Noninterfering synthetic peptides as internal controls for amino acid sequencing of sample unknowns.

Abstract Noninterfering synthetic peptides have been designed that may be used as internal sequencing standards (ISS-1 and ISS-2) by placing them in an amino acid sequencer with the sample. The peptides are composed of four unnatural amino acids which all yield phenylthiohydantoin derivatives having unique retention times compared with those obtained from the commonly observed natural residues. These internal standards indicate how the entire sequencing system was functioning during the actual analysis of an unknown by providing an initial yield and numerous repetitive yields. Verifying proper operation is extremely important when cycles appear blank due to the presence of modified amino acids or a blocked N-terminus. In addition, the ISS peptides can detect and identify different types of sequencing errors. This sometimes eliminates the need to rerun a sample due to blank cycles caused by mechanical malfunctions which result in failure to cleave the N-terminal residues. ISS-1 or ISS-2 may also be utilized during method development to compare different sample supports and to normalize sequencing data from proteins or peptides that have been treated differently.