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Fig. 3 | BMC Bioinformatics

Fig. 3

From: ProteoModlR for functional proteomic analysis

Fig. 3

ProteoModlR computes exact and approximate abundance and PTM stoichiometry based on the available set of peptides for a given protein. Exact and approximate calculations for abundance and stoichiometry were tested on simulated datasets modeling a hypothetical protein producing four peptides, two of which bear a PTM. If the input file contains all ‘Q’, ‘M’ and ‘NM’ peptides, then ProteoModlR computes ‘exact’ relative peptide abundance, expressed as fold change compared to Sample #1 (a) and stoichiometry (c) If ‘Quantification’ (‘Q’) or non-modified (‘NM’) peptides are not available, ProteoModlR can calculate ‘approximate’ relative abundances (b) and 'approximate stoichiometry (d) resembling the exact values (Pearson product–moment correlation coefficient = 0.98)

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