Proteomics
Part I: Technologies & Markets
ByProf. K. K. Jain
MD, FRACS, FFPM
Jain PharmaBiotechBasel, Switzerland
July 2012
A Jain PharmaBiotech Report
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A U T H O R ' S B I O G R A P H Y
Professor K. K. Jain is a neurologist/neurosurgeon by training and has been working inthe biotechnology/biopharmaceuticals industry for several years. He received graduatetraining in both Europe and USA, has held academic positions in several countries, and isa Fellow of the Faculty of Pharmaceutical Medicine of the Royal College of Physicians of UK. Currently, he is a consultant and CEO at Jain PharmaBiotech.Prof. Jain is the author of 440 publications including 21 books (4 as editor) and 50 specialreports which have covered important areas in biotechnology, gene therapy and biopharmaceuticals. He has also written a textbook of gene therapy which is the first book on this subject to be translated into the Chinese language. A book on gene therapy companies was published in 2000 by John Wiley & Sons. Both of these are now incorporated in a special report on gene therapy published in 2004 by JainPharmaBiotech with the latest edition in 2011. His latest books include "Handbook of Nanomedicine" (Humana/Springer 2008; Chinese edition, Peking University Press 2011,2
nd
ed Springer 2012), Textbook of Personalized Medicine (Springer 2009), "Handbook of Biomarkers" (Springer 2010), "Handbook of Neuroprotection" (Springer 2011),
“Applications of Biotechnology in Cardiovascular Therapeutics” (Springer 2011)
, and
“Applications of Biotechnology in Neurology” (Springer 2012).
A B O U T T H I S R E P O R T
The proteomics report started as an expansion of the chapter on proteomics in Prof.Jain's report on "The Impact of Genomics on Drug Discovery and Development"published by Decision Resources Inc in 1999 and has been constantly updated since itspublication as a separate report in 2000 by Jain PharmaBiotech. It has been rewrittenseveral times since then.
July 2012 (first edition published in 2000)Copyright
2012 byJain PharmaBiotechBläsiring 7CH-4057 BaselSwitzerlandTel & Fax: +4161-6924461Email: info@pharmabiotech.chWeb site: http://pharmabiotech.ch/
All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmittedin any form or by any means, electronic, mechanical, photocopying, or otherwise without the prior writtenpermission of the Publisher. This report may not be lent, resold or otherwise traded in any manner without theconsent of the Publisher. While all reasonable steps have been taken to ensure the accuracy of the informationpresented, the Publisher cannot accept responsibility for inadvertent errors or omissions.
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T A B L E O F C O N T E N T S
0.
Executive Summary .............................................................................. 17
1.
Basics of Proteomics ............................................................................. 19
Introduction....................................................................................................................... 19
History ............................................................................................................................... 19
Nucleic acids, genes and proteins ...................................................................................... 20
Genome .......................................................................................................................... 20
DNA ............................................................................................................................... 21
RNA ............................................................................................................................... 21
MicroRNAs .................................................................................................................. 21
Decoding of mRNA by the ribosome ............................................................................... 22
Genes ............................................................................................................................. 23
Alternative splicing ........................................................................................................... 23
Transcription ................................................................................................................... 24
Gene regulation ............................................................................................................... 24
Gene expression .............................................................................................................. 25
Chromatin ....................................................................................................................... 25
Golgi complex .................................................................................................................. 26
Proteins .......................................................................................................................... 26
Spliceosome ............................................................................................................... 27
Functions of proteins ................................................................................................... 27
Inter-relationship of protein, mRNA and DNA .................................................................. 28
Proteomics ......................................................................................................................... 29
Mitochondrial proteome .................................................................................................... 30
S-nitrosoproteins in mitochondria.................................................................................. 30
Proteomics and genomics .................................................................................................. 31
Classification of proteomics ............................................................................................... 33
Levels of functional genomics and various "omics" ............................................................... 33
Glycoproteomics .............................................................................................................. 34
Transcriptomics ............................................................................................................... 34
Metabolomics .................................................................................................................. 34
Cytomics......................................................................................................................... 35
Phenomics ......................................................................................................................... 35
Proteomics and systems biology ........................................................................................ 35
Functional synthetic proteins ............................................................................................. 36
2.
Proteomic Technologies ........................................................................ 37
Key technologies driving proteomics ................................................................................. 37
Sample preparation ........................................................................................................... 38
New trends in sample preparation ...................................................................................... 38
Pressure Cycling Technology ............................................................................................. 39
Protein separation technologies ........................................................................................ 39
High resolution 2DGE ....................................................................................................... 39
Variations of 2D gel technology.......................................................................................... 40
Limitations of 2DGE and measures to overcome these .......................................................... 40
1-D sodium dodecyl sulfate (SDS) PAGE ............................................................................. 40
Capillary electrophoresis systems ....................................................................................... 41
Head column stacking capillary zone electrophoresis ............................................................ 41
Removal of albumin and IgG ............................................................................................. 41
Companies with protein separation technologies .................................................................. 42
Protein purification ............................................................................................................ 43
Technologies for protein purification ................................................................................... 44
Applications of protein purification ..................................................................................... 44
Protein detection ............................................................................................................... 44
Protein identification and characterization ........................................................................ 44
Mass spectrometry (MS) ................................................................................................... 44
Companies involved in mass spectrometry ..................................................................... 45
Electrospray ionization ................................................................................................. 46
Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry ....................................... 47
Cryogenic MALDI- Fourier Transform Mass Spectrometry ................................................. 48
Stable-isotope-dilution tandem mass spectrometry ......................................................... 49
HUPO Gold MS Protein Standard ................................................................................... 49
High performance liquid chromatography ............................................................................ 49
Multidimensional protein identification technology (MudPIT) .................................................. 49
Peptide mass fingerprinting ............................................................................................... 50
Combination of protein separation technologies with mass spectrometry ................................. 50
Combining capillary electrophoresis with mass spectrometry ............................................ 50
Proteomics - Technologies, Markets and Companies Part 1
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This report describes and evaluates the proteomic technologies that will play an important role in drug discovery, molecular diagnostics and practice of medicine in the post-genomic era - the first… (More)
http://www.bioportfolio.net/report/3791-proteomics-technologies-markets-and-companies.html
This report describes and evaluates the proteomic technologies that will play an important role in drug discovery, molecular diagnostics and practice of medicine in the post-genomic era - the first… (More)
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