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Protein Identification by Mass Spectrometry (PIMS) Services

Our Protein Identification by Mass Spectrometry (PIMS) Services are designed to identify antibody cross-reactive proteins that reveal interesting changes in expression or phosphorylation in cells and tissues as uncovered with our Kinetworks™ multi-immunoblotting services and our Kinase-Substrate Profiling services. This service can also be used to identify purified preparations of proteins that are submitted by clients.

The identification of antibody cross-reactive proteins provides for discovery of novel biomarkers and new targets for existing antibodies that may be more exciting than the originally intended targets. Antibody-driven protein discovery permits immediate follow up with other immunological methods such as immunoprecipitation, immunohostochemistry and ELISA assays.
With our standard PIMS services, clients submit about 4 to 10 mg of lysate protein from which Kinexus attempts to immunoprecipitate the desired cross-reactive proteins. Typically, about half of the antibodies used by Kinexus are able to successfully immunoprecipitate cross-reactive proteins. Successful immunoprecipitations are confirmed by immunoblotting at Kinexus for clients as part of these services. The immunoprecipitated cross-reactive proteins are then excised from the SDS-PAGE gel, digested with trypsin, and the peptide fragments identified by mass spectrometry on a Thermo Electron LTQ MS/MS Orbitrap.

From the charge to mass ratio of one or more trypsin peptides, it is feasible to identify the parent protein from queries of the charge to mass ratios of all of the tryptic peptide from proteins encoded by the human genome and the genomes of other organisms that have been partially or fully sequenced. Successful identification is further supported with the knowledge of the molecular mass of the cross-reactive protein on SDS-PAGE and the presence of the epitope of the cross-reacting antibody that detected it. These bioinformatics analyses are provided by Kinexus as part of our PIMS services and documented in a final report for clients.