Consultation on experimental design and general procedures


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)