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Proteomics Core Facility

Empowering research through mass spectrometry-based proteomics

The Proteomics Core Facility offers comprehensive protein and peptide analyses using state-of-the-art LC-MS/MS mass spectrometry. Our services are complemented by advanced sample processing workflows and expert support in experimental design, data interpretation and statistical analysis.

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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 LC-MS/MS experiments.

Services

  • 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 LC-MS/MS (Q-Exactive plus, Fusion Lumos, Exploris 480, Astral) for identification and quantification of proteins
  • Protein quantification by stable-isotope labelling (e.g. TMT labelling) and label-free (e.g. DDA and DIA) approaches
  • Identification of post-translational modifications on purified proteins
  • Determination of N- and C-termini of proteins and products of limited proteolysis
  • Global phosphoproteome and acetylome analyses
  • Crosslinking MS on purified protein complexes

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 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 desalting using C18 cartridges
  • Peptide labelling with stable isotopes (TMT) for relative protein quantification
Peptide enrichment
  • Fe-IMAC-based enrichment of phosphorylated peptides
  • Antibody-based enrichment of acetylated peptides
Peptide Separation
  • Offline high pH reverse phase chromatography, as a pre-fractionation step in peptide-based proteomics to enhance sensitivity
  • Peptide-size exclusion chromatography for crosslinked peptides for non-enrichable crosslinker
LC-MS/MS
  • Peptide separation by C18 nano-HPLC
  • Peptide ionization by electrospray ionization (ESI)
  • Peptide fragmentation by collision-induced dissociation (CID), higher-energy collisional dissociation (HCD) and electron-transfer dissociation (ETD)
  • Data-dependent (DDA) and data-independent acquisition (DIA)
Data analysis
  • Data analysis with MS Fragger, DIA-NN, pLink3, Skyline or MaxQuant
  • Statistical analysis
  • Data visualization
  • Data discussion

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

About the PCF

  • More than 600 projects per year
  • Supporting research groups at all EMBL sites and external groups
  • Active member of the Proteomics working group Core for Life
  • Managing currently five mass spectrometers and seven HPLC systems
  • Instrumentation is aimed to run 24h/7days

Service fees

ConsumablesEURO €
Sample processing fee (per sample)3
TMT6-plex labelling reagent100
TMT10/11-plex labelling reagent200
TMT16/18-plex labelling reagent280
Phosphoenrichment (per sample)20
Desalting (per sample)20
Offline high pH reverse phase chromatography (per sample)20
Peptide-size exclusion chromatography (per sample)20
Measurement time (per hour) EURO €
Academia 100
Industry150

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.

Contact

Proteomics Core Facility

EMBL Heidelberg
Meyerhofstraße 1
69117 Heidelberg
Germany

Tel: +49 6221 387-8388
Email: pcf@embl.de

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