Systems and methods for characterizing low molecular weight (LMW) protein drug product impurities are provided. One embodiment uses hydrophilic interaction chromatography (HILIC) coupled to mass spectrometry analysis. After removal of the N-linked glycans from the protein drug product, for example an antibody drug product, the elution of LMW impurities from the HILIC column was determined by the size of the molecular weight species. In some embodiments, the HILIC separation is performed under denaturing conditions, making the detection of LMW forms using this method highly comparable to both SDS-PAGE and CE-SDS methods. LMW drug product impurities include, but are not limited to light chain, half antibody, H2L, H2, HL, HC, peptide backbone-truncated species, and combinations thereof.

In one aspect, the present disclosure provides GlcNAc-Asn analogs of the formula (I): wherein the variables are as defined herein. In another aspect, the present disclosure also provides pharmaceutical compositions and methods of using the compounds disclosed herein. Additionally, the present disclosure also provides methods of treating cancer comprising inhibiting NGLY1. ##STR00001##

Provided herein are methods for assessing cell surface glycans, e.g., N-glycans, by assessing a sample of released surface glycans, and determining the presence, absence, or level of glycans present in the sample. Also provided are methods of assaying and/or evaluating a cell composition by assessing the cell surface glycan profile of the cell composition and comparing the profile to a reference sample. Methods for manufacturing and/or culturing a plurality of cell compositions having consistent surface glycan expression with low variability are also provided.

Materials and methods of in vivo possessing of target proteins in plants by co-expressing with proprotein processing enzyme, human Furin, are provided. A method of expressing highly soluble and functional active human Furin in plants also is provided.

Provided herein are methods for assessing cell surface glycans, e.g., N-glycans, by assessing a sample of released surface glycans, and determining the presence, absence, or level of glycans present in the sample. Also provided are methods of assaying and/or evaluating a cell composition by assessing the cell surface glycan profile of the cell composition and comparing the profile to a reference sample. Methods for manufacturing and/or culturing a plurality of cell compositions having consistent surface glycan expression with low variability are also provided.

Provided are pharmaceutical compositions each comprising a glycosylation agent, an antibody that binds to human CD47, and a pharmaceutically acceptable carrier. Also provided are novel CD47 antibodies that bind to human CD47, wherein the antibodies bind to at least one epitope that is at one of the glycosylation sites of the CD47 protein of red blood cells (e. g, at least a glycosylation site near the epitope residues Gln31 and Thr34 in CD47).

Provided herein are methods of detecting glycosylated proteins, such as immune checkpoint proteins. Further provided are methods of treating cancer, such as by administering immune checkpoint inhibitors.

In one aspect, the present disclosure provides GlcNAc-Asn analogs of the formula (I): wherein the variables are as defined herein. In another aspect, the present disclosure also provides pharmaceutical compositions and methods of using the compounds disclosed herein. Additionally, the present disclosure also provides methods of treating cancer comprising inhibiting NGLY1.

##STR00001##

In one aspect, the present disclosure provides GlcNAc-Asn analogs of the formula:

##STR00001## wherein the variables are as defined herein. In another aspect, the present disclosure also provides pharmaceutical compositions and methods of using the compounds disclosed herein. Additionally, the present disclosure also provides methods of treating cancer comprising inhibiting NGLY1.

The invention provides modular cell-free de-novo synthesis of glycans with immobilized bionanocatalysts. The invention provides materials, and in particular, magnetic materials, for producing glycans of defined length and sequences using one or more enzymes that are immobilized within bionanocatalysts (BNCs) which in turn are embedded within scaffolds to control the synthesis in batch or continuous processes manufacturing. In some embodiments, the scaffolds are high magnetism and high porosity composite blends of thermoplastics or thermosets comprising magnetic particles that form powders. In some embodiments, Selective Laser Sintering (SLS) is used to design and produce objects via 3D printing by sintering composite magnetic powders. The modular flow cells may be mixed and matched for a highly customizable and highly efficient cell-free manufacturing process. In some embodiments the elementary and system modules provided by the invention are employed. In preferred embodiments, human milk oligosaccharides (HMOs) are produced.