Pre-MS Immuno Precipitation (IP) pull down sample pre-treatment

Application Service Description
IP sample pull downs
Parallel Reaction Monitoring
  • Specific enrichment of target protein(s)
  • Isolation of protein complexes
  • Ultra-sensitive assays when antibody pairs not available


  • By selecting the correct pull-down method the sensitivity of the resulting assay can be significantly improved.
  • Customer customisable, can use proprietary user reagents or off-the-shelf commercial products

The sensitivity of mass spectrometry to detect a particular protein(s) can be significantly enhanced when combined with selective enrichment tools  like an upfront, often custom made, immuno-precipitation using antibodies, aptamers or other affinity agent.  This approach can be beneficial when no suitable ELISA exists to this protein(s), or matrix effects make the ELISA impracticable due to interferences in the matrix of choice compared to buffer.   We do not even require a highly specific antibody as long as the target protein is recovered quantitatively, the resolution and speed of modern mass spectrometry platforms can handle some limited contamination during the pull-down step.

Pull-downs are also widely used to map and, in some cases quantify, Protein/Protein Interactions (PPI) from simple to highly-ordered complexes and the individual networks they represent.

Our typical pull-down workflow involves production of the affinity matrix (typically magnetic particle-based), capturing the protein(s) of interest, washing, on bead digestion and mass spectrometry.  For some analytes we will adapt the workflow to provide maximum recovery, which we always ensure is quantitative across the expected physiological range. 

We have also used immunoprecipitation to deliver clinical-grade assays where LOD, LLOQ, ULOQ, dilutional linearity etc are determined and sensitivity in the low pg/ml range is possible. This results in a Targeted Assay that can be used routinely on future samples submitted by the client.

Customers can supply samples where we perform the immuno-pull down, or the proteins already captured onto a matrix.

What’s included
  • Incoming sample QC to check sufficient protein in samples for a satisfactory analysis
  • Protein capture/elution
  • Computational proteomics and full bioinformatics analysis
  • Comprehensive report summarising the proteins, peptides and if applicable the peptide-PTM’s.  Data interpretation, pathway analysis and biological relevance
  • An Excel based QuantSheet detailing qualitative and quantitative protein  identification data.
  • Provision of all raw data if required
  • All stages to ELISA equivalent custom assay development 
Material required
  • This is analyse and assay specific - please contact us to discuss your specific target(s) 
Typical turnaround time
  • Generally 6 to 8 weeks from receipt of samples and completion of incoming sample QC for a Proof of Principle determination via LC-MS2.   For subsequent SRM/PRM Assay Development up to GCLP if required is subject to quotation