Peptide Mapping

Applied Biomics’ Peptide Mapping by LC-MS/MS offers maximum sequence coverage of a target protein. Our peptide mapping service offers a powerful analytical technique to identify and characterize different proteins. Our platform uses the Orbitrap Exploris with Biopharma option for maximum detection and quantitation of all target protein peptides. Following are some main applications:

• Confirmation of the target protein sequence
• Difference in coverage between samples
• Visualize and quantify the purity of target protein
• Post translational modifications (PTMs)

We have optimized our peptide mapping protocols starting from sample preparation, protease digestion to mass spectrometry scan settings for various kinds of proteins. The following is an example of a typical peptide mapping analysis output in BioPharma Finder 5.1:

Figure 1: Peptide Map for a section of protein sequence

In addition, intensity maps show the intensity of target protein peptides over the total ion chromatogram (all detected peptides). This allows visualization how much of the total protein in a sample is composed of the target protein, providing insight into the sample purity.

Figure 2: MS1 Intensity Map of Bovine Serum Albumin

Peptide Mapping Experimental Procedure:

1. Sample preparation: Sample clean up, measure/adjust protein concentration
2. Reduction, alkylation, and trypsin (and/or other protease) digestion
3. nanoLC-MS/MS: Peptides separated and analyzed by nanoLCMSMS
4. Data analysis: Peptide identification and quantitation in BioPharma Finder

Data Report covers the following:

1. Peptide List: identification / sequence, positions, m/z, and confidence metrics for all matching peptides of target protein
2. Coverage Data: sequence coverage and matching spectra for peptide
3. Peptide Map: visual showing the entire amino acid sequence and the match quality for each identified peptide
4. Intensity Map: visual of the peptide intensity of target protein over total ion chromatogram