Protein identification based on matrix assisted laser desorption/ionization-post source decay-mass spectrometry

Due to its very short analysis time, its high sensitivity and ease of autom ation, matrix-assisted laser desorption/ionization (MALDI)-peptide mass fin gerprinting has become the preferred method for identifying proteins of whi ch the sequences are available in databases. However, many protein samples cannot be unambiguously identified by exclusively using their peptide mass fingerprints (e.g., protein mixtures, heavily posttranslationally modified proteins and small proteins). In these cases, additional sequence informati on is needed and one of the obvious choices when working with MALDI-mass sp ectrometry (MS) is to choose for post source decay (PSD) analysis on select ed peptides. This can be performed on the same sample which is used for pep tide mass fingerprinting. Although in this type of peptide analysis, fragme ntation yields are very low and PSD spectra are often very difficult to int erpret manually, we here report upon our five years of experience with the use of PSD spectra for protein identification in sequence (protein or expre ssed sequence tag (EST)) databases. The combination of peptide mass fingerp rinting and PSD and analysis described here generally leads to unambiguous protein identification in the amount of material range generally encountere d in most proteome studies.