de Botton Institute for Protein Profiling

Overview

Mision statement

To produce the best data possible from any mass spectrometry based proteomics experiment. 

How?
  
We can use either a 'bottom-up' proteomics approach where proteins are extracted from the biological samples, subjected to enzymatic digestion followed by liquid chromatography - mass spectrometric analysis. Post-acquisition, the protein identity and quantity is reconstructed using cutting edge bioinformatics. Or we can perfrom top down analysis of small proteins using our Fusion Lumos mass spectrometer, equipped with multiple fragmentation technologies. We apply rigorous quality control and criteria for generating the best data from our instruments.

 

 

Methodologies

Discovery proteomics

MethodologiesIn a ‘discovery’ type experiment we aim to identify and quantify as many proteins as possible from the samples we receive. We can perform such analyses either label-free or using SILAC (whichever is most appropriate to the experiment at hand). The main advantage of the discovery approach is the unbiased, wide range screen of thousands of proteins at a time. In a label-free experiment such wide-scale proteomic profiling can be performed across dozens of samples.

Targeted proteomics

In a ‘targeted’ type experiment we quantify a specific set of proteins using their serrate tryptic peptides. This is conducted using synthetic, stable heavy isotopically labeled peptide standards. The analysis is conducted either on our tandem quadrupole mass spectrometer, in Selective Reaction Monitoring (SRM) mode or on our high resolution quadrupole Orbitrap mass spectrometer, in Parallel Reaction Monitoring mode (PRM). The main advantage of these techniques is the sensitive, specific and reproducible quantification of peptides and proteins.