Services

Sample
preparation

  • Protein extraction
  • Protein quantification
  • Digestion
  • Peptide clean-up
  • Phosphopeptide enrichment

Simple Western

  • Automated capillary electrophoresis
  • Targeted quantitation of proteins using antibodies
  • Data analysis and statistical tests

Mass
spectrometry

  • Protein identification
  • Protein quantitation by
    • label-free (LFQ)
    • isobaric labelling (TMT)
    • metabolic labelling ( SILAC)
  • Analysis of Post-Translational Modifications (PTM)
  • Data Dependant or Data Independent Acquisition workflows (DDA/DIA)
  • Data analysis and statistical tests

Typical workflows & applications

Total proteome profiling

Typical outputAmount neededFormat
6’000-8’000 protein groups identified and quantitated with high data completeness20 ug proteinAny number of samples
  • Extraction of proteins from cells or tissue samples, measurement of concentration
  • Protein digestion (miST or SP3) and peptide clean-up
  • MS analysis by DIA on Bruker TIMS-TOF Pro (90-min gradient). Identification by DIA-direct or via project-specific library (DDA on 6 basic-RP fractions)
  • Data processing, filtering and normalization. Statistical tests to identify significant changes. Full reporting

Protein interactions

Typical outputAmount neededFormat
500 – 2’500 protein groupsExperiment-dependentAny number of samples
  • Following affinity purification, proteins are digested on-beads or after elution.
  • MS analysis on Thermo Orbitrap instruments (Exploris 480 or Fusion) using 90-min gradients. Label-free quantitation.
  • Data processing, filtering, QC and normalization. Statistical tests to identify significant changes. Full reporting
  • Variants :
    • dedicated digestion procedures are used for proximity labelling samples ( streptavidin beads).
    • MS analysis on the Orbitrap Fusion with FAIMS interface can be used for increasing depth by ion mobility fractionation of peptides.
    • The classical geLC-MS/MS workflow is available on demand

Phosphoproteomics (Phospho-TMT 16-plex)

Typical outputAmount neededFormat
10’000-15’000 phosphosites identified and quantitated with data completeness > 80%150 ug proteinBatches of 16 samples to be compared directly
  • Extraction of proteins from cells or tissue samples in denaturing conditions and measurement of concentration
  • Protein digestion (SP3 method) and peptide clean-up
  • Labelling with TMT Pro reagents and QC
  • Phosphopeptide enrichment by IMAC
  • MS analysis on FAIMS-Orbitrap instrument with fractionation by ion mobility to increase depth
  • Parallel profiling of total proteomes on the same samples
  • Data processing, filtering, QC and normalization. Statistical tests to identify significant changes. Full reporting

See our technology page for more information on our instrumentation and our data analysis workflows.