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In this bottoms up approach, the protein is broken down into smaller peptides that are then ionized and analyzed by mass spectrometry (as opposed to peptide mapping, where the intact protein is analyzed). The peptide composition is compared to a database of protein sequences. Successive iterations with different digesting enzymes allow for the identification of the correct sequence, in a manner termed shotgun peptide sequencing or shotgun proteomics. When the peptide fragments must be separated by HPLC, the technique is termed multidimensional protein identification technology (MudPIT).
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