Targeted Proteomics

* These are bundled prices, for our official prices please see http://proteomics.ucdavis.edu/prices-jan-2015

You may notice the actual service is considerably less expensive than our Protein ID service. The reason for this is that we did not include any data analysis, or method development in the service cost. Some projects take a lot of method development and some do not, so we felt it was fair to charge for that seperatly. Also once you have the method developed, you usually only have to pay for the LC-MS/MS. Please call if you have any questions

Targeted Proteomics targets specific peptides in a complex mixture of other peptides and determines their presence (if they are above our detection limit) and quantity in one sample or across multiple samples. You can think of it as a mass spectrometer version of a western blot, but far more accurate and not requiring any antibodies.This analysis usually utilizes a triple quadrupole mass spectrometer (QQQ) which has been used for a long time to quantitate small molecules. Only recently has it been utilized for peptides. Parallel Reaction monitoring (PRM) and data independent analysis (DIA) are also options and can be far cheaper than developing a method for a QQQ…but preliminary runs are also an important part of that analysis as well.

Here are some examples where you would utilize this type of analysis.

• If you want to verify that your knockdown target is knocked down.
• If you want to know the quantity of a peptide/protein  in a complex mixture of other peptides or proteins (PSA in blood serum, oxytocin in cerebral spinal fluid, a protein in a cell lysate or cell fraction)
• If you want to see if a specific protein is differentially expressed across samples or during a time course experiment.

This method actually “targets” peptides enzymatically digested from your target protein, so it is important to pick your peptides and method conditions carefully. Please come and talk to us if you are considering this type of experiment. This analysis also requires a good bit of preliminary analysis to ensure the method is robust and quantitative and thus cannot usually be done with 1 or 2 mass spectrometry runs.

Here is a nice collection of recent Targeted proteomics applications and research papers

• Estimation of Absolute Protein Quantities of Unlabeled Samples by Selected Reaction Monitoring Mass Spectrometry
• Biochemical Fractionation and Stable Isotope Dilution Liquid Chromatography-Mass Spectrometry for Targeted and Microdomain-Specific Protein Quantification in Human Postmortem Brain Tissue 
• Targeted Proteomic Quantification on Quadrupole‐Orbitrap Mass Spectrometer
• Current affairs in quantitative targeted proteomics: multiple reaction monitoring mass spectrometry
• Quantification of Activated NF-κB/RelA Complexes Using ssDNA Aptamer Affinity – Stable Isotope Dilution—Selected Reaction Monitoring—Mass Spectrometry
• Methods for Peptide and Protein Quantitation by Liquid Chromatography-Multiple Reaction Monitoring Mass Spectrometry
• Isotope coded protein label quantification of serum proteins—Comparison with the label-free LC–MS and validation using the MRM approach
• Determination of Protein Stoichiometry within Protein Complexes Using Absolute Quantification and Multiple Reaction Monitoring
• Increased Selectivity, Analytical Precision, and Throughput in Targeted Proteomic
• Skyline Software (the open source software we use to analyze targeted proteomics data)
• The development of selected reaction monitoring methods for targeted proteomics via empirical refinement
• Multiple Reaction Monitoring of Multiple Low-Abundance Transcription Factors in Whole Lung Cancer Cell Lysates
  • Nice Recent (2013) Targeted proteomics paper