de Botton Institute for Protein Profiling


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Global quantification of protein expression (‘Discovery’ type experiments):

We can analyse almost any biological sample, including cell lines, tissue, formalin fixed paraffin embedded tissue, bio-fluids, plants, fungi, and more. 

Our main application where we aim to quantify as many proteins as possible using either label free or SILAC based methods, in simple and complex biological samples. ‘Discovery’ type experiments can be performed using either 1DLC, where the typical coverage is ~3,000 proteins from ~3e5 cells. When using 2DLC(prefractionation), we can reach as many as 9,000 proteins from 1e6 cells.

Analysis of protein-protein interactions:
Analysis of samples after Co-IP.

Global quantification of the phosphoproteome (Fe-IMAC):
Enrichment of phosphopeptides followed by either discovery or targeted analysis. From 2mg protein we can identify >5,000 phosphopeptides.

Targeted quantification of proteins and PTMs (SRM, PRM):
A powerful technique for specific and sensitive quantification of proteins and their PTMs. Targeted quantification is suitable for hypothesis driven experiments, where the proteins of interest are already known.

Intact protein analysis

Analysis of intact proteins for MW determination

De novo sequencing of single proteins using our DiPS method

We developed a novel method for full-length, de novo sequencing of single proteins or antibodies.

Global detection of ubiquitination sites (using anti k-GG enrichment). 

Analysis of serum/plasma including immunodepletion:
Immunodepletion of abundant proteins using the MARS14 column, followed by either targeted or discovery analysis.

Analysis of histone modifications.

Global analysis of S-nitrosylation (SNO-RAC method):
Enrichment of S-nitrosylated peptides using the SNO-RAC method.

Global analysis of protein redox states (OxiCAT):
Analysis of redox sensitive proteins in complex samples using the OxiCAT method.