Protein Analytical Service

Empowering High-Quality Antibody Production with Advanced Protein Analysis Technology

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Overview

GenScript’s Comprehensive Protein Analysis Platform is an advanced, integrated system designed for in-depth study and evaluation of protein characteristics. It offers a wide range of services, including qualitative & quantitative analysis, protein modification analysis, impurity analysis, molecular interaction analysis, and more customized analysis. Together, these capabilities make the platform an essential tool in protein research, drug development, and biopharmaceutical production.

Qualitative & Quantitative Analysis

Concentration
Purity (SDS-PAGE, CE-SDS, icIEF, SEC-HPLC, RP-HPLC, HIC-HPLC, etc.)
Intact mass /Native mass
(in gel) Peptide mapping
N/C terminal sequencing

Protein Modification Analysis

PTM analysis
Disulfide bond mapping
N-glycan and O-glycan profiling
Sialic acid analysis

Impurity
Analysis

Endotoxin quantification
HCP identification /quantification
Residual DNA quantification
Residual Protein A quantification

Molecular Interaction
Analysis

Antibody-antigen affinity analysis >>
Protein-protein/DNA /small molecule interactions
Fc effector function
Enzyme activity assay

Customized
Analysis

Monoclonal antibody self-interactions
Monoclonal antibody polyspecificity
Thermal stability analysis
Mutation site analysis
Free-thaw stability analysis
Antibody de novo sequencing
More customized services available

Talk to an Expert Quote/Order

Advanced instruments for protein analysis

Waters BioAccord LC-MS

Thermo QE Orbitrap LC-MS/MS

Waters Xevo G3 QTOF

Biacore 8K

Octet RED

qPCR

Plate reader

TR-FRET

LabChip CE-SDS

Maurice iCIEF

Agilent GC

Cedex analyzer

Waters UPLC

Optimize Your Research with Precision-Fit Assays

Identify your research stage and discover tailored services to accelerate your progress!

Antibody Drug Discovery

Gene to Hits

Hits to Leads

Candidates Selection

Discovery & Target
Identification

Hits Screening

Lead Indentifaction
& Validation

Lead Optimization

In vivo & vitro Assays

GLP Tox

0.05mg

500mg

200g

TurboCHO™ HT

TurboCHO™ Express

TurboCHO™ HP/TurboCHO™ Stable

Qualitative & Quantitative Analysis
Molecular Interaction Analysis

Purity by CE-SDS or HPLC
Affinity screening/ranking >>
HT antibody stability screening
More customized services available

Qualitative & Quantitative
Analysis

Purity by HPLC
Intact mass
Peptide mapping
N/C terminal sequencing
More customized
services available

Protein Modification & Molecular
Interaction Analysis

Identification by mass
PTM analysis
Disulfide bond mapping
N-/O- glycan profiling
Sialic acid analysis
Fc binding affinity >>
More customized services available

In Vitro Diagnostic Development

Target Screening

Assay Development

Assay Validation and Optimization

Diagnostic
Commercialization

Biomarker
Discovery

Replication
Confirm markers and reproducibility of assays

Analytical Development
Translation onto a clinical diagnostic platform

Phase I
Sensitivity & Specificity

Phase II
PPV and NPV

Phase III
Clinical benefit
& Cost effectiveness

Registration

0.05mg

500mg

10g

TurboCHO™ HT

TurboCHO™ Express

TurboCHO™ HP/TurboCHO™ Stable

TurboCHO™ Stable

Qualitative & Quantitative Analysis
Molecular Interaction

Purity by CE-SDS or HPLC
Affinity screening/ranking >>
More customized services available

Protein Modification & Molecular Interaction Analysis

Identification by mass
PTM analysis
Glycan analysis
Binding affinity assay >>
More customized services available

Interested in learning more about protein assay method?

Discover their applications, benefits, and explore case studies below.

Qualitative & Quantitative Analysis
Protein Modification Analysis
Molecular Interaction Analysis
Impurity Analysis

Qualitative & Quantitative Analysis
Applications	Assay list	Benefits
Purity Analysis	SDS-PAGE	High acceptance
	CE-SDS	High accuracy Automated High resolution
	HPLC	Broad applicability
	UPLC	Ultra-high pressure resistance Minimal delay volume Minimal sample residue
Routine molecular weight detection	Non-deglycosylated detection: Intact mass Reduced mass	Suitable for characterization of glycosylation modifications and protein assembly
Routine molecular weight detection	N-glycan removal detection: De-glycosylated mass Reduced and de-glycosylated mass	High intensity mass spectrometry More accurate determination of protein chain Suitable for bispecific antibody identification
Characterization of heavily glycosylated proteins	Denatured N-glycan removal detection: De-glycosylated mass(denatured) Reduced and de-glycosylated mass(denatured)	Suitable for the identification of complete molecular weight measurement of proteins with complex modifications.
Characterization of heavily glycosylated proteins	Denatured N-glycan and O-glycan removal detection: De-O-glycosylated mass Reduced and de-O-glycosylated mass	Simultaneous removal of N-glycans and O-glycans Elimination of their interference with protein detection
Characterization of complex formation under the native state	Native mass	Mild detection conditions and native state preservation Suitable for analysis of protein complexes linked by non-covalent bonds Suitable for analyzing the degree of small protein aggregation
Characterization of the complete protein sequence	Sequence coverage	Minimal impact of protein purity 100% sequence coverage
Characterization of the complete protein sequence	in-gel sequence coverage	Qualitative analysis of the band of interest
Characterization of protein N-terminal and C-terminal sequences	N/C-terminal sequence	Confirm full protein expression Detect breaks in protein expression Identify N/C-terminal modifications

Case1 Native mass - BsAb – Identification of the non-covalently linked chain

Native mass spectrometry is often used to identify the components of bispecific antibodies. The molecular weights of the marker bands in Fig 1A are 150 kDa, 120 kDa, 100 kDa, 74 kDa, and 23 kDa. Under denaturing conditions, the 150 kDa light chain was not identified by conventional mass spectrometry. This indicates that non-covalent interactions between proteins were disrupted under these conditions (Fig 1B). In contrast, native mass spectrometry reflected the original state of the proteins and successfully identified the light chain (Fig 1C).

Figure 1 SDS-PAGE and Mass analysis of BsAb1

Case 2 In-gel sequence coverage - Biotinylated protein – Identification for low concentration protein

Detection of biotinylation efficiency for protein-1 was requested by the customer. However, its concentration is far below the requirement and it is difficult to concentrate. Nevertheless, the SDS-PAGE bands were relatively clear (Fig 1). By excising the target band from the gel and performing coverage analysis, the biotinylation efficiency was successfully identified (Fig 2, Tab 1).

Figure 1 SDS-PAGE of protein-1

Figure 2 Fragment coverage map of protein-1

Table 1 Peptide coverage analysis of protein-1

Site	Mod	M/Z	Charge St.	Mono Mass Exp.	Mono Mass Theo.	△ ppm	Biotinylation ratio %
K1296	Biotinylation	980.803	3	2938. 385	2938.392	-2.36	99.3

Protein Modification Analysis
Assay List	Benefits
Glycosylation mirror comparison	Suitable for the analysis and determination of glycosylation sites and their respective proportions in proteins.
Biotinylation ratio (peptide mapping)	Targeted enzymatic cleavage for Avi tag analysis High accuracy
Disulfide bond analysis	Suitable for determination of sites and proportions of disulfide bond formation between cysteine residues in proteins
N-glycosylation site	Suitable for determination of sites and proportions of N-glycosylation
PTM-phosphorylation	Suitable for determination of sites and proportions of protein modifications
PTM-deamidaton
PTM-oxidation

Case1 Glycosylation mirror comparison – Glycoprotein – Production process optimization and selection

Ab-1 and Ab-2 are the same protein produced by different hosts with different glycosylation patterns. Glycosylation mapping analysis identifies the glycosylation sites and proportions of Ab-1 and Ab-2, facilitating process optimization and selection.

Figure 1 Reduced Mass analysis of Ab-1 & Ab-2

Table 1 Glycosylation analysis of Ab-1 & Ab-2

NO.	Mass (Da)	Glycan Name	Ratio%
NO.	Mass (Da)	Glycan Name	Ab-1	Ab-2
1	50063	N Glycosylation Man5	3.3%	1.4%
2	50086	N Glycosylation G0F-GlcNac	5.9%	4.2%
3	50290	N Glycosylation G0F	84.5%	85.9%
4	50452	N Glycosylation G1F	6.3%	8.6%

Note：Mass value is from Ab-1.

Molecular Interaction Analysis
Applications	Assay List	Benifits	Recommendation
Antigen-antibody affinity analysis Protein-protein interaction Protein-DNA interaction Protein-small molecule interaction	Bio-Layer Interferometry >>	Target-free, real-time detection, high throughput Relatively low cost High sample compatibility Sample recovery available	Suitable for the detection of supernatants BLI and SPR perform comparably when used to detect samples with moderate affinity(KD µM~nM).
	Surface Plasmon Resonance >>	Target-free, real-time detection, high throughput High sensitivity, broader affinity detection range Capable of detecting small molecules (100 Da)	Suitable for detecting low-affinity(KD ~µM) and higher affinity (KD ~0.1 nM) samples

Case 1 SPR – IgG Affinity –SPR has high sensitivity and broad affinity detection range (KD = 10^-3-10^-15)

As shown in Fig 1 and Tab 1, SPR has higher sensitivity and a wider affinity detection range than BLI. SPR is suitable for both low-affinity (KD ~µM) and high-affinity (KD ~0.1 nM) samples, which may not be successfully detected by BLI.

Figure 1 Affinity binding curves of human IgG-1, 2, 3

Human IgG-1

Human IgG-2

Human IgG-3

Table 1 Affinity binding detailed analysis report of human IgG-1, 2, 3

Ab	Chip	Affinity	Test item	Chi² (RU²)	Ka (1/Ms)	kdis (1/s)	KD (M)
Human IgG-1	ProA	Medium	Affinity	4.90e-02	1.39e+05	2.07e-03	1.49e-08
Human IgG-2	ProA	High	Affinity	3.41e-01	2.75e+04	3.59e-05	1.30e-09
Human IgG-3	ProA	Low	Kinetics	4.75	-	-	3.818E-07

Case2 BLI v.s. SPR – IgG Affinity - BLI and SPR results are comparable for most antibody-antigen interactions

Most antigen-antibody interactions fall into the category of medium affinity samples, for which the detection results (KD) of BLI and SPR are nearly identical.

Rabbit IgG

Mouse IgG

Impurity Analysis
Applications	Test Items	Benefits
Host cell protein analysis	ELISA or LCMS	Provides reference for upstream manufacturing and downstream applications
Residual DNA	qPCR based	/
Residual Protein A	ELISA	/

Case 1 Host cell protein analysis – Impurity protein – SDS-PAGE unknown band Identification

An unknown band was detected in several production batches of the protein (Fig 1). After excluding protein contamination, this band was suspected to be a host cell protein (HCP). HCP analysis preliminarily identified the band as phosphopyruvate hydratase (Tab 1). Further sequence analysis revealed a sequence coverage of 90.9% for this protein, confirming the band as the host cell protein phosphopyruvate hydratase (Fig 2).

Figure 1 SDS-PAGE of expression sample

Table 1 Sequence coverage map report of the unkown band

Figure 2 Sequence coverage map of the unkown band

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Protein Analytical Service

Empowering High-Quality Antibody Production with Advanced Protein Analysis Technology

Overview

Advanced instruments for protein analysis

Interested in learning more about protein assay method?

Qualitative & Quantitative Analysis

Protein Modification Analysis

Molecular Interaction Analysis

Impurity Analysis

Get in Touch with GenScript Protein Analytical Service

REQUEST A QUOTE

EMAIL

PHONE

ONLINE FORM

ONLINE FORM

Get in Touch
with GenScript Protein Analytical Service