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Proteomics Core Facility

This facility provides a full proteomics infrastructure for the identification and characterisation of proteins.

Infrastructure in this facility is centered around state-of-the-art mass spectrometry for MS and LC-MSMS experiments. This is complemented by chromatographic and electrophoretic systems for protein and peptide separation.
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Mikhail Savitski

Team Leader, Senior Scientist and Head of Proteomics Core Facility

ORCID: 0000-0003-2011-9247

The Proteomics Core Facility provides a full proteomic infrastructure for the identification, quantification and characterization of proteins. This includes various platforms for protein and peptide separation, and state-of-the-art mass spectrometry for MS and LC-MS/MS experiments.

This website intends to give guidelines for sample submission to the PCF, and to provide practical information on sample preparation.

Services

Proteomics:

Project planning, sample preparation, data acquisition and data analysis/ visualization
Protein identification from in-gel or in-solution samples
High resolution and high mass-accuracy MS, MS/MS, and LC-MS/MS (Q-Exactive plus, Fusion Lumos, Exploris 480) for identification and quantification of proteins in complex mixtures
Protein quantification by stable-isotope labeling (e.g TMT labelling)
Identification of post-translational modifications on purified proteins
Multi-dimensional peptide separation (liquid chromatography)
Determination of N- and C-termini of proteins and products of limited proteolysis
Verification of incorporation of non-natural amino acids

Techniques and approaches

The Proteomics Core Facility offers a range of techniques for the identification, characterization and quantification of proteins and proteomes. These include the following techniques and approaches, often used in combination:

Protein and Peptide Separation

High pH (pH 10) reverse phase chromatography, for offline fraction collection, as a pre-fractionation step in peptide-based proteomics, prior to LC-MS/MS analyses
Peptide-Size Exclusion Chromatography for crosslinked peptides (only internal service)

Protein Digestion and Labelling

Protein digestion in-gel or in-solution, using a variety of proteases (trypsin, LysC, chymotrypsin, ArgC, GluC, AspN)
In-gel acid hydrolysis for determination of N- /C- termini (eg. for samples from limited proteolysis experiments)
Peptide purification using Oasis HLB μElution plates (Waters), Sep-Pak C18 cartridges (Waters)
Peptide labelling with stable isotopes (TMT) for relative protein quantification

Mass Spectrometry: MS, LC-MS and LC-MS/MS

Identification of proteins from coomassie stained gels (please see here for MS compatible staining recipe)
Complex proteome analysis, often combined with additional protein or peptide fractionation techniques (listed above)
Peptide fragmentation by CID, HCD and ETD
Relative quantification of proteins and proteomes by stable isotope labelling (TMT), or data-independent acquisition (DIA) using high resolution and high mass accuracy LC-MS and LC-MS/MS
Identification of phosphorylation and other post-translational modifications on single protein level
Data analysis for all of the services listed above
For protein identification: databases can be customized to the user’s needs
For protein quantification, we analyse data with MS Fragger, DIA-NN or MaxQuant

Please contact us for additional applications that may fit your needs.

About the PCF

More than 400 projects per year
Supporting research groups at all EMBL sites and external groups
Manages currently five mass spectrometers and seven HPLC sytems
Instrumentation is aimed to run 24h/7days

Service fees

Consumables	EURO €
TMT6-plex labelling reagent	100
TMT10/11-plex labelling reagent	200
TMT16/18-plex labelling reagent	280
Desalting (per sample)	20
High pH reverse phase offline fractionation (per sample)	20
Peptide-Size exclusion chromatography (per sample)	20

Measurement time (per hour)	EURO €
Academia	100
Industry	150

In order to estimate the total price for a specific type of a proteomics experiment such as, for instance, a full proteome analysis, please contact the PCF (pcf@embl.de) to discuss.