While previous "Validation Viewpoint" columns have focussed on conventional and recombinant pharmaceutical products, and at times, bioanalytical methods, we think it is also appropriate to address method validation as it relates to -omics-type studies. Over the last decade, there have been enormous advances in the technology for such methods by which large numbers of analytes are identified and determined. These fields have matured to the extent that there are new journals focused on them. Most such publications and presentations make little to no mention of analytical method validation. It does not appear that the US Food and Drug Administration (FDA) or its European or Japanese counterparts have promulgated firm guidelines to be followed when performing method validation in any -omics studies, likely reflecting the fact that such studies are not yet widely included in regulatory filings. Today's journals are very protective of limited pages, and quality control components expected of good scientific practice frequently are not included in publications. It is assumed that pipettes, thermometers, and pH meters have been calibrated. It is assumed that extraction recoveries and linear ranges have been established. In the good laboratory practices (GLP) and current good manufacturing practice (cGMP) worlds, it is expected that laboratories can withstand a rigorous audit covering method validation, very little of which is ever expected to be published, nor need that be required. Good validation practice is established and is expected to be followed.

On the other hand, for -omics methods we are not at the state of maturity where such assumptions can be applied with confidence. The number of analytes is huge. Often there are no absolute reference standards for each compound. In many cases, the compounds detected are not of known structure and are quantitated in a relative way comparing biological cohorts such as disease vs. health or treatment versus not or cell line A versus cell line B. Given the large number of substances varying over many orders of magnitude, we can be totally sure that analytes are behaving independently of each other, and that their absolute or even relative concentrations are preserved by the sample preparation procedure. There are no single methods or technologies capable of a linear response over 10 orders of magnitude, given that four orders of magnitude is often described as optimistic. In fact, rarely is anything reported about linearity, lower limits of quantitation, or even the precision for various analytes when samples are repeated within-run or day-to-day or between laboratories. It is also clear that many types of instrument platforms and software are used for -omics and it is not even known how much difference that makes. No doubt these are challenges. It is about time that this area of bioanalytical chemistry receives some attention so that collectively, government, academia, and industry can begin to establish validation standards. It is encouraging that the Human Proteome Organization (HUPO) and others are beginning to address this issue (1). We encourage the International Conference on Harmonization (ICH) and similar organizations devoted to analytical method validation to also give attention to this important, albeit difficult topic, in its workshops and guidelines (2–5).

In addition to these challenges, there also are the related challenges of "valid structural assignments" and "biological validation." We say related because without reliable methods, it is likely that biological validation will be more noise than signal. No doubt we need good numbers for known molecules that can be reproduced, and proteomics has come under this scrutiny as of late. Proteomics has come under scrutiny of late. It clearly has disappointed vs. the expectations that were declared as the millennium turned. It is no doubt early and approaches are still being refined, but it is not too early to ignore basic principles of method validation.

This column was conceived in the hopes that we might be able to shed some light on how and when analytical methods could or should be validated in the proteomics and peptidomics areas. These same suggestions apply to low molecular weight (MW) analytes, as in the metabolomics field, but in that case a greater percentage of the analytes are known and available in reasonable standards. We are working from the current USP and ICH guidelines on analytical method validation for conventional, low MW pharmaceuticals, as discussed in past "Validation Viewpoint" columns (6,7). What we are suggesting is that the proteomics–peptidomics communities-at-large might start considering how they could begin to institute method validation protocols or guidelines for future studies, no matter what the sample type or analytical method employed.