragment_ions that do not fall into same SWATH(s) as precursor swa_conflict_assay 5 Number of precursor that have at least one failing fragment swa_5 652 Number of fragment ions that fall within 5 Th of precursor ion swa_25 9395 Number of fragment ions that fall within 25 Th of precursor ion problem_assays 5 Assays whose precursor or any fragment m/z values do not match SWATHs file or differ significantly from theoretical values