ORIGINAL ARTICLE Identification and characterization of protein composition in Withania somnifera—an Indian ginseng Rekha Sapru Dhar & Suphla Bajpai Gupta & Parvinder Pal Singh & Sumeer Razdan & Wajid Waheed Bhat & Satiander Rana & Surrinder Kumar Lattoo & Shabnam Khan Received: 27 May 2011 /Accepted: 13 September 2011 # Society for Plant Biochemistry and Biotechnology 2011 Abstract To have better understanding of the processes that occur in Withania somnifera L. Dunal, proteome analyses were initiated on two tissues (seeds & leaves) of this plant. Protein extracts were separated by two- dimensional gel electrophoresis (2-DE) across a broad 3.0–10.0 immobilized pH gradient (IPG) strip that yielded 434 protein spots. A total of 167 individual spots (82 from seeds and 85 from leaves) were excised from the gel and were characterized by peptide mass fingerprinting. From these analyses, 70 individual proteins from seeds and 74 from leaves were identified by protein sequence database interrogation and were catalogued accordingly to different protein functions. A comparative analysis of the two tissues indicated that some enzymes/proteins involved in housekeeping pathways were common to both, whereas some were exclusively tissue specific with specialized metabolic complement. The knowledge gained by this study towards the tissue specific protein expression in W. somnifera would form the basis for our future endeavor of characterization of proteins to understand the physiology and the associated complex metabolic network during its ontogenetic development. Keywords Proteomics . Withania somnifera . Mass spectrometry . Protein identification . Metabolic enzymes Abbreviations 2-DE Two-dimensional gel electrophoresis IPG Immobilized pH gradient SGTL1 Sterol glucosyltransferases TCA Trichloroacetic acid CHAPS 3-[(3-cholamidopropyl) dimethylammo- nio]-1-propanesulfonate DTT Dithiothreitol SDS-PAGE Sodium dodecyl sulfate–polyacrylamide gel electrophoresis IEF Isoelectric focusing IAA Iodoacetamide MALDI-TOF-MS Matrix-assisted laser desorption/ioniza- tion-time of flight mass spectrometry PMF Peptide mass fingerprinting. Introduction Withania somnifera L. Dunal (Solanaceae) commonly known as ashwagandha or Indian ginseng is of immense therapeutic utility in traditional health care system of India and finds an extensive use in Indian herbal preparations. It has important hepatoprotective, immunomodulatory and anti-cancer properties. It also increases physiological endurance and protects against stress—related disorders such as arthritis, hypertension, diabetes and premature aging. All these attributes are ascribed to a group of compounds called phytosteroids that include withanolides, withaferins, withanones and sitoindosides. The commom name of Indian ginseng for W. somnifera is based on the fact that the phytosteroids bear a resemblance both in their R. S. Dhar (*) : S. B. Gupta : S. Razdan : W. W. Bhat : S. Rana : S. K. Lattoo : S. Khan Plant Biotechnology, Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu, Tawi 180001, India e-mail: rsapru@iiim.ac.in P. P. Singh Medicinal Chemistry, Indian Institute of Integrative Medicine (CSIR), Canal Road, Jammu, Tawi 180001, India J. Plant Biochem. Biotechnol. DOI 10.1007/s13562-011-0083-0