Review Approaches for systematic proteome exploration Ronny Falk, Margareta Ramstro ¨m, Stefan Sta ˚hl, Sophia Hober * Royal Institute of Technology, Albanova University Center, School of Biotechnology, SE-106 91 Stockholm, Sweden Received 4 December 2006; received in revised form 24 January 2007; accepted 25 January 2007 Abstract With the completion of the human genome project (HUGO) during recent years, gene function, protein abundance and expression patterns in tissues and cell types have emerged as central areas for the scientific community. A mapped human proteome will extend the value of the genome sequence and large-scale efforts aiming at elucidating protein localization, abundance and function are invaluable for biomarker and drug discovery. This research area, termed proteomics, is more demanding than any genome sequencing effort and to perform this on a wide scale is a highly diverse task. Therefore, the proteomics field employs a range of methods to examine different aspects of proteomics including protein localization, protein–protein interactions, posttranslational modifications and alteration of protein composition (e.g. differential expression) in tissues and body fluids. Here, some of the most commonly used methods, including chromatographic separations together with mass spectrometry and a number of affinity proteomics concepts are discussed and exemplified. # 2007 Elsevier B.V. All rights reserved. Keywords: Proteomics; Protein atlas; Protein array; Protein localization; Mass spectrometry; Protein quantification Contents 0. Introduction ................................................................................. 156 1. Expression analysis ............................................................................ 157 1.1. Expression proteomics using mass spectrometry .................................................... 157 1.1.1. Two-dimensional gel electrophoresis and mass spectrometry ..................................... 157 1.1.2. Shotgun proteomics ................................................................. 157 2. Localization ................................................................................. 158 2.1. Fractionation and MS-based Localization ........................................................ 158 2.2. Affinity-based localization ................................................................... 159 2.2.1. Protein expression atlases ............................................................. 159 2.2.2. Localization enabled via reporter systems .................................................. 161 3. Interactions .................................................................................. 161 3.1. Yeast two hybrid (YTH) .................................................................... 161 3.2. Tandem affinity purification (TAP) ............................................................. 162 3.3. Immunoaffinity capture ..................................................................... 162 4. Quantification ................................................................................ 163 4.1. MS-based biomarker discovery and quantitative proteomics............................................ 163 4.2. Biomarker discovery and quantitative proteomics by protein arrays ...................................... 164 5. Conclusions.................................................................................. 165 Acknowledgements ............................................................................ 166 References .................................................................................. 166 www.elsevier.com/locate/geneanabioeng Biomolecular Engineering 24 (2007) 155–168 * Corresponding author. Tel.: +46 5537 8330; fax: +46 5537 8481. E-mail address: sophia.hober@biotech.kth.se (S. Hober). 1389-0344/$ – see front matter # 2007 Elsevier B.V. All rights reserved. doi:10.1016/j.bioeng.2007.01.001