Identification of biomarkers capable of differentiating between pathophysiological states of an individual is a laudable goal in the field of proteomics. well as improper statistical analysis of the resulting data. This review will discuss in detail the importance of experimental design and provide some insight into the overall workflow required for biomarker identification experiments. Proper balance between the degree of biological technical replication is required for confident biomarker identification. or experimentation have been profiled in an effort to bring biomarkers to the clinical setting. Problematically despite numerous claims of success no test derived using MS-based proteomic techniques is currently FDA approved. Acknowledging the dynamic complexity of any proteome this lack of validated biomarkers is ultimately attributed to flaws in experimental design [17 18 the use of biased or inconsistent methodology [19 20 or inadequate statistical analyses [21 22 23 Innate errors in biomarker discovery experimentation coupled with irreproducible results in some high- profile cases have delayed progress and shaken confidence in the field of biomarker research [24 25 26 27 Figure 1 (Top) The number of PubMed search results as a function of year; (Bottom) The growth in number of publications corresponds directly to the application of numerous technologies and methods [9 10 11 12 13 14 15 16 used to improve throughput and sensitivity. … Scope of Review This review will discuss the current state of biomarker research as well as the inherent challenges associated with proteomic technologies for identification of disease biomarkers. It should be noted that a biomarker discovery experiment extends beyond the analytical lab. For example proper consideration must be given to the number (e.g. multiple patient samples or multiple samples from one patient) and type (e.g. proximal fluid or tissue) of samples to be taken for analysis the GDC-0068 method of sample collection (e.g. anesthetization of the patient or catheterization) and preservation (e.g. storage conditions or inclusion of protease inhibitors). Following discovery of a putative biomarker a validation phase must be included to determine the efficacy (e.g. sensitivity and specificity) of the biomarker at the clinical level. Methods for validation of biomarkers have been reviewed [28 29 and introduction of a pipeline geared towards bringing proteomic biomarkers into routine clinical use have been suggested [30]. Most importantly consideration of the points raised in this review must be given during all phases of the biomarker identification process. For example standardization of collection methods and storage conditions will eliminate bias in the early stages of biomarker discovery while implementation of the good experimental practices discussed below will reduce bias in data accumulation allowing the greatest potential for identification of true biomarkers. Acknowledging that most reliable biomarker would arise from analysis of the ‘normal’ state of a single individual compared with the ‘diseased’ state of the same individual this may not be possible. A lack of baseline comparisons such as in paediatric populations or knowledge of what sample to analyze and what to search for make this form of biomarker Rabbit polyclonal to ODC1. discovery not feasible for the discovery phase. This review focuses on the fundamentals of experimental design and provides an in-depth analysis of common errors in biomarker discovery experiments that must be addressed prior to execution of the experiment. 2 Sample Description 2.1 Characteristics of an Ideal Biomarker The National Institute of Health defines a biomarker as a [31]. With respect to biomarker discovery through genomic or proteomic approaches the indicating characteristic may be gene(s) or protein(s) that present quantifiable changes in expression across a clinically obtainable sample. What constitutes an ideal biomarker depends heavily GDC-0068 on the disease GDC-0068 in question though universal characteristics of the ideal biomarker are summarized in Table 1. Table 1 Universal characteristics of an ideal biomarker. The stringent requirements for ideal biomarkers presented in Table 1 GDC-0068 imply the identification of a single gene or protein biomarker for a given disease to be extremely unlikely. To combat this issue investigators often turn to panels of GDC-0068 genes or proteins which together may provide.