Comparison of peptide identifications based on measured peptide sequence tags containing 2-9 AA residues with UStags-derived peptide identification. Both peptide fragment measured masses are filtered using a 10 ppm MMA cutoff. Top: ○ and ◇ indicate the number of peptides and proteins, respectively, identified with 2-9 AA-residues; ○ and ◆ indicate the number of peptides and proteins, respectively, that overlap between the “peptide sequence tag” and “UStag” sets of identifications. Venn diagrams compare peptides and proteins identified using “peptide sequence tags” with ≥2 AA residues requirement (mass (MS) and sequencing error (MS/MS) histograms from are shown in the upper right corner) and UStags with unconstrained peptide C-termini. Bottom: An example of ambiguous peptide identification using the “peptide sequence tag” approach, even with two AA segments GQ and SLLL (labeled in blue), which was unambiguously identified using UStag approach.