De Novo and Hybrid Modified Protein Identification
Using tandem mass spectrometry and mixed-integer linear optimization, a comprehensive list of proteins along with their corresponding post-translational modifications can be derived. Given a mixture of unknown proteins that may be post-translationally modified, liquid chromatography and tandem mass spectrometry (LC-MS/MS) is used to separate, ionize, and fragment the digested peptides from the mixture. A set of unmodified peptides extracted from the de novo algorithm PILOT or the hybrid de novo/database algorithm PILOT_SEQUEL is used to generate a list of proteins that are present in the sample. All MS/MS that are not annotated with an unmodified peptide are searched for a sequence tag of unmodified amino acids that can be found in one of the derived proteins. Using the known sequence of the protein, the PILOT_PTM algorithm is used to check for every possible post-translational modification that can exist and assign the proper modifications to the protein.