Fig. 2

ProteoModlR annotates peptides based on their PTM status and controls potential sources of technical variation. a Peptide annotation of peptides from a hypothetical protein depends on available quantified chemoforms. b Quantitation across three replicate measurements (shades of red) of five peptides from a protein. c ProteoModlR corrects errors introduced by differential ionization efficiency and technical variability, equalizing the signal recorded for equimolar reference isotopologues (d–e)