A research team has developed a reliable and economical laboratory method that uses tiny magnetic beads for studying proteins with sugar molecules attached to them in blood and tissue samples. Gaining a better understanding of their pathological changes has the potential to help researchers as they diagnose and treat diseases, including cancer.
Their work was published in the journal Molecular & Cellular Proteomics on August 11, 2026.
Scientists in Japan started the Human Glycome Altas (HGA) Project in April 2023 to create a catalog of human sugar molecules, called glycans, related to disease. The catalog is created using glycoproteomics on a large cohort of samples. In glycoproteomics, scientists study proteins, called glycoproteins, that have sugar molecules attached to them. Glycoproteomics is a branch of proteomics, the large-scale study of all proteins’ function and structure in an organism, tissue, or cell. For the HGA Project to achieve its goals, researchers needed to develop faster and more efficient sample preparation methods that increased analytical throughput. A research team from Japan has developed a robust method using low-cost, commercially available magnetic particles.
Glycosylation, the process of attaching a sugar molecule to a protein or lipid, is the most common chemical change of a protein that occurs after it has been built by a cell. How the sugar molecule attaches to the protein affects the protein’s interactions with other cells. Scientists have noted changes in the glycosylation patterns of proteins occurring in several diseases, including cancer. Cancer damages the sugar molecules. These changed sugar-proteins are important biomarkers in the body because scientists can find and track cancer by studying these changes in the sugar molecules.
Bottom-up glycoproteomics is a promising approach for biomarker discovery because it provides scientists qualitative and quantitative information on carrier glycoproteins, glycosylation sites, and glycan composition. In bottom-up glycoproteomics, scientists use enzymes to cut the proteins with their attached sugar molecules into smaller pieces called peptides, purify them using a laboratory technique called hydrophilic interaction liquid chromatography (HILIC), and study them using mass spectrometry. However, bottom-up glycoproteomics has limited usefulness because the mass spectrometry testing cannot easily detect the glycopeptides because the plain proteins are so plentiful. The biological samples also can contain impurities such as salts and detergents. These impurities can interfere with scientists’ analysis of proteins.
Single-pot, solid-phase-enhanced sample preparation (SP3) is a useful sample preparation method in glycoproteomics. SP3 involves sample preparation for facilitating automation using magnetic beads. “The SP3 method has also been adapted for glycopeptide preparation, however, seamless workflow in series of sample preparation using appropriate magnetic beads has not been reported,” said Dr. Kazuki Nakajima, a professor at the Institute for Glyco-core Research in Japan.
The research team evaluated a streamlined, cost-effective method for N -glycopeptide preparation using commercially available magnetic particles. They compared two types of magnetic particles, carboxylated polymer beads and cellulose resin. They found that the magnetic particles made of cellulose worked via HILIC to gather the N -glycopeptides from the sample while allowing the non-glycopeptides to pass through. The team evaluated this method for blood-derived samples of plasma and serum and then with tissue samples. They tested their method on samples from patients with gastric cancer and were able to detect cancer-related changes in the glycoproteins.
“The SP3-based N -glycopeptide preparation method using commercially available cellulose magnetic beads is a robust and automate-friendly approach for N -glycoproteomics,” said Nakajima. Preparation using the cellulose magnetic particles exhibited higher glycopeptide recovery and non-glycopeptide removal efficiencies in the preparation of various sample types. “The method is believed to be a global standard method for analyzing glycoproteomics profiles,” said Nakajima.
Looking ahead the team hopes to adapt this process on a larger scale for automation. “In the HGA project, we are developing a homemade fully automated system implementing the robotic protocol. The system will be applied for plasma/serum and tissue sample preparation, and further in-depth glycoproteomics,” said Nakajima.
The research team includes Ken Hanzawa, Matej Nemcic, and Kazuki Nakajima from the Institute for Glyco-core Research, Gifu University; Miki Tanaka-Okamoto from the Department of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute; and Yasuhide Miyamoto from the Department of Clinical Laboratory, Osaka International Cancer Institute.
The research is funded by the Human Glycome Atlas Project, KAKENHI, and the joint research program of the J-GlycoNet Cooperative Network.
Molecular & Cellular Proteomics
Experimental study
Human tissue samples
N-Glycoproteomics sample preparation using commercially available cellulose magnetic particles
11-Aug-2026