In this issue: Proteomics – Clinical Applications 6/2008

Abstract

AbstractIn this issue of Proteomics – Clinical Applications you will find the following highlighted articles:Try again and again and again? NO: QC of unlabeled mass spectraThe choice of appropriate controls and instrument settings are not immediately obvious for unlabeled serum samples from a simulated myocardial infarction. These are some of the challenges Sutton, et al. faced as they worked on characterizing a Fourier transform LC/MSn system for (mostly) automated high throughput proteomic analysis. Their ultimate method is to introduce pure, non‐human protein samples at specified steps in the procedure and follow the quality of these standards as the samples progress through the protocol. This includes bovine fetuin for plasma partitioning; beta casein, carbonic anhydrase, glycogen phosphorylase, and lactoperoxidase for digestion, desalting and delipidation; angiotensin I and II for injection and fractionation standards. Sensitivity is in the fmol range. These standards were also helpful in minimizing the problems due to chromatography bandwidth, sample frequency and sample concentration. These same QC practices apply in improving the analysis of metabolic components of cells.Sutton, J. et al., Proteomics Clin. Appl. 2008, 2, 862–881.A battle royal: cetuximab vs thymidylate synthase, and EGF receptor in colorectal cancerDeveloping an understanding of the mechanism of a therapeutic candidate is not a trivial part of drug development. Take the case of cetuximab (CM), please. It is a monoclonal antibody targeted at the epidermal growth factor receptor (EGFR), a major player in maintenance and progression of colorectal and other cancers. CM is best described as a chemisensitizer. When used with 5‐flurouracil, an inhibitor of thymidylate synthase (TS), the 5‐FU effects are enhanced. Skvortsov, et al. observed that the CM‐enhanced inhibition of TS was only seen when the cells expressed EGFR and was roughly proportional to the level of EGFR, as judged by Western blots. Blocking EGFR signaling with CM reduced angiogenesis and metastasis, and enhanced apoptosis. The mechanisms remain to be explicated.Skvortsov, S. et al., Proteomics Clin. Appl. 2008, 2, 908–914.Pick a peck of perked‐up markers for CRC (colorectal cancer)Colorectal cancer ranks high on the “nasty” lists: it is third in frequency and second in mortality for the developed nations. A major part of the problem is that it is stealthy – no reliable early symptoms. CEA is neither specific nor timely and transcriptome work has not paid off yet, so Watanabe, et al. set out to look hard at the proteome. This time they used the 2‐nitrobenzenesulfenyl method of labeling tryptophan‐containing peptides before digestion and LC‐MS/MS or before subjecting undigested proteins to MALDI/TOF for quantitation. Analysis of a cytosolic fraction and a 2% CHAPS‐soluble fraction, they identified 320 intensity‐shifted peaks. Looking at 23, they picked 6 up‐regulated proteins for Western blot validation and further testing – ZYX, RAN, RCN1, AHCY, LGALS1, and VIM. Pursuing these six leads to the traditional roadblock how to evaluate proteins for early stage biomarkers without the early stage patients. Chicken or egg?Watanabe, M. et al., Proteomics Clin. Appl. 2008, 2, 925–935.