Protein Analysis

Proteins play a decisive role in determining the function of cells and tissues—not only through their sequence, but also through their structure, interactions, and post-translational modifications. Modern protein analytics provides access to this molecular level in both qualitative and quantitative terms, enabling detailed characterization of biological processes, material properties, and quality-related parameters.

At Fraunhofer IMWS, we possess in-depth technical expertise and state-of-the-art analytical technologies for the comprehensive characterization of proteins in complex samples. Our latest-generation Orbitrap Astral (Thermo Fisher Scientific) mass spectrometer (the first of its kind in the Fraunhofer Society) enables high-resolution analyses with high sample throughput.

We provide precise protein analyses from minimal sample quantities, even in challenging matrices such as the extracellular matrix (ECM). Our services include the untargeted identification and quantification of post-translational modifications (e.g., phosphorylation, degradation, and aging markers, AGEs), de novo sequencing of antibodies and unknown proteins, contamination analysis of protein preparations (e.g., host cell proteins), and the generation of protein profiles in animal and plant-based foods, including bioactive or flavor-influencing peptides.

Our methodological portfolio comprises state-of-the-art LC-MS/MS workflows, including data-dependent acquisition (DDA) and data-independent acquisition (DIA), de novo sequencing, and developing targeted approaches (PRM). This is complemented by isobaric labelling strategies (TMT) and label-free quantification (LFQ), enabling precise and efficient solutions for complex analytical questions.

Furthermore, we combine these analytical techniques with a broad portfolio of in-house physical and cell biological characterization methods for biomaterials. Embedded in an active research environment, we also draw on extensive expertise in peptide synthesis, protein structure analysis, protein modelling, amino acid analysis, and the analysis of small molecules.

 

Astral Promotional Video

Discover our LC-MS/MS platform: modern high-throughput proteomics with high precision, sensitivity, and reproducibility for research and quality control.

Post-translational modifications (PTMs)

High-resolution analysis of known PTMs (e.g., phosphorylations, AGEs), complemented by untargeted screening for novel or unexpected PTMs, for example, to elucidate biochemical signaling pathways. 

Extracellular matrix

Precise characterization of the extracellular matrix: high-resolution analysis of collagen and elastin, including age-related PTMs—relevant for skin (aging, fibrosis) and vascular diseases (atherosclerosis, aneurysm).

 

Antibody Sequencing

Sequence characterization and quality control: de novo sequencing for antibodies and unknown proteins, including host cell proteins (HCP) analysis to support development, process control, and release testing

Peptidomics

Quantitative peptide profiling for bioactive and flavor-relevant peptides, including assessment of degree of hydrolysis, stability, and batch consistency in animal and plant-based foods.

Identifying proteins in complex samples—and understanding how they interact—is a critical foundation for many forward-looking applications in medicine, biotechnology, and nutrition science. Advanced analytical capabilities enable, for example, the discovery of biomarkers for diagnostics and prognosis, as well as the identification and validation of targets for new therapeutics. In addition, they provide essential insights for toxicology, food quality control, and understanding of complex biological systems.

 

Clinical Research

Comprehensive characterization of tissue and cell culture samples—from single-cell analysis to complete tissue lysates—supporting diagnostics and target validation in drug development.

Nutrition

Precise analysis of proteins in animal- and plant-based foods, including the quantification of bioactive peptides and the identification of taste-relevant di- and tripeptides.

Extracellular Matrix (ECM)

Detailed analysis of extracellular matrix samples, for example, to identify and quantify post-translational modifications in proteins such as elastin associated with aging processes.

Post-Translational Modifications (PTMs)

In-depth analysis of canonical and non-canonical PTMs, including advanced glycation end products (AGEs) and fibrosis-associated modifications, enabling a deeper understanding of biochemical pathways and inflammatory responses.

De Novo Sequencing

Sequencing of antibodies and unknown proteins to identify novel biomarkers and uncover molecular mechanisms underlying diseases.