For the de novo sequencing of monoclonal antibody (mAb) proteins, the sequence accuracy is an essential factor. There are some cases that a single amino acid error can cause a total loss of antibody activity.
There are two major difficulties in mAb de novo sequencing by LC-MS based technique. First, it is difficult to determine antibody variable region sequences with error, especially in CDRs. Due to the great diversity of the antibody sequences, virtually each newly isolated mAb sample has a unique sequence. So it is not possible to depend on sequence homology search accurately determine its sequence. An IgG antibody contains six CDRs with average ten amino acids in length. There are 1E13 possible sequences for each of six CDRs. Finding the only correct from 1E13 possible sequence is already a difficult task. Second, amino acids Leucine and isoleucine have same mass and similar chemical properties. Distinguishing those two amino acids is also very difficult. Due to those reasons, a recent publication stated correctly that “Modern mass spectrometry-based sequencing will rarely, if ever, provide a single unambiguous sequence for the variable domains “(MAbs. 2016 Apr;8(3):501-12)
To meet this challenge, we have been continuing our effort in developing new technology for antibody de novo sequence, including various procedures and over a dozen bioinformatics tools, including the software package for distinguishing Leu/Ile residues. With over a hundred antibody samples sequenced and the many of them have been functionally validated by our clients, we are now confident we can deliver the world best mAb de novo sequencing technology to our clients.