PROTEOMICS TECHNIQUES

Protein Identification (Code #ID-BAND-001)

  • Protein identification of a sample submitted in a gel band

High Throughput Protein Profiling (Code HD#ID-PROFILE-002/003)

  • Identification of proteins in a complex sample; optional fractionation depending on sample complexity, objective, protein amount or budget

Quantitative Analysis – High Throughput chemical & enzymatic labeling (Code HT#QUANT-C&E-004/005)

  • Quantitative analysis of two different samples, providing a catalogue of the proteins present, and a statistical analysis reflecting the changes at the protein levels observed across conditions. Optional fractionation

Quantitative Analysis – High Throughput Metabolic labeling (Code HT#QUANT-SILAC-006/007)

  • Quantitative analysis of two different samples, providing a catalogue of the proteins present, and a statistical analysis reflecting the changes at the protein levels observed across conditions. Labeled samples are provided by the user. Optional fractionation.

Quantitative Analysis – High Throughput Isobaric labeling (Code HT#QUANT-iTRAQ-4plex-008/009)

  • Quantitative analysis of four different samples, providing a catalogue of the proteins present, and a statistical analysis reflecting the changes at the protein levels observed across conditions. Optional fractionation.

Quantitative Analysis – High Throughput Isobaric labeling (Code HT#QUANT-iTRAQ-8plex-010/011)

  • Quantitative analysis of eight or ten different samples, providing a catalogue of the proteins present, and a statistical analysis reflecting the changes at the protein levels observed across conditions. Optional fractionation.

PTM Profiling (Code #PTM-PROFILE-012)

  • Identification of proteins and several stable PTMs readily identifiable by database searching, such as acetylation, methylation, deamidation, etc. Optional fractionation.

Functional interaction Profiling (Code #IPP-PROFILE-013)

  • Protein identification from pull-down experiments, comparing control samples and different conditions.

Custom analysis

  • Please contact the Unit for other particular analyses

PROTEOMICS EQUIPMENT

Mass spectrometry systems

  • A Thermo Scientific Orbitrap Fusion Tribrid mass spectrometer with ETD (incorporated at 2015). This spectrometer combines a quadrupole, an Orbitrap, and an ion trap mass analyser in a novel Tribrid architecture that delivers unprecedented capabilities and depth of analysis. It enables scientists analyzing low-abundance, high-complexity, or difficult samples to identify more compounds more quickly, and quantify more accurately.
  • A Thermo Scientific Q Exactive HF mass spectrometer (incorporated at 2013). This instrument features an ultra-high-field Orbitrap analyzer which doubles its speed and resolution – more samples run and better data quality. The system utilizes also an advanced quadrupole design for high analytical performance. The combination is optimal for quantitation challenges where the combination of speed and highest performance are essential for the highest spectra quality and depth.
  • A Thermo Scientific Orbitrap Elite mass spectrometer (incorporated at 2011). This spectrometer combines a dual-pressure linear ion trap (Velos Pro) with a high-field Orbitrap mass analyzer to increase sensitivity and reliability, a greater dynamic range for better precursor detection, and the power of MSn identification. It is especially useful when analyzing samples of high complexity and targeting analytes of low abundance in applications such as proteomics, metabolomics and lipidomics.
  • A Thermo Scientific Q Exactive mass spectrometer (incorporated at 2011). This hybrid quadrupole-Orbitrap mass spectrometer combines high-performance quadrupole precursor selection with high-resolution, accurate-mass Orbitrap detection for a wide range of qualitative and quantitative applications.
  • A Thermo Scientific LTQ Orbitrap XL with ETD mass spectrometer (incorporated at 2008). Combining fast, sensitive linear ion trap MSn with high-resolution, accurate-mass Orbitrap technology, is the instrument of choice for confident, reliable detection, identification, and characterization. The standard higher-energy collisional dissociation (HCD) collision cell provides exceptional flexibility in fragmentation for advanced proteomics and small-molecule research. The electron transfer dissociation (ETD) mode generates information for complementary analyses.
  • An Sciex QTRAP 4000 mass spectrometer (incorporated at 2003). This hybrid system houses a triple quadrupole/linear ion trap (LIT) analyzers to improve the sensitivity in ion trap scan modes to excel at metabolite identification, detection and confirmation, and in protein/peptide quantitation for biomarker verification and validation.

Commercial mass spectrometry software packages for database searches running on two HPC clusters (Thermo Proteome Discoverer v2.1; Scaffold Q+ from Proteome Software) and in-house algorithms and open source tools for data analysis are available.

Other resources

  • SpeedVac
  • Agilent HPLC 1290 Infinity
  • A Typhoon 9400 scanner equipped with 3 laser lines from GE Healthcare