Proteomics Services

The main area of expertise of the proteomics facilities, that are part of the X-omics research infrastructure, consists of quantification of cellular proteome, phosphoproteome, and protein complexes. The services offered by the facilities are described in more detail below.

Quantification of cellular proteome

Whole cell lysate quantitative proteomics (starting from cell pellet or sample lysate)

Quantification of phosphoproteome

Whole cell lysate quantitative phosphoproteomics (starting from cell pellet or sample lysate)

Quantification of protein complexes

LC-MS analysis of protein complexes (starting from purified samples or elution from beads/columns)

Data analysis

MaxQuant
Proteome Discoverer
MSFragger

Available equipment for these analyses

Q-Exactive Orbitrap Exploris MS
Orbitrap Fusion Lumos Tribrid MS
TimsTOF Pro MS

All services mentioned above are custom services.
Please contact our helpdesk for a quote with turnaround times and prices based on your research question.

Service	Description	Turnaround time	Costs	Equipment	Data Analysis
Whole cell lystate quantitative proteomics	Quantitative analysis of cell proteome starting from cell pellet or sample lysate	1 - 6 months, depending on the size of the sample set	Custom*	Q-Exactive HF Orbitrap MS	MaxQuant
				Q-Exactive HF-X Orbitrap MS	Proteome Discoverer
				Maxis Plus MS	Proteome Discoverer
Whole cell lystate quantitative phosphoproteomics	Quantitative analysis of cell phosphoproteome starting from cell pellet or sample lysate	3 - 6 months	Custom*	Q-Exactive HF Orbitrap MS	MaxQuant
Whole cell lystate quantitative phosphoproteomics		3 - 6 months	Custom*	Q-Exactive HF-X Orbitrap MS	Proteome Discoverer
Affinity purification- MS for analysis of protein complexes	LC-MS analysis of protein complexes starting from purified samples on beads or elution from beads/columns	1 - 4 months	Custom*	Q-Exactive HF Orbitrap MS	MaxQuant
				Q-Exactive HF-X Orbitrap MS	Proteome Discoverer
				Maxis Plus MS	Proteome Discoverer
Quantitative proteomics in body fluids	Quantitative proteomics in body fluids with and without enrichment and/or fractionation	1 - 6 months, depending on the size of the sample set	custom*	Maxis Plus MS	MaxQuant

Costs
* Depending on size of sample set.