Not just a protein identity test

Peptide mapping is not only a regulatory requirement under ICH Q6B for structural characterization and confirmation.

It provides a whole suite of information to help inform the drug development process.

One of the key benefits of engaging us in your research projects is that we’ll both fulfill regulatory requirements and provide you with full data interpretation, giving you all the information we uncover.

We pioneered the mass spectrometry analysis service for the biopharmaceutical industry and have been leaders for almost 15 years, making us your peptide mapping specialists.

Our bioinformatics staff, who dedicate their time to analyzing mass spectrometry outputs, know that there are a number of ways in which peptides can be mapped in a laboratory. But each method has strengths and weaknesses depending on your situation.

We design the study so that we are using the method with the greatest strengths for your specific project. Other protein service providers don’t have a similar breadth of options when it comes to peptide mapping with mass spectrometry.

Mapping peptides was once the domain of chromatography and UV research. However, these simple methods of analysis did not allow for the identification of individual peptides without great difficulty.

Now, with our superior understanding of modern mass spectrometry, we can identify and analyze individual peptides within a protein with great certainty. And because Protagen’s scientists were at the forefront of mass spectrometry software development when it emerged almost 15 years ago, clients benefit from our finely tuned skills in this area.

Technical information

Peptide mapping is commonly undertaken to analyze the protein primary structure after cleavage of the protein into proteolytic peptides. The power of peptide mapping lies in the large number of site specific molecular features that can be detected.

When using one digestion enzyme (for example, Trypsin), peptide mapping is typically carried out for protein identification. The analysis is performed using MALDI-MS/MS or LC-ESI-MS/MS, for example during protein identification after electrophoresis, such as 1D or 2D PAGE.

When using multiple enzymes, peptide mapping is applied for the confirmation of a complete amino acid sequence, for example when confirming the amino acid sequence of a biosimilar and comparing it with the originator molecule.

Depending on the experimental setup, peptide mapping can also be used to determine the N- and C-terminus of a protein. This is sometimes crucial information for our clients, for example in the case of monoclonal antibodies, where the truncation level of the C-terminal Lysine can be monitored.

Proteins and peptides are ionized and fragmented in the mass spectrometer. The resulting MS/MS spectra is used to sequence the individual amino acids in order of their appearance in a protein or peptide.

In combination with additional sample preparation, peptide mapping can also be used to determine:

If the protein sequence is not found in a protein database, it can be deduced by de-novo sequencing.

Up to 100% sequence coverage confirms the amino acid sequence. The identification is based on LC-ESI-MS/MS data, which allows the sequencing of peptides with high confidence. Overlapping peptide sequences confirm the order of amino acids in the sequence.

Your contact for Peptide Mapping at Protagen Protein Services GmbH


Dr. Marcus Mreyen

Director Business Development
Our business development team will be happy to assist you with your project.

Phone: +49 (0) 231 9742-6100