REVIEW Proteomic technologies for the identification of disease biomarkers in serum: Advances and challenges ahead Sandipan Ray 1 , Panga J. Reddy 1 , Rekha Jain 1 , Kishore Gollapalli 1 , Aliasgar Moiyadi 2 and Sanjeeva Srivastava 1 1 Wadhwani Research Center for Biosciences and Bioengineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India 2 Advanced Center for Treatment Research and Education in Cancer, Tata Memorial Center, Khargar, Navi Mumbai, India Received: July 23, 2010 Revised: February 28, 2011 Accepted: March 7, 2011 Serum is an ideal biological sample that contains an archive of information due to the presence of a variety of proteins released by diseased tissue, and serum proteomics has gained considerable interest for the disease biomarker discovery. Easy accessibility and rapid protein changes in response to disease pathogenesis makes serum an attractive sample for clinical research. Despite these advantages, the analysis of serum proteome is very challenging due to the wide dynamic range of proteins, difficulty in finding low-abundance target analytes due to the presence of high- abundance serum proteins, high levels of salts and other interfering compounds, variations among individuals and paucity of reproducibility. Sample preparation introduces pre-analytical variations and poses major challenges to analyze the serum proteome. The label-free detection techniques such as surface plasmon resonance, microcantilever, few nanotechniques and different resonators are rapidly emerging for the analysis of serum proteome and they have exhibited potential to overcome few limitations of the conventional techniques. In this article, we will discuss the current status of serum proteome analysis for the biomarker discovery and address key technological advancements, with a focus on challenges and amenable solutions. Keywords: Abundant proteins / Biomarker / Label-free / Nanowires and nanotubes / Serum / Technology 1 Introduction The genomic revolution successfully accomplished the sequencing of human genome and that of other organisms, which has accelerated the pace of proteomics research for disease expression profiling. During the last decade, proteomics has manifested significant impact on various aspects of clinical research, including understanding of disease pathogenesis, discovery of novel biomarkers for early disease diagnosis as well as identification of new drug and vaccine targets [1–4]. The biomarkers are biomolecules that are used to aid in monitoring disease progression and following prognosis in response to the therapeutic interventions. Identification of protein biomarkers is useful for early detection of various fatal diseases such as cancer or autoimmune disorders and has significant impact on human health [5, 6]. Determining the protein expression changes in different biological fluids is a promising approach for an early disease diagnosis and it may have implications as a complementary strategy to histopathology [7]. Abbreviations: BTB, bric-a-brac, tramtrack, broad-conplex; CD, Crohn’s disease; CEA, carcinoembryonic antigen; CRP, C reac- tive protein; DS, Down syndrome; FET, field effect transistor; HT, high-throughput; PPP, plasma proteome project; LMW, low molecular weight; MRM, multiple reaction monitoring; NAFLD, non-alcoholic fatty liver disease; PIs, protease inhibitors; PSA, prostate-specific antigen; Q-TOF, quadrupole-TOF; RA, rheuma- toid arthritis; SARS, severe acute respiratory syndrome; siNW, silicon nanowire; SLE, systemic lupus erythematosus; SPR, surface plasmon resonance; SPRi, surface plasmon resonance imaging; T-PSA, total prostate-specific antigen Colour Online: See the article online to view Figs. 2 and 3 in colour. Correspondence: Professor Sanjeeva Srivastava, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India E-mail: sanjeeva@iitb.ac.in Fax: 191-22-2572-3480 & 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.com Proteomics 2011, 11, 2139–2161 2139 DOI 10.1002/pmic.201000460