In the MALDI analysis of peptides and proteins, these analytes appear as a single species, usually in protonated form, in the linear TOF mass spectra. MS/MS spectra can be collected, since post-source decay appears to occur . However, by using a combination of sample preparation methods and delayed extraction, fragment ions can be generated in the linear TOF MALDI spectrum due to ?prompt fragmentation? (PF) in the ion source. If PF can be optimized, then structural information becomes available from MALDI TOF instruments that only offer the linear TOF option. More importantly, these fragment ions can be selected for the PSD experiment, and spectra of the fragment ions can be obtained. This leads to MSn capabilities that are not currently available in the MALDI TOF instruments that use reflectron technology. Consider the PSD spectrum of an intact protonated peptide molecule. The peptide has many basic sites, so the PSD spectrum contains fragments from many structural forms of the precursor. The fragment ions observed reflect preferred sites of protonation. In contrast, consider PSD on a high mass fragment ion such as a yn ion, which has a specific structure - with the fragment peptide protonated at the N-terminus. MS/MS spectra of this ion will be very different than that of the protonated molecule, yielding products of charge-remote reactions, similar to those we encounter when working with charged derivatives. The ability to generate prompt fragments in the ion source of the MALDI experiment for peptides offers additional options for obtaining sequence information.
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