Investigation of VUV photodissociation propensities using peptide libraries

PSD does not usually generate a complete series of y-type ions, particularly at high mass, and this is a limitation for de novo sequencing algorithms. It is demonstrated that b2 and b3 ions can be used to help assign high mass xN−2 and xN−3 fragments that are found in vacuum ultraviolet (VUV) photofragmentation experiments. In addition, vN-type ion fragments with side chain loss from the N-terminal residue often enable confirmation of N-terminal amino acids. Libraries containing several thousand peptides were examined using photodissociation in a MALDI-TOF/TOF instrument. 1345 photodissociation spectra with a high S/N ratio were interpreted.

Graphical abstractFigure optionsDownload full-size imageDownload high-quality image (29 K)Download as PowerPoint slideHighlights► We study the VUV photodissociation of peptides found in synthetic libraries. ► The propensities for forming various unusual high-energy fragment ions are examined. ► The potential for using high-energy fragment ions in de novo sequencing is discussed.