The proteome analytics unit is associated with the Romeis group. Our group primarily engages in LC-MS/MS-based (phospho)-protein and (phospho)-proteome analyses. Deep proteomics, allowing quantification of up to 7000 proteins in a plant tissue sample is established. Discovery proteomics is complemented by protein interaction analyses and targeted approaches allowing accurate quantification of individual peptides in complex protein extracts. 
 

Phosphorylation 

Reversible, multi-site phosphorylation has as much an impact on protein function as translation of the polypeptide itself. We help to elucidate the function and mechanisms of calcium-dependent protein kinase (CDPK) signaling, and the dynamics changes on the levels of protein abundance, phosphorylation, and interaction in multiple biological scenarios. Our key questions are the following: 

• How does the plant (phospho)-proteome change due to CDPK activity?
• What are the immediate molecular kinase substrates of CDPKs?
• Can we identify single amino acids as key positions for protein activity regulation of CDPKs and their targets?

We have established phospho-peptide-enrichment strategies to detect phosphorylation of purified proteins (CDPK (auto)-phosphorylation and downstream substrate phosphorylation), targeted proteomics for single-site analysis, or phospho-proteome analysis to characterize global and comprehensive changes in the phosphorylation pattern dependent on CDPK activity. 
 

IPB and external collaborations

Alongside our own research, we provide proteomics services across all departments of the IPB, collaborate externally, and contribute to multiple projects and publications with a variety of approaches: protein identification, interaction studies, modification analysis (phosphorylation, ubiquitination, ADP-ribosylation, fluorescent labelling of specific amino acids, etc.), and proteome analysis. 

We aim to continuously improve our methods and repertoire, as well as service to the IPB and collaborators. 
 

Equipment: 

State-of-the-art LC-MS systems

• Orbitrap Fusion Lumos Tribrid Mass Spectrometer (ThermoFisher) with nLC1200 HP-LC (with link to the other web page)
• QExactive Plus (ThermoFisher) with nLC1000 HP-LC (with link to the other web page)

Application for a Orbitrap Astral Mass Spectrometer system (ThermoFisher) is pending.