Proteomics is the largescale study of proteins, including protein, protein complexes, protein signaling networks, protein structures and functions, etc. One of its most important tasks of proteomics study is to develop efficient and rapid approaches to identify various proteins. Peptide mapping is a efficient method to rapidly map the protein sequence, and thus is commonly used strategy in protein identification. Peptide mapping is also an important technique for investigating protein primary structures and determining surface-exposed sites or epitopes within proteins. Prior to peptide mapping, the proteins and peptides usually need to be separated and purified by a variety of separation approaches, such as gel electrophoresis, liquid chromatograph, capillary electrophoresis, etc. Then proteins are digested into peptide fragments. These resultant fragments are subsequently identified by mass spectrometry to obtain peptide mass fingerprints.
Peptide mapping is a rapid method to identify the amino acid sequence of the target proteins. Unlike Edman degradation sequencing, which analyzes each amino acid identity from the N-terminal end, peptide mapping methods only analyze the mass peptide, which are then compared to the theoretical peptide masses of known proteins, to speculate the identity and sequence of the target protein. Since only peptide mass are measured, contamination from other protein can be interference to the accuracy of protein analysis, hence should be eliminated. Therefore, proteins are often separated by 1D or 2D PAGE before proceed to LC-MS/MS analysis. We strictly follow the ICH Q6B Guidelines in support our customers’ needs.
To increase the accuracy of peptide mapping and post-translational modification analysis, proteins are usually digested by several proteolytic enzymes, including trypsin, Lys-C, Glu-C, chymotrypsin, Asp-N, and Arg-C.
Theoretically, peptide fragments can be analyzed by both ESI-TOF and MALDI-TOF. MALDI-TOF is preferred in our service, as MALDI-MS/MS has high sample throughput and even enables analyzing several proteins at the same time.
As peptide mapping service compares the peptide masses with protein databases, only protein from the database can be identified using this method. Proteins, whose sequence is not found in a protein database, such as antibodies or novel proteins, can be deduced by our service of de-novo sequencing.
Workflow of peptide mapping service:
1D/2D-PAGE separation & breakage of disulfide bond (optional)
Digestion of protein by 1-6 proteolytic enzymes
HPLC-MALDI MS/MS analysis