Proteomics methods and applications for the practicing clinician

Abstract

Objective: To describe clinical proteomics from discovery techniques and their limitations, to applications in allergy, asthma, and immunology, and finally to how proteomics can be integrated into clinical practice.

Data sources: Despite many inherent challenges, proteomics-based methods have become a powerful and popular means of profiling clinical samples for the purpose of biomarker discovery. Although several strategies exist, clinical proteomics for the purpose of biomarker discovery generally focuses on 1 of 3 basic workflows: (1) 2-dimensional gel electrophoresis to quantitate relative protein levels followed by mass spectrometry (MS) to identify proteins of interest, (2) non-gel-based methods that rely on liquid chromatography MS (LCMS) for both quantitation and identification of proteins, and (3) protein profiling methods that do not directly result in the identification of proteins but rather generate "fingerprints" that are compared among individuals or samples.

Study selection: Regardless of the strategy being pursued, a few general experimental steps are followed that will be expounded on in the text. These proteomics techniques have been applied to discover new biomarkers in biofluids and tissues from individuals with a variety of conditions, including allergy, asthma, atopic dermatitis, inflammatory diseases, chronic obstructive pulmonary disease, and other lung diseases.

Results: After biomarker discovery, LCMS-based proteomics offers several advantages over traditional antibody-based clinical assays, including greater specificity, cost- and time-effectiveness, and the potential to multiplex up to hundreds of peptides in a single assay.

Conclusion: With many guidelines now in place and model studies on which to design future experiments, there is reason to be optimistic that candidate protein biomarkers will be discovered using proteomics and translated into clinical assays.