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Side Reactions in Peptide Synthesis

A working reference for synthetic chemists — indexed by Δmass, residue, and category.

← Peptide Analysis Suite
Use it like this:
① "I see +X Da" → click the Δmass row
② "About to synth M-W-C" → click the residue keys
③ "How do I avoid X" → click categories or search by name
Δmass (Da) — observed minus parent
Or enter exact: ± Da
Affected residue
Category
Free text
of reactions
drag to pan · scroll to zoom · click node = detail
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Edges
shares amino acid
similar Δmass (≤2 Da)
same category

Each node = one side reaction. Same filters above apply (residue, category, search). Hover to see name; click to open the full entry.

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All side reactions (A-Z)
Acetone-induced N-terminal imidazolidinone Acetonitrile-derived cyanohydrin Acid-catalyzed N→O acyl migration Arg δ-lactam formation Asn / Gln deamidation Asn / Gln side-chain dehydration to nitrile Aspartimide formation Asp hydrazide protection (modern Asp protection) -Asp-Pro- acidolysis NCA-mediated dipeptide impurity C-terminal N-Me-Xaa acidolysis Cys β-elimination + piperidine adduct Cys β-elimination → dehydroalanine Cys disulfide scrambling / mis-pairing Cys-EDT and Cys-EDT-tBu adducts Cys over-oxidation (sulfenic / sulfinic / sulfonic) Dibenzofulvene (Fm) adduct on Nα Deguanidination of Arg DKP (2,5-diketopiperazine) formation Eschweiler-Clarke N-methylation Methanol esterification of Asp/Glu/C-term FITC-induced N-terminal Edman degradation Formaldehyde-induced methylene-bridge crosslinking DMF-induced formylation H-phosphonate impurity HBTU / HATU guanidination of free amine Disulfide desulfurization (Cys → Ser) N-terminal H-His-Pro-Xaa autodegradation Hydantoin formation Sluggish coupling at lipidated Lys (semaglutide / tirzepatide) Met alkylation by DODT scavenger Met over-oxidation to sulfone Met oxidation to sulfoxide MTBE-induced tert-butylation N-Acylurea formation (DIC byproduct) Acidolysis of N-Ac-N-alkyl-Xaa N-terminus N-α acetylation Pbf protecting-group residue on Arg Side-chain sulfonation (Pbf-derived) β-elimination of phosphopeptide Redundant coupling via premature Fmoc loss Pyroglutamate formation from N-terminal Glu Pyroglutamate formation from N-terminal Gln Pyrophosphate side product Cα racemization Trifluoroacetate counterion alkylation Aib²-mediated DKP (tirzepatide-class peptides) Trifluoroacetylation Trp-EDT and Trp-EDT-TFA adducts Trp alkylation by resin linker cations Trp oxidation (kynurenine, oxindolylalanine, NFK) Trp tert-butylation Trt protecting-group residue