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The proteins are typically cleaved by trypsin into peptides (in-gel, in-solution or filter-aided sample preparation (FASP)) and analyzed by nano LC MS-MS. The detected peptides are matched against the sequence of the purified protein or against a publicly available protein database as SwissProt using Proteome Discoverer.
For complex samples an optional off-line fractionation step as High pH liquid chromatography can be included in the workflow to facilitate identification of low abundant proteins and to improve the number of protein identifications.

Samples can be either in-solution, as a protein pellet or a protein band from a gel separation. Avoid the use of detergents as NP40, Triton X100 and Tween in any buffers since their presence significantly interferes with the downstream MS analysis.

Gel cuts are submitted in a tube and covered by 3% acetic acid in ultra-pure water. We prefer Coomassie blue-visible protein bands. In case of silver staining, please use an MS compatible silver staining method (e.g. Pierce Silver Staining for Mass Spectrometry Kit, Thermo #24600). 

This platform supports large-scale, reproducible, and quantitative proteomic profiling from various clinical sample types, including fresh frozen tissue and formalin-fixed paraffin-embedded (FFPE) specimens.

Samples are lysed and processed in a fully automated workflow using the BioMek i7 liquid handling workstation, ensuring high reproducibility and throughput suitable for clinical research settings. For data acquisition, the platform utilizes the TimsTOF HT and Orbitrap Astral MS instruments, providing next-generation sensitivity and throughput optimized for deep clinical proteome analysis.

The recent developments in MS-based plasma proteomics have opened completely new opportunities with significantly improved proteome coverage and throughput. A breakthrough in plasma proteomics is the development of nanoparticle-based enrichment strategies for low-abundance proteins and Data-Independent Acquisition (DIA).

The Proteomics Core Facility (PCF) has implemented Biognosys' P2 Enrichment technology, enabling quantification of 4500-7000 plasma proteins dependent on disease. Integrated with automated sample preparation workflows, and TimsTOF HT and Orbitrap Astral MS instruments, the platform for precision medicine delivers high-throughput, reproducible and clinically relevant data for biomarker discovery, disease understanding, and precision medicine.

Glycobiosynthesis is a non-template driven process, where complex structures (branched and linear) are produced from monosaccharide building blocks by multiple and competitive enzymatic actions. This complexity of the glycobiosynthesis presents an analytical challenge for studies of protein glycosylation.

Due to the structural complexity and the diversity of glycans, protein glycosylation studies are traditionally carried out on the released glycans. The analysis of released glycans (glycomics) provides detailed quantitative and structural glycan data, however, it lacks their protein site-specific information and glycoproteomics should be applied for studies that require characterization of the glycans on the proteome level.

Analogous to proteomics, glycoproteomics is based on advanced Mass Spectrometry technologies optimized for either global or directed analysis of glycoproteins in biological samples. Depending on the selected methodologies, glycoproteomics is capable to provide:

• identification and quantification of the proteins carrying glycosylation
• identification of the glycosylation sites and site occupancies
• site-specific characterization of the glycan structures (monosaccharide compositions and micro heterogeneity)

Protein glycosylation studies often demand a complex design and addressing even one of the above listed questions would frequently require application of multiple advanced technologies for sample preparation and analysis as well as an in-depth knowledge of systems biology and medicine. Therefore, we encourage you to come and discuss with us about your glycoproteomic projects to ensure optimal design in respect to the available material and your biological question.

Glycoproteomics has been identified as an important research field and is currently supported by the national BioMS infrastructure () as well as SciLifeLab (). 

Phosphoproteomics is the study of changes in the protein phosphorylation pattern due to different treatments or conditions. Quantification of phosphorylation sites among different conditions is often accomplished using labeling with isobaric tags (see quantitative MS).

Especially the treatment and harvest of samples for phosphoproteomics experiments require attention; therefore please contact the Proteomics Core Facility already during study design. 

Phosphoprotein samples are lysed in the presence of phosphatase inhibitors and digested with trypsin. The resulting peptides are labeled with different versions of isobaric tags, and combined into one sample. A small aliquot is used for quantitative proteomics in order to check the protein level background, whereas the majority is subjected to phosphopeptide enrichment. Typically, (phospho)peptides originating from whole cell lysates are pre-fractionated to reduce complexity. Phosphorylation sites are detected by their additional mass of 80 Da on the modified amino acid. Quantification is performed on TMT reporter ions created during fragmentation in the mass spectrometer.