FDR at the peptide & spectra level (from valid hits)

FDR at the protein level

   Group proteins across all directories
    Grouping method: 1 shared peptide 1 shared, expand subgroups

Precursor mass error mean (ppm)

Precursor charge count (from valid spectra)

Precursor Isolation Purity & Averagine Chi²

Precursor Acquisition Uncertainty: m/z and z

MS1 intensity stats for each run.

Precursor Ion Fragmentation Table

Identification Scores

Fragmentation Metrics

Fragmentation Mode

Variable modification site localization

Chromatography metrics for each run
     Middle RT portion of validated spectra in LC run: 90 80 50 (%)

Peptide pI median for each run

RT scatter plot & peptide subset reports for each directory (seqdb/peptideQMlists/*.txt)

Isobaric label incorporation for each run Control: 114 115 116 117

Digestion completeness

Observed modifications by: Peptide Spectrum Matches Distinct Peptides

Distinct Peptide Fraction Overlap Table

Distinct peptide comparison method: Case Insensitive(CI) Case Sensitive(CS) Case/Charge Sensitive(CzS)

For fraction overlap, sample handling, or pI choose CS or CI.
FDR calculations always use CI.
Filtering to distinct peptides retains each highest scoring representative
after CS or CI string comparison of sequences. Variable mods are lowercase.