Growing evidence demonstrates widespread deficiencies in the reporting of health research studies. The EQUATOR Network is an international initiative that aims to enhance the reliability and value of the published health research literature. EQUATOR provides resources, education and training to facilitate good research reporting and assists in the development, dissemination and implementation of robust reporting guidelines. This paper presents a collection of tools and guidelines available on the EQUATOR website (http://www.equator-network.org) that have been developed to increase the accuracy and transparency of health research reporting.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2362.2009.02234.x

A catalogue of reporting guidelines for health research.

Next-generation sequencing allows the analysis of genomes, including those representing disease states. However, the causes of most disorders are multifactorial, and systems-level approaches, including the analysis of proteomes, are required for a more comprehensive understanding. The proteome is extremely multifaceted owing to splicing and protein modifications, and this is further amplified by the interconnectivity of proteins into complexes and signalling networks that are highly divergent in time and space. Proteome analysis heavily relies on mass spectrometry (MS). MS-based proteomics is starting to mature and to deliver through a combination of developments in instrumentation, sample preparation and computational analysis. Here we describe this emerging next generation of proteomics and highlight recent applications.

/pdf/next-generation-proteomics-towards-an-integrative-view-of-2ccbo2dtdc.pdf

Next-generation proteomics: towards an integrative view of proteome dynamics

Clinical analysis of blood is the most widespread diagnostic procedure in medicine, and blood biomarkers are used to categorize patients and to support treatment decisions. However, existing biomarkers are far from comprehensive and often lack specificity and new ones are being developed at a very slow rate. As described in this review, mass spectrometry (MS)-based proteomics has become a powerful technology in biological research and it is now poised to allow the characterization of the plasma proteome in great depth. Previous "triangular strategies" aimed at discovering single biomarker candidates in small cohorts, followed by classical immunoassays in much larger validation cohorts. We propose a "rectangular" plasma proteome profiling strategy, in which the proteome patterns of large cohorts are correlated with their phenotypes in health and disease. Translating such concepts into clinical practice will require restructuring several aspects of diagnostic decision-making, and we discuss some first steps in this direction.

/pdf/revisiting-biomarker-discovery-by-plasma-proteomics-s6lnwmqry8.pdf

Revisiting biomarker discovery by plasma proteomics.

The role of heat shock proteins in cancer.

“Omics” research poses acute challenges regarding how to enhance validation practices and eventually the utility of this rich information. Several strategies may be useful, including routine replication, public data and protocol availability, funding incentives, reproducibility rewards or penalties, and targeted repeatability checks.

/pdf/improving-validation-practices-in-omics-research-23dyqebtfy.pdf

Improving validation practices in "omics" research.

Clinical proteomics has yielded some early positive results-the identification of potential disease biomarkers-indicating the promise for this analytical approach to improve the current state of the art in clinical practice. However, the inability to verify some candidate molecules in subsequent studies has led to skepticism among many clinicians and regulatory bodies, and it has become evident that commonly encountered shortcomings in fundamental aspects of experimental design mainly during biomarker discovery must be addressed in order to provide robust data. In this Perspective, we assert that successful studies generally use suitable statistical approaches for biomarker definition and confirm results in independent test sets; in addition, we describe a brief set of practical and feasible recommendations that we have developed for investigators to properly identify and qualify proteomic biomarkers, which could also be used as reporting requirements. Such recommendations should help put proteomic biomarker discovery on the solid ground needed for turning the old promise into a new reality.

/pdf/recommendations-for-biomarker-identification-and-3b0x6k6mkn.pdf

William B. Mattes

Papers

Recommendations for Biomarker Identification and Qualification in Clinical Proteomics