Please cite this article in press as: M.F. Khan, et al., Proteomics by mass spectrometry—Go big or go home? J. Pharm. Biomed. Anal. (2011), doi:10.1016/j.jpba.2011.02.012 ARTICLE IN PRESS G Model PBA-8055; No. of Pages 10 Journal of Pharmaceutical and Biomedical Analysis xxx (2011) xxx–xxx Contents lists available at ScienceDirect Journal of Pharmaceutical and Biomedical Analysis journal homepage: www.elsevier.com/locate/jpba Review Proteomics by mass spectrometry—Go big or go home? Morgan F. Khan, Melissa J. Bennett, Chanelle C. Jumper, Andrew J. Percy, Leslie P. Silva, David C. Schriemer * University of Calgary, Department of Biochemistry and Molecular Biology, 3330 Hospital Drive NW, Calgary, Alberta, Canada T2N 4N1 article info Article history: Received 4 November 2010 Received in revised form 3 February 2011 Accepted 10 February 2011 Available online xxx Keywords: Proteomics Mass spectrometry Selected reaction monitoring Chromatography Bioinformatics abstract Mass spectrometry is an important technology for mapping composition and flux in whole proteomes. Over the last 5 years in particular, impressive gains in the depth of proteome coverage have been real- ized, particularly for model organisms. This review will provide an update on advancements in the key analytical techniques, methods and informatics directed towards whole proteome analysis by mass spec- trometry. Practical issues involving sample requirements, analysis time and depth of coverage will be addressed, to gauge how useful data-driven approaches are for solving biological problems. Targeted mass spectrometric methods, based on selected reaction monitoring, are presented as a powerful alternative to data-driven methods. They offer robust, transferable protocols for hypothesis-directed monitoring of limited yet biologically significant tracts of any proteome. © 2011 Published by Elsevier B.V. Contents 1. Introduction .......................................................................................................................................... 00 2. Whole proteome analysis ............................................................................................................................ 00 2.1. The basic method ............................................................................................................................. 00 2.2. Proteomics of simple model organisms ...................................................................................................... 00 2.3. Proteomics of complex organisms ........................................................................................................... 00 2.4. On the discrepancy between simple and complex organisms ............................................................................... 00 2.5. An assessment ................................................................................................................................ 00 3. Technological developments in whole proteome analysis .......................................................................................... 00 3.1. Improving LC–MS/MS performance .......................................................................................................... 00 3.2. Recent developments in peptide and protein fractionation ................................................................................. 00 3.3. Improvements in peptide ion fragmentation ................................................................................................ 00 3.4. Departing from the data-driven experiment ................................................................................................ 00 3.5. Developments in bioinformatics ............................................................................................................. 00 4. Targeted proteomics ................................................................................................................................. 00 4.1. SRM methods ................................................................................................................................. 00 4.2. SRM applications ............................................................................................................................. 00 5. Conclusions and perspective ......................................................................................................................... 00 References ........................................................................................................................................... 00 1. Introduction Proteomics as a discipline may be defined as the monitoring of all proteins within an organism, in both temporal and spa- tial terms. That is, at any given point in time, what proteins are expressed and where are they? While this sort of question defines * Corresponding author. Tel.: +1 403 210 3811; fax: +1 403 283 8727. E-mail address: dschriem@ucalgary.ca (D.C. Schriemer). the core technical issue for many endeavors in molecular biology, proteomics differentiates itself on the basis of the number of pro- teins monitored—all vs. a select few. A comprehensive analysis would have the advantage of avoiding bias when monitoring a dis- ease state or a biological mechanism, and thus has considerable appeal. As the field has existed for approximately 15 years, it is reason- able to evaluate how close we are to providing reliable methods for proteome analysis. Can established methods be placed into individual labs to deliver proteome characterization within a rea- 0731-7085/$ – see front matter © 2011 Published by Elsevier B.V. doi:10.1016/j.jpba.2011.02.012