Peptide fragmentation caused by Ar cluster ions depending on primary ion energy

Rationale Time‐of‐flight secondary ion mass spectrometry (TOF‐SIMS) with an Ar cluster ion beam as a primary ion source provides useful information in terms of peptide analysis. It is, however, difficult to interpret the spectra. The ToF‐SIMS peptide spectra obtained with Ar clusters having different energies have been investigated in order to classify the secondary ions into the peptide fragment ions and those related to contaminants or the substrate. Methods Three peptides having different molecular weights from 600 to 1300 u were measured with Ar cluster beams having different energies per atom from 4 to 40 eV/atom. Results In the spectra normalized to a geometric average of all the spectra, the amino acid fragment ions are distinguished from other secondary ions. In the mass range above 600 u, the peptide fragment ions increase with mass while those not related to the peptide decrease with mass. Conclusions Energy‐dependence fragmentation helps in understanding the peptide spectra. Specific peptide fragment ions of the larger peptides are likely to be detected under lower energy than energy higher than 10 eV/atom. Although it is difficult to interpret the TOF‐SIMS spectra of a peptide obtained with an Ar cluster ion beam, the secondary ions can be classified by comparing those obtained with different energy Ar cluster ion beams. Copyright © 2015 John Wiley & Sons, Ltd.