Agilent Spectrum Mill - Quality Metrics and False Discovery Rates (FDR)

FDR Metrics (spectra, peptide, protein)
Precursor Ion Metrics
MS/MS Interpretation Metrics
MS/MS Spectral Identifiability Metrics (define thresholds below)
Peptide Separation Metrics

     Middle RT portion of validated spectra in LC run: (%)
Sample Handling Metrics
Peptide Fraction Overlap
Distinct peptide comparison method:
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.
Data Directories
(None Selected)