Peptide mapping

Sometimes, you need to confirm the whole sequence of a protein. Using a combination of several proteases and high resolution mass spectrometry, our experts will determine the exact amino acid sequence of your target protein.

Screenshot of a peptide mapping software

Peptide mapping workflow overview

In silico digestion

The first step of confirming the complete amino acid sequence of a protein by mass spectrometry is to cut it into smaller peptides using a protease. The enzyme of choice for many proteomics workflows is trypsin, as it reliably cuts after every lysine and arginine residue (with some exceptions). However, for some regions of your protein, a tryptic digestion may produce peptides that are either too small or too big for a proper detection by the machine. This would result in a lack of sequence information for these regions, which is undesirable for a peptide mapping experiment. To prevent this, our experts will first proceed to an in silico digestion of your protein of interest to determine which combination of protease would yield peptides that, when bio-informatically merged, cover 100% of the sequence. We generally achieve full coverage with a combination of two to three different proteases.

Digestion and LC-MS/MS

Once the choice of proteases is set, we will perform the real-life digestion of your protein in the lab.  Peptides resulting from each digestion will be analyzed on a short LC-MS/MS gradient using a data-dependent acquisition workflow.

Data analysis

A protein identification software will first associate the recorded data to a peptide sequence for each protease. This will result in a list of regions that were covered by peptides in each individual protease. Finally, we will pool and align every confirmed peptide from each digestion on the theoretical sequence of the protein to get the final peptide mapping.

Data report

Peptide mapping data reports include the list of every detected peptide, separated by protease. We will provide the total protein coverage, as well as the confidence associated with every peptide.

Contact us for your peptide mapping needs

My personal experience of collaborating with PhenoSwitch Bioscience was really amazing and great. Ribosomal protein paralogs have very limited number of amino acid differences. If it were not for PhenoSwitch, it would not have been possible to get such a high quality identification and quantification of duplicated ribosomal proteins in yeast. I am highly indebted and thankful for their perseverance, commitment, help and guidance during the tough times of optimization. If you you need to use MS for identification and quantification of your molecules, I strongly recommend you to talk to these guys!
Mustafa Malik Ghulam, Post Doctoral Fellow, RNA Therapeutic Institute, Umass Medical School, Worcester, Massachussetts

"PhenoSwitch Bioscience Inc has provided us with outstanding efficacious service, high quality data and exemplary data analysis over the past three years."

Stephen Naylor, Ph.D., CEO at ReNeuroGen LCC, Milwaukee, USA
"They have provided excellent data in a timely manner on a number of metabolism and protein studies ongoing in my group"
Klaus Klarskov, Ph.D., Professor at Université de Sherbrooke, Canada
Looking for advice?

PhenoSwitch Bioscience will be happy to help

Are you interested in our services? Please fill out this form and our experts will write back to you in less than 24 hours!

Plan a consultation