Quantitative proteomics and Biomarker Discovery often focuses on the selective identification and quantitation of a protein of interest from an array of proteins. In addition to the selection power of mass spectrometers, multi-step sample preparations (e.g. separations) are often needed for a highly complex sample prior to MS analysis. We can routinely identify and quantitate the differences in low level (sub-femtomole) peptides and proteins.
Working with our partners in the Mass spectrometry, Metabolomics and Proteomics Facility (MMPF), we have identified multiple different peptides present in serum at 0.1-0.5 fmole per component using selective reaction monitoring (SRM, also known as MRM) using our Agilent 6410 triple quadropole (QQQ) mass spectrometer. This approach allows us to identify peptides from a protein of interest in a "discovery" run on our LTQ-FT Ultra or Orbitrap Velos Pro then develop a list of target peptides to quantitate that protein using the QQQ. Using our Agilent Chip Cube interfaced to our LTQ-FT or Orbitrap Velos Pro during identification we can proceed to quantitate using the same column running on the Chip Cube on our Agilent 6410. Using software such as Skyline (MacCoss lab, Univ. Washington) simplifies the generation of a list of peptide targets and transitions for rapid assay development.
to discuss your quantitation needs.