AbstractNano‐electrospray tandem mass spectrometry (nano‐ES‐MS/MS) was used to record collision‐induced dissociation (CID) spectra of a set of peptoid–peptide hybrids and the complete peptoid derived from the phosphopeptide Ac‐pTyr‐Glu‐Thr‐Leu‐NH2 (1). The presence of B and Y″‐type fragment ions in the tandem mass spectra of the protonated molecular ions [M + H]+ allowed confirmation of sequence similar to mass spectrometric sequence analysis in peptides. In the isomeric peptoid compounds studied, one or several amino acid residues were replaced by peptoid residues (N‐substituted glycine residues), which resulted in characteristic tandem mass spectra with differently increased relative abundances of Y″‐and B‐type fragment ions. The increment of a particular Y″‐ion was directly correlated to the position of a peptoid residue present. In addition to these increased peak intensities, other characteristic peaks were also observed compared with the spectrum of reference peptide 1. When a peptoid phosphotyrosine was incorporated, the presence of this residue was apparent from the occurrence of a relatively intense peak at m/z 187 representing the positively charged side‐chain of phosphotyrosine, which was almost absent in the spectrum of the reference peptide 1. Since the threonine side‐chain had to be translated into the homo peptoid analog this substitution was apparent from the presence of [M + H]+ and fragment ions 14 mass units higher than observed in the spectrum of the reference phosphopeptide 1. The presence of an NLeu peptoid residue could be confirmed by the specific fragmentation of the immonium ion showing an intense peak in its tandem mass spectrum at m/z 57, which results from the loss of an neutral imine molecule leading to a positively charged [C4H9]+ ion. By means of these mass spectrometric characteristics, all isomeric peptoid compounds could be distinguished from each other and characterized. The methods used appear to be very useful in future studies of peptoids and peptoid–peptide hybrids. Copyright © 2001 John Wiley & Sons, Ltd.