Nanoproteomics and Biomarkers

Nanoproteomics - application of nanobiotechnology to proteomics - improves on most current protocols including protein purification/display and automated identification schemes that yield unacceptably low recoveries with reduced sensitivity and speed while requiring more starting material. Low abundant proteins and proteins that can only be isolated from limited source material (e.g. biopsies) can be subjected to nanoscale protein analysis - nano-capture of specific proteins and complexes, and optimization of all subsequent sample handling steps leading to mass analysis of peptide fragments. This is a focused approach, also termed targeted proteomics, and involves examination of subsets of the proteome, e.g., those proteins that are either specifically modified, or bind to a particular DNA sequence, or exist as members of higher order complexes, or any combination thereof. This approach is used at Memorial Sloan-Kettering Cancer Center and Cornell University, New York, to identify how genetic determinants of cancer alter cellular physiology and response to agonists.

High-Field Asymmetric Waveform ion Mobility Mass Spectrometry

An ion mobility technology - high-field asymmetric waveform ion mobility mass spectrometry (FAIMS) - has been introduced as online ion selection methods compatible with electrospray ionization (ESI). FAIMS uses ion separation to improve detection limits of peptide ions when used in conjunction with electrospray and nanoelectrospray MS. This facilitates the identification of low-abundance peptide ions often present at ppm levels in complex proteolytic digests and expand the sensitivity and selectivity of nanoLC-MS analyses in global and targeted pro- teomics approaches. This functionality likely will play an important role in drug discovery and biomarker programs for monitoring of disease progression and drug efficacy.

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