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 output
Amount needed
Format
6’000-8’000 protein groups identified and quantitated with high data completeness
20 ug protein
Any 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 output
Amount needed
Format
500 – 2’500 protein groups
Experiment-dependent
Any 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 output
Amount needed
Format
10’000-15’000 phosphosites identified and quantitated with data completeness > 80%
150 ug protein
Batches 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 ourtechnology page for more information on our instrumentation and our data analysis workflows.