NONINTERFERING SYNTHETIC PEPTIDES AS INTERNAL CONTROLS FOR AMINO-ACIDSEQUENCING OF SAMPLE UNKNOWNS

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 derivat ives having unique retention times compared with those obtained from t he commonly observed natural residues. These internal standards indica te how the entire sequencing system was functioning during the actual analysis of an unknown by providing an initial yield and numerous repe titive yields. Verifying proper operation is extremely important when cycles appear blank due to the presence of modified amino acids or a b locked N-terminus. In addition, the ISS peptides can detect and identi fy different types of sequencing errors. This sometimes eliminates the need to rerun a sample due to blank cycles caused by mechanical malfu nctions 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 protei ns or peptides that have been treated differently. (C) Academic Press, Inc.