Fig 1.
Diagram showing deamidation reaction mechanisms.
(A) Deamidation of asparagine to aspartic acid. (B) Deamidation of glutamine to glutamic acid. Diagrams illustrate both direct hydrolysis and cyclic intermediate pathways. Note: the formation of isoaspartic acid and isoglutamic acid is not depicted.
Fig 2.
Diagram showing reaction mechanisms for conversion of N-terminal Glutamine and Glutamic Acid to Pyroglutamic Acid.
Note: formation of pyroglutamic acid from isoaspartic acid and isoglutamic acid is not depicted.
Fig 3.
Schematic overview illustrating The Demodifier’s pipeline.
Figure created in Mermaid.live.
Fig 4.
The Demodifier’s process of making sequence permutations for an imaginary peptide.
First, all possible deamidations of N/Q to D/E are simulated up to the number detected by search software and ignoring N-terminal Q if the pyroGlu modification was detected, next reverse deamidation permutations of D/E to N/Q are simulated, ignoring previously altered positions and N-terminal E if the pyroGlu modification was detected, and then if N-term pyroGlu formation was detected, Q to E or E to Q substitutions are simulated depending on starting amino acid. Peptide permutation duplicates are removed (if present) before LCA is assigned for each MISP using Unipept pept2LCA. In the case of this imaginary peptide, the LCA of the input peptide is Unicorn, however the MISPs yield LCAs matching to several other Mythical Equus. Figure created in Biorender.com.
Fig 5.
Graphical overview of The Demodifier’s output for the test dataset.
(A) Proportional figure showing the total number of peptides in the test dataset, number of peptides with MISPs, number of peptides with MISPs that match to real protein sequences, those which additionally match to multiple distinct sequences, and those which have previously been reported, (B) Number of LCAs per input peptide by input peptide count (C) MISP LCA categories by input peptide count including: LCAs which were different to the input peptide’s LCA, identical to the input peptide’s LCA, less taxonomically specific than the input peptide’s LCA, or more taxonomically specific than the input peptide’s LCA.