Consultation on experimental design and general procedures
- Arrange an intake meeting with Jeroen Demmers
Sample preparation
- Extraction of proteins from tissue, cell lysates, body fluids, IP-ed proteins, etc.
- Protein clean-up and digestion (various proteases), also for middle-down analysis
- Complete workflows for post-translational modifications (PTM) enrichment (ubiquitination, phosphorylation, acetylation and many more)
- Depletion of highly abundant proteins for plasm / serum profiling
- Orthogonal fractionation of proteins and peptides (HILIC, high pH, SCX, etc.)
Mass spectrometry
- Orbitrap Exploris 480 (Thermo)
- Orbitrap Eclipse (Thermo)
- Orbitrap Fusion Lumos Tribrid (Thermo)
- Orbitrap Q Exactive Plus (Thermo)
All systems are set up in a nanoflow LC-MS configuration – see Equipment for details.
Protein analysis
- Protein identification from gel bands
- Co-immunoprecipitations and protein complex characterization
- In-depth global proteome profiling
- Characterization of PTMs // analysis of PTM subproteomes
- Quantitative proteomics (LFQ, SILAC, TMT(Pro), dimethyl, etc.)
- Targeted quantitative proteomics (parallel reaction monitoring, PRM) w/ or w/o AQUA peptides
- Data independent acquisition (DIA)
- Plasma / serum proteome profiling
- HLA peptide analysis
- De novo peptide sequencing
- Intact protein analysis
- Exosome profiling
Data analysis and bioinformatics
The software packages we use include:
- Proteome Discoverer (Thermo)
- Mascot (MatrixScience)
- MaxQuant / Perseus (Cox/Mann labs)
- Spectronaut (Biognosys)
- DIA-NN (Demichev/Ralser labs)
- PEAKS (Bioinformatics Solutions Inc.)
- R
- Various customized software tools
Data analysis and interpretation include basic statistical procedures (t tests > volcano plots, etc.)
Description of experimental procedures & data sharing
- Description of proteomics workflow for materials & methods section
- Raw data deposition (ProteomeXchange)