REPRODUCTION REVIEW Proteomics and the search for biomarkers of female reproductive diseases Katie L Meehan, Adam Rainczuk, Lois A Salamonsen and Andrew N Stephens Prince Henry’s Institute of Medical Research, Level 4, PO Box 5152, Clayton, Victoria 3168, Australia Correspondence should be addressed to K L Meehan; Email: katie.meehan@princehenrys.org K L Meehan and A Rainczuk contributed equally to this work Abstract Over the past decade, high-throughput proteomics technologies have evolved considerably and have become increasingly more commonly applied to the investigation of female reproductive diseases. Proteomic approaches facilitate the identification of new disease biomarkers by comparing the abundance of hundreds of proteins simultaneously to find those specific to a particular clinical condition. Some of the best studied areas of female reproductive biology applying proteomics include gynaecological cancers, endometriosis and endometrial infertility. This review will discuss the progress that has been made in these areas and will highlight some of the emerging technologies that promise to contribute to better understanding of the female reproductive disease. Reproduction (2010) 140 505–519 Introduction Diseases of the female reproductive tract contribute significantly to the global burden of diseases and as such are an important target for the development of better diagnostic, prognostic and therapeutic strategies. The use of proteomics technologies, enabling the simul- taneous comparison of hundreds or thousands of proteins to identify disease-specific biomarkers, offers an attractive approach to the identification and develop- ment of new clinically relevant tools. The increasing availability of proteomics technologies, development and application of better sample preparation techniques and recent advances in mass spectrometry (MS) instrumentation are now enabling identification and quantitation of lower abundance proteins involved in the disease. Such developments are likely to make a significant impact on reproductive biology research. To date, the most common proteomics technologies applied to investigate the female reproductive diseases include ‘gel-based’ proteomics such as two-dimensional gel electrophoresis (2DE) or differential in-gel electro- phoresis (DIGE). A technique known as surface- enhanced laser desorption/ionisation time-of-flight MS (SELDI TOF MS) has also been widely used. These have been applied to identify changes in protein abundance between normal and disease states, or to decipher the underlying molecular mechanisms of tumour chemore- sistance. Sample types that have been commonly used include entire or laser capture microdissection (LCM) dissected tissues, minimally fractionated plasma/serum, uterine lavage, and both primary and immortalised cell systems. Other more advanced ‘gel-free’ proteomics technologies including multidimensional proteomics identification technology (Mudpit), quantitative MS-based proteomics and matrix-assisted laser de- sorption ionisation imaging (MALDI-IMS) have also been applied, although in a more limited context. Despite these ongoing efforts, research initiatives have yet to develop widely applicable clinical tools for the diagnosis of disease. In this review, we provide an overview of proteomics technologies as applied to research targeting reproduc- tive disease. We discuss the challenges of applying proteomics to the analysis of commonly used sample types in reproductive biology, and detail the progress made thus far in some of the best studied areas including gynaecological cancers, endometriosis (EOS) and endometrial infertility. In addition, several emerging technologies that promise to contribute to better under- standing of the reproductive disease will be highlighted. Proteomics technologies for biomarker discovery Proteomic analyses permit the global comparison of proteins from almost any biological sample, enabling the identification of multiple proteins of interest within a single experiment. Differential protein expression between conditions (for example, healthy versus disease), relative protein abundance, the presence of post- translational modifications, sub-cellular localisation q 2010 Society for Reproduction and Fertility DOI: 10.1530/REP-10-0226 ISSN 1470–1626 (paper) 1741–7899 (online) Online version via www.reproduction-online.org