Amino Acid Sequencing of Synthetic Peptides Using a MALDI-TOF Mass Spectrometer and Protein Sequencer

User Benefits

- Amino acid sequences of peptides can be determined with the MALDI-ISD analysis. - By combining protein sequencer results with MALDI molecular weight measurements or MALDI-ISD results in a complementary way, all amino acid sequences can be determined regardless of the peptide structure.

Introduction

Compared to large molecular weight antibody therapeutics, peptide therapeutics have been attracting attention in recent years because they are more readily absorbed in oral form, and offer higher cell membrane permeability, lower production costs based on chemical synthesis, and other benefits. In order for peptide therapeutics to offer a particular function, they must have a specific amino acid sequence. However, during the synthesis process, by-products can be formed if the peptide bond elongation reaction is accidentally stopped or missed, etc. It is therefore necessary to confirm the amino acid sequence of the final synthesized product. Technical advances in mass spectrometers now enable high-throughput analysis of amino acid sequences of peptides and proteins by using mass spectrometers and corresponding databases. However, that can result in problems, such as inaccurate or uncertain database search results due to amino acid side chain modifications or other factors causing the mass spectrometry results to differ from the theoretical masses. Also, if the genome database of a biological species is incomplete, amino acid sequencing with a mass spectrometer can be complicated and unreliable. In contrast, when sequencing amino acids by Edman degradation, respective amino acids are identified one at a time starting from N-terminals, which eliminates problems with mass and database dependence. However, sequencing by Edman degradation has limitations, such as decreased efficiency when analyzing long sequences or difficulty analyzing modified amino acids. This Application News describes the combined use of sequence information obtained with the MALDI-8030 benchtop MALDI-TOF mass spectrometer and a PPSQ-50A series protein sequencer with conventional Edman degradation to determine the amino acid sequences in two types of synthetic peptides.

April 14, 2025 GMT