Mass spectrometry-based biomarker discovery: toward a global proteome index of individuality

Direct analysis of biological tissue by paper spray mass spectrometry

Paper spray mass spectrometry (PS-MS) is explored as a fast and convenient way for direct analysis of molecules in tissues with minimum sample pretreatment. This technique allows direct detection of different types of compounds such as hormones, lipids, and therapeutic drugs in short total analysis times (less than 1 min) using a small volume of tissue sample (typically 1 mm(3) or less). The tissue sample could be obtained by needle aspiration biopsy, by punch biopsy, or by rubbing a thin tissue section across the paper. There exists potential for the application of paper spray mass spectrometry together with tissue biopsy for clinical diagnostics.

Measuring the intra-individual variability of the plasma proteome in the chicken model of spontaneous ovarian adenocarcinoma

The domestic chicken (Gallus domesticus) has emerged as a powerful experimental model for studying the onset and progression of spontaneous epithelial ovarian cancer (EOC) with a disease prevalence that can exceed 35% between 2 and 7 years of age. An experimental strategy for biomarker discovery is reported herein that combines the chicken model of EOC, longitudinal plasma sample collection with matched tissues, advanced mass spectrometry-based proteomics, and concepts derived from the index of individuality (Harris, Clin Chem 20: 1535-1542, 1974). Blood was drawn from 148 age-matched chickens starting at 2.5 years of age every 3 months for 1 year. At the conclusion of the 1 year sample collection period, the 73 birds that remained alive were euthanized, necropsied, and tissues were collected. Pathological assessment of resected tissues from these 73 birds confirmed that five birds (6.8%) developed EOC. A proteomics workflow including in-gel digestion, nanoLC coupled to high-performance mass spectrometry, and label-free (spectral counting) quantification was used to measure the biological intra-individual variability (CV(W)) of the chicken plasma proteome. Longitudinal plasma sample sets from two birds within the 73-bird biorepository were selected for this study; one bird was considered "healthy" and the second bird developed late-stage EOC. A total of 116 proteins from un-depleted plasma were identified with 80 proteins shared among all sample sets. Analytical variability (CV(A)) of the label-free proteomics workflow was measured using a single plasma sample analyzed five times and was found to be ≥CV(W) in both birds for 16 proteins (20%) and in either bird for 25 proteins (31%). Ovomacroglobulin (ovostatin) was found to increase (p < 0.001) over a 6 month period in the late-stage EOC bird providing an initial candidate protein for further investigation.

Measurement of biomarker proteins for point-of-care early detection and monitoring of cancer

This critical review evaluates progress toward viable point-of-care protein biomarker measurements for cancer detection and diagnostics. The ability to measure panels of specific, selective cancer biomarker proteins in physicians' surgeries and clinics has the potential to revolutionize cancer detection, monitoring, and therapy. The dream envisions reliable, cheap, automated, technically undemanding devices that can analyze a patient's serum or saliva in a clinical setting, allowing on-the-spot diagnosis. Existing commercial products for protein assays are reliable in laboratory settings, but have limitations for point-of-care applications. A number of ultrasensitive immunosensors and some arrays have been developed, many based on nanotechnology. Multilabel detection coupled with high capture molecule density in immunosensors and arrays seems to be capable of detecting a wide range of protein concentrations with sensitivity ranging into the sub pg mL(-1) level. Multilabel arrays can be designed to detect both high and ultralow abundance proteins in the same sample. However, only a few of the newer ultrasensitive methods have been evaluated with real patient samples, which is key to establishing clinical sensitivity and selectivity.

Electrochemical aspects of electrospray and laser desorption/ionization for mass spectrometry

Soft-ionization methods, namely electrospray ionization and laser desorption/ionization, are widely used to transfer large molecules as intact gas-phase ions either from a solution or from a solid substrate. During both processes, in-source electrochemical and photoelectrochemical reactions occur. These electrode reactions, which take place at interfaces, play important roles in influencing the ionization products, but they have received little attention. We show that having good control over both types of electrochemical reactions can lead to new analytical applications. Examples include online tagging by grafting of mass tags and in-source photooxidation of peptides.

Industrialized MS-based proteomics in the search for circulating biomarkers

Proteomics is the study of the expression, structure and function of proteins under a range of cellular conditions. A rapidly evolving component of this field is clinical proteomics, which focuses on proteins involved in human disease and how they are affected by therapeutic intervention. MS is the main analytical technology for identifying and quantifying proteins whose expression is modulated across the normal to disease continuum. Applying this technology to clinical samples, however, is particularly challenging due to high biological variability in the population, a variety of disease stages, nonuniform response to therapy, multiple concomitant treatments and special requirements for handling samples from clinical trials. Given these challenges, an ‘industrialized’ approach is best suited to clinical biomarker development, with its standard operating procedures, process control and ‘chain of custody’. This review will focus, therefore, on MS-based industrialized proteomics for the discovery and verification of circulating candidate clinical protein biomarkers.